installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: Rcpp
Loading required package: coda
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'icenReg.tex' failed.
LaTeX errors:
! LaTeX Error: File `epsf.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {enumerate}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.6Mb
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  24.3Mb
Package suggested but not available for checking: ‘PROcess’
Package unavailable to check Rd xrefs: ‘PROcess’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pritikin-schmidt.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  14.6Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ilc.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 28.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    include   2.8Mb
    libs     17.9Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Package required but not available: ‘imputeLCMD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘pcaMethods’ ‘impute’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'imputeTS-Time-Series-Missing-Value-Imputation-in-R.tex' failed.
LaTeX errors:
! LaTeX Error: File `environ.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.317 ^^M
         
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘rsprng’ ‘Rmpi’
Error in re-building vignettes:
  ...
Loading required package: permute
Warning in wilcox.test.default(indvar.barcelona$B, indvar.moia$B) :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(Spec.ind.barcelona, Spec.ind.moia) :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(O.barcelona.ind, O.moia.ind) :
  cannot compute exact p-value with ties
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'PigeonExample.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package unavailable to check Rd xrefs: ‘minfi’
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
sh: line 1: 77241 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/x13binary/bin/x13ashtml /tmp/RtmpRkk1xD/x1312db639bdee37/iofile -n -s 2> /dev/null
Warning: running command '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/x13binary/bin/x13ashtml /tmp/RtmpRkk1xD/x1312db639bdee37/iofile -n -s 2>/dev/null' had status 133
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x128b10579
#1  0x128b0f945
#2  0x7fff9fea9529
Error: X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Error in re-building vignettes:
  ...
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: survival

Attaching package: 'InformativeCensoring'

The following object is masked from 'package:survival':

    cox.zph

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gamma_imputation_Jackson_2014.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.57 \usepackage
                {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘easypackages’ ‘pacman’
Packages unavailable to check Rd xrefs: ‘easypackages’, ‘pacman’
Missing link or links in documentation object 'ask.user.yn.question.Rd':
  ‘winDialog’

Missing link or links in documentation object 'check.for.updates.R.Rd':
  ‘winDialog’

Missing link or links in documentation object 'installr.Rd':
  ‘winDialog’

Missing link or links in documentation object 'os.manage.Rd':
  ‘winDialog’

Missing link or links in documentation object 'updateR.Rd':
  ‘winDialog’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Package which this enhances but not available for checking: ‘psgp’
Package required but not available: ‘a4Core’

Packages suggested but not available for checking:
  ‘MLP’ ‘biomaRt’ ‘org.Hs.eg.db’ ‘a4Base’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Interatrix.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: def)

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
Package required but not available: ‘Rdisop’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Icens’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
.nndsvd.internal: no visible global function definition for ‘runif’
nmf.mnnals: no visible global function definition for ‘runif’
nmf.opt.k: no visible global function definition for ‘points’
nmf.opt.k: no visible global function definition for ‘lines’
nmf.opt.k: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  lines mtext points runif
Consider adding
  importFrom("graphics", "lines", "mtext", "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
Package required but not available: ‘Biostrings’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rhdf5’
File ‘iotools/libs/iotools.so’:
  Found non-API call to R: ‘getConnection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: MASS
Loading required package: nlme
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'IPMpack_Vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.15 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Package unavailable to check Rd xrefs: ‘HH’
Errors in running code in vignettes:
when running code in ‘IPSUR.Rnw’
  ...
> library(TeachingDemos)

> plot(z.test(PlantGrowth$weight, stdev = 0.7), "Conf")
Loading required package: HH
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'HH'

  When sourcing 'IPSUR.R':
Error: could not find function "normal.and.t.dist"
Execution halted
Error in re-building vignettes:
  ...

    mnorm

The following object is masked from 'package:grDevices':

    cm

Warning in sqrt(sigma2) : NaNs produced
Warning in sqrt(sigma2) : NaNs produced

Attaching package: 'TeachingDemos'

The following objects are masked from 'package:aplpack':

    faces, slider

Loading required package: HH
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'HH'

Error: processing vignette 'IPSUR.Rnw' failed with diagnostics:
 chunk 250 
Error in normal.and.t.dist(mu.H0 = mu, obs.mean = obs.mean, std.dev = std.dev,  : 
  could not find function "normal.and.t.dist"
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'iqLearn.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'irace-package.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.70 \usepackage
                {booktabs}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespaces in Imports field not imported from:
  ‘coda’ ‘lattice’
  All declared Imports should be used.
Running examples in ‘IRATER-Ex.R’ failed
The error most likely occurred in:

> ### Name: clean.admb
> ### Title: delete IRATE (ADMB) run files
> ### Aliases: clean.admb clean.IRATE
> 
> ### ** Examples
> 
> example.setup <- IRATE.examples()
> new.setup <- new.setup.path <- example.setup[1] # select old IRATE setup to reparameterize
> print(new.setup) # print setup name to be run
[1] "HoenigNonMixing"
> old.setup.path <- system.file(paste0("IRATE.examples/",new.setup,".dat"), package = "IRATER")
> 
> system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
> system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder
> setwd(new.setup.path)
> 
> run.IRATE(new.setup) # compile and run setup
sh: admb: command not found
Error in R2admb::compile_admb(setup.file, safe = safe, re = re, verbose = verbose,  : 
  base admb command failed: run setup_admb(), or check ADMB installation
Calls: run.IRATE -> <Anonymous>
Execution halted
Packages required but not available: ‘graph’ ‘RBGL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'isocir.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10  \usepackage
                 [latin1]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'isotone.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘test.R’ [1s/1s]
Running the tests in ‘tests/test.R’ failed.
Last 13 lines of output:
  > setwd(tempdir())
  > 
  > testMD <- issuesData2md()
  > 
  > # Use default data to generate PDF
  > issuesGenPDF(style = "tint",
  +              RmdLocation =  system.file("rmarkdown/templates/", "tint.Rmd",
  +                                         package = "issueReporter"),
  +              outputFile = tempfile(pattern="ir", fileext=".pdf"),
  +              outputDir = tempdir(),
  +              md = testMD,
  +              setTitle = "Example Notes",
  +              setAuthor = "Author Name")
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Execution halted
Package required but not available: ‘lfa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'JADE-BSSasymp.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.15 \usepackage
                {authblk}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
 1: .Call(rmd_b64encode_data, readBin(inFile, "raw", n = fileSize))
 2: paste("data:", mime::guess_type(inFile), ";base64,", .Call(rmd_b64encode_data,     readBin(inFile, "raw", n = fileSize)), sep = "")
 3: .b64EncodeFile(inFile)
 4: sub(src, .b64EncodeFile(inFile), imgSrc, fixed = TRUE)
 5: FUN(X[[i]], ...)
 6: lapply(regmatches(html, m)[[1]], .b64EncodeImgSrc)
 7: unlist(lapply(regmatches(html, m)[[1]], .b64EncodeImgSrc))
 8: .b64EncodeImages(ret)
 9: eval(quote({    oldwd <- setwd(filedir)    on.exit(setwd(oldwd))    .b64EncodeImages(ret)}), new.env())
10: eval(quote({    oldwd <- setwd(filedir)    on.exit(setwd(oldwd))    .b64EncodeImages(ret)}), new.env())
11: eval(expr, p)
12: eval(expr, p)
13: eval.parent(substitute(eval(quote(expr), envir)))
14: local({    oldwd <- setwd(filedir)    on.exit(setwd(oldwd))    .b64EncodeImages(ret)})
15: markdown::markdownToHTML(out, output, encoding = encoding, ...)
16: knit2html(..., force_v1 = TRUE)
17: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$",     file)) knit2pdf else knit)(file, encoding = encoding, quiet = quiet,     envir = globalenv())
18: vweave(...)
19: engine$weave(file, quiet = quiet, encoding = enc)
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) {    stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)), domain = NA, call. = FALSE)})
24: buildVignettes(dir = "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Jdmbs.Rcheck/vign_test/Jdmbs")
An irrecoverable exception occurred. R is aborting now ...
Packages required but not available: ‘org.Hs.eg.db’ ‘AnnotationDbi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("jiebaR")
  Loading required package: jiebaR
  Loading required package: jiebaRD
  Error in library(devtools) : there is no package called 'devtools'
  Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval -> library
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.3Mb
Package required and available but unsuitable version: ‘psych’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'technical.tex' failed.
LaTeX errors:
! LaTeX Error: File `biblatex.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.17 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'JOUS.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {algorithmicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'json-opencpu.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.62 \usepackage
                {xspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘KEGGgraph’ ‘biomaRt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kcirt.tex' failed.
LaTeX errors:
! LaTeX Error: File `supertabular.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ade4
Loading required package: lattice
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'simulation.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \title
          {KDETrees Simulations}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `titling.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kernlab.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.18 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘org.Hs.eg.db’
Package suggested but not available for checking: ‘stsm’
Package unavailable to check Rd xrefs: ‘stsm’
Running examples in ‘KFKSDS-Ex.R’ failed
The error most likely occurred in:

> ### Name: DS
> ### Title: Disturbance Smoother for State Space Models
> ### Aliases: DS DS.deriv
> ### Keywords: ts, model
> 
> ### ** Examples
> 
> # local level plus seasonal model with arbitrary parameter values
> # for the 'JohnsonJohnson' time series
> m <- stsm::stsm.model(model = "llm+seas", y = JohnsonJohnson, 
+   pars = c("var1" = 2, "var2" = 15, "var3" = 30))
Error in loadNamespace(name) : there is no package called ‘stsm’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'examples.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \input
          {header}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘illustration.png’, ‘kinn.Rmd’
Package has no Sweave vignette sources and no VignetteBuilder field.
Package required but not available: ‘git2r’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/kmcudaR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: knotR
Warning in plot.window(...) : "box" is not a graphical parameter
Warning in plot.xy(xy, type, ...) : "box" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "box" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "box" is not a graphical parameter
Warning in box(...) : "box" is not a graphical parameter
Warning in title(...) : "box" is not a graphical parameter
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'knot.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
    rename, round_any

Warning: Removed 27 rows containing missing values (geom_path).
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 8 rows containing missing values (geom_point).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kobe.tex' failed.
LaTeX errors:
! LaTeX Error: File `framed.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.24 \usepackage
                {color}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.2Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'koRpus_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: def)

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘pcalg’ ‘graph’

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Loading required package: relations
Loading required package: sets
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Rgraphviz’
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Rgraphviz’
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kst.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {amsfonts,hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'variablekey.tex' failed.
LaTeX errors:
! LaTeX Error: File `cancel.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.33 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: boot
Loading required package: MASS
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'laeken-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `soul.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.98 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package unavailable to check Rd xrefs: ‘R2jags’
Packages required but not available: ‘GOstats’ ‘GOSemSim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs           9.9Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    dataset   1.4Mb
    include  11.8Mb
    libs      3.4Mb
Packages suggested but not available for checking: ‘Rgraphviz’ ‘graph’
Running ‘test-all.R’ [45s/65s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  testthat results ================================================================
  OK: 300 SKIPPED: 0 FAILED: 2
  1. Error: Effects (@test-inference.R#27) 
  2. Error: Graph attributes (@test-model.R#82) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: ‘geojsonio’
Running ‘test-all.R’ [10s/15s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Actual value: "c++ exception (unknown reason)"
  
  
  2. Failure: lawn_centroid fails correctly (@test-centroid.R#50) ----------------
  error$message does not match "Unexpected number".
  Actual value: "c++ exception (unknown reason)"
  
  
  testthat results ================================================================
  OK: 805 SKIPPED: 0 FAILED: 2
  1. Failure: lawn_centroid fails correctly (@test-centroid.R#47) 
  2. Failure: lawn_centroid fails correctly (@test-centroid.R#50) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.19 \usepackage
                {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘topicmodels’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'details.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.60 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘chopsticks’

Packages suggested but not available for checking:
  ‘rtracklayer’ ‘GenomicRanges’ ‘GenomeInfoDb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RBGL’ ‘qvalue’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘sf’ ‘rgdal’ ‘rgeos’
Running examples in ‘leaflet-Ex.R’ failed
The error most likely occurred in:

> ### Name: addRasterImage
> ### Title: Add a raster image as a layer
> ### Aliases: addRasterImage projectRasterForLeaflet
> 
> ### ** Examples
> 
> library(raster)
Loading required package: sp
> 
> r <- raster(xmn=-2.8, xmx=-2.79, ymn=54.04, ymx=54.05, nrows=30, ncols=30)
> values(r) <- matrix(1:900, nrow(r), ncol(r), byrow = TRUE)
> crs(r) <- CRS("+init=epsg:4326")
> 
> leaflet() %>% addTiles() %>%
+   addRasterImage(r, colors = "Spectral", opacity = 0.8)
Error in .requireRgdal() : package 'rgdal' is not available
Calls: %>% ... projectRasterForLeaflet -> <Anonymous> -> .requireRgdal
Execution halted
Running ‘test-all.R’ [3s/4s]
  Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(leaflet)
  > 
  > test_check("leaflet")
  Error in library(sf) : there is no package called 'sf'
  Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval -> library
  testthat results ================================================================
  OK: 41 SKIPPED: 0 FAILED: 0
  Execution halted
File ‘leaps/libs/leaps.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘leaps.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: lhs
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'augmentLHS_Example.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {graphicx}                  % for figure inclusion^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/libstableR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
BugReport: http://github.com/spedygiorgio/lifecontingencies/issues

Loading required package: markovchain
Package:  markovchain
Version:  0.6.9.6
Date:     2017-07-10
BugReport: http://github.com/spedygiorgio/markovchain/issues

Loading required package: parallel
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'an_introduction_to_lifecontingencies_package.tex' failed.
LaTeX errors:
! LaTeX Error: File `pict2e.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.59   \DeclareRobustCommand
                            {\overanglebracket}{%^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: parallel

DEoptim package
Differential Evolution algorithm in R
Authors: D. Ardia, K. Mullen, B. Peterson and J. Ulrich

Loading required package: ggplot2
Loading required package: gtools
Loading required package: rtf
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'usage.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
For a step-by-step guide to using linkcomm functions:
   > vignette(topic = "linkcomm", package = "linkcomm")
To run an interactive demo:
   > demo(topic = "linkcomm", package = "linkcomm")
To cite, see:
   > citation("linkcomm")
NOTE: To use linkcomm, you require read and write permissions in the current directory (see: help("getwd"), help("setwd"))

The "ward" method has been renamed to "ward.D"; note new "ward.D2"
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'linkcomm.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {caption}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'LinRegInteractive.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {booktabs}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.8Mb
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    libs      18.2Mb
    testdata   1.5Mb
Package required but not available: ‘LDheatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'lmm-tr.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {amsmath,epsfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: lmodel2
RMA was not requested: it will not be computed.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mod2user.tex' failed.
LaTeX errors:
! LaTeX Error: File `ucs.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 \usepackage
               [utf8x]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘samr’

Package suggested but not available for checking: ‘graph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error: has.localsolver(ls.path) is not TRUE
Execution halted
Error in re-building vignettes:
  ...
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
Execution halted
Error in re-building vignettes:
  ...
Loading required package: LogConcDEAD
Loading required package: MASS
Loading required package: mvtnorm
Loading required package: logcondens
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'LogConcDEAD.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \renewcommand
                 {\textfraction}{0.05}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'plotGlm.tex' failed.
LaTeX errors:
! LaTeX Error: File `morefloats.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.67 \usepackage
                [section]{placeins}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘graph’ ‘PairViz’ ‘Rgraphviz’ ‘RDRToolbox’
Running examples in ‘loon-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.graph
> ### Title: Convert a loongraph object to an object of class graph
> ### Aliases: as.graph
> 
> ### ** Examples
> 
> library(graph)
Error in library(graph) : there is no package called ‘graph’
Execution halted
Running ‘demos.R’ [1s/1s]
Running the tests in ‘tests/demos.R’ failed.
Last 13 lines of output:
  + }
  need the tkimg tcl extension installed to run this demo.
  
  
  	demo(l_glyphs)
  	---- ~~~~~~~~
  
  > require(PairViz) || stop("Package PairViz is required.")
  Loading required package: PairViz
  Error in eval(ei, envir) : Package PairViz is required.
  Calls: demo -> source -> withVisible -> eval -> eval
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'PairViz'
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: tcltk

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 689-693 (minorities.Rmd) 
Error: processing vignette 'minorities.Rmd' failed with diagnostics:
there is no package called 'PairViz'
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: lucid
Loading required package: lattice
Loading required package: rjags
Quitting from lines 269-293 (lucid_printing.Rmd) 
Error: processing vignette 'lucid_printing.Rmd' failed with diagnostics:
could not find function "jags.model"
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bdt.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.15 \usepackage
                [margin=1.0in]{geometry}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages which this enhances but not available for checking:
  ‘rgdal’ ‘rgeos’
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs  16.4Mb
Error in re-building vignettes:
  ...
Loading required package: magree
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'landis.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘Biostrings’ ‘pdInfoBuilder’ ‘convert’ ‘marray’ ‘GEOquery’
  ‘GEOmetadb’ ‘annotate’ ‘GO.db’ ‘RGtk2’ ‘gWidgetsRGtk2’ ‘RBGL’
  ‘genefilter’ ‘simpleaffy’ ‘impute’ ‘oligo’ ‘beadarray’ ‘lumi’
  ‘GOstats’ ‘globaltest’ ‘WGCNA’ ‘Rgraphviz’ ‘ssize’ ‘KEGGREST’
  ‘KEGGgraph’ ‘graph’ ‘Category’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: quadprog
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Mangrove.tex' failed.
LaTeX errors:
! LaTeX Error: File `moreverb.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.6 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Warning in arrange_impl(.data, dots) :
  '.Random.seed' is not an integer vector but of type 'NULL', so ignored
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot875a24484c01.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot875a24484c01.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshotca4c591575d8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotca4c591575d8.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
Checking rgeos availability: TRUE
Warning: use rgdal::readOGR or sf::st_read
Warning: use rgdal::readOGR or sf::st_read
Warning: use rgdal::readOGR or sf::st_read
Warning: use rgdal::readOGR or sf::st_read
Warning: use rgdal::readOGR or sf::st_read
Warning: use rgdal::readOGR or sf::st_read
Warning: non-unique values when setting 'row.names': ‘37055’, ‘37095’

Error: processing vignette 'combine_maptools.Rnw' failed with diagnostics:
 chunk 18 
Error in unionSpatialPolygons(nc90, IDs = paste(nc90$ST, nc90$CO, sep = "")) : 
  package rgeos required for unionSpatialPolygons
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: def)

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Chunk margins3a:
  lm(formula = mpg ~ wt * I(wt^2) * hp * I(hp^2), data = mtcars) 

m <- lm(mpg ~ wt * I(wt^2) * hp * I(hp^2), data = mtcars)
margins(m)

Number of messages:
message 
      6 
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TechnicalDetails.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.58 \usepackage
                {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.1Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'AsymptoticMarkowitz.tex' failed.
LaTeX errors:
! LaTeX Error: File `paralist.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.92 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'EMDerivation.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   4.4Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
**************************************************|
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'matching.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.54 \usepackage
                {tikz}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘ASGSCA’
Package which this enhances but not available for checking: ‘graph’
Error in re-building vignettes:
  ...
<sparse>[ <logic> ] : .M.sub.i.logical() maybe inefficient
<sparse>[ <logic> ] : .M.sub.i.logical() maybe inefficient
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Intro2Matrix.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 \usepackage
               [authoryear,round]{natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  ‘MaxentVariableSelection.Rmd’, ‘MaxentVariableSelection.html’,
    ‘auto/library.el’, ‘library.bib’
Error in re-building vignettes:
  ...
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Number of samples considered (number of samples found): 100(0) 
Finished

Loading required package: sp

Version 3.3 of the spsurvey package was loaded successfully.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'MBHdesign.tex' failed.
LaTeX errors:
! LaTeX Error: File `nicefrac.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.93 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘kangar00’
Package unavailable to check Rd xrefs: ‘kangar00’
Error in re-building vignettes:
  ...

Loading required package: sandwich

Attaching package: ‘party’

The following object is masked from ‘package:mboost’:

    varimp

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SurvivalEnsembles.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.31 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘Rglpk’ ‘glpkAPI’

Packages suggested but not available for checking: ‘Rgraphviz’ ‘cplexAPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CourseNotes.tex' failed.
LaTeX errors:
! LaTeX Error: File `tocbibind.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {makeidx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mcmcse_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.78 \title
           {An Introduction to Estimating Monte Carlo Standard Errors with R...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 228-229 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   6.4Mb
Error in re-building vignettes:
  ...
Loading required package: meteoland
Loading required package: sp
Loading required package: qmap
Loading required package: fitdistrplus
Loading required package: MASS
Loading required package: survival
Loading required package: spdep
Loading required package: Matrix
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'FireBehaviour.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

Effect decomposition on the scale of the linear predictor
conditional on: gender, educ, age 
with x* = 0, x = 1

Effect decomposition on exp(scale of the linear predictor)
conditional on: gender, educ, age 
with x* = 0, x = 1

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'medflex.tex' failed.
LaTeX errors:
! LaTeX Error: File `nccmath.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.12 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mediation-old.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.47 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘medSTC/libs/medSTC.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘medstc/medstc.o’, ‘medstc/corpus.o’,
      ‘svmlight/svm_common.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘medstc/corpus.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required but not available: ‘pcaMethods’ ‘seqLogo’

Depends: includes the non-default packages:
  ‘seqinr’ ‘pcaMethods’ ‘Matrix’ ‘ROCR’ ‘Hmisc’ ‘KernSmooth’ ‘seqLogo’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘untb’
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'memgeneTutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.65 \usepackage
                {parskip}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘aws.s3’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'memuse-guide.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.189 \usepackage
                 {fancyhdr}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘RGtk2’ ‘RGtk2Extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘gWidgetsRGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rstanarm’
Error in re-building vignettes:
  ...

arm (Version 1.9-3, built: 2016-11-21)

Working directory is /Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/merTools.Rcheck/vign_test/merTools/vignettes

Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:MASS':

    select

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 320-333 (Using_predictInterval.Rmd) 
Error: processing vignette 'Using_predictInterval.Rmd' failed with diagnostics:
there is no package called 'rstanarm'
Execution halted
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.4Mb
Package required but not available: ‘crmn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘EBImage’ ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘GEOquery’ ‘GEOmetadb’

Package suggested but not available for checking: ‘BiocStyle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘GEOquery’ ‘org.Hs.eg.db’ ‘annaffy’ ‘hgu133plus2.db’ ‘hgu133a.db’
  ‘hgu95av2.db’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'metaMA.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading 'metafor' package (version 2.0-0). For an overview 
and introduction to the package please type: help(metafor).

Attaching package: ‘metafor’

The following objects are masked from ‘package:metansue’:

    forest, funnel, leave1out

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'metansue.tex' failed.
LaTeX errors:
! LaTeX Error: File `supertabular.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.6 \usepackage
               {enumitem}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘GSEABase’ ‘genefilter’ ‘impute’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘GEOquery’ ‘affy’ ‘hgu133plus2.db’ ‘doSMP’ ‘impute’
Packages suggested but not available for checking:
  ‘HTSFilter’ ‘DESeq’ ‘DESeq2’
Errors in running code in vignettes:
when running code in ‘metaRNASeq.Rnw’
  ...

> options(width = 60)

> library(metaRNASeq)

> library(DESeq2)

  When sourcing ‘metaRNASeq.R’:
Error: there is no package called ‘DESeq2’
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
 chunk 2 (label = loadparameters) 
Error in library(DESeq2) : there is no package called ‘DESeq2’
Execution halted
Running examples in ‘metaSEM-Ex.R’ failed
The error most likely occurred in:

> ### Name: indirectEffect
> ### Title: Estimate the asymptotic covariance matrix of standardized or
> ###   unstandardized indirect and direct effects
> ### Aliases: indirectEffect
> ### Keywords: compute effect sizes
> 
> ### ** Examples
> 
> ## A correlation matrix as input
> x <- matrix(c(1, 0.4, 0.2, 0.4, 1, 0.3, 0.2, 0.3, 1), ncol=3)
> dimnames(x) <- list( c("y", "m", "x"), c("y", "m", "x") )
> indirectEffect(x, n=300)
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  c++ exception (unknown reason)
Calls: indirectEffect -> mxRun -> runHelper
Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
Loading required package: qmap
Loading required package: fitdistrplus
Loading required package: MASS
Loading required package: survival
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Meteorology.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  10.5Mb
    misc   1.1Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'basic-dutils.ltx' failed with diagnostics:
Running 'texi2dvi' on 'basic-dutils.ltx' failed.
LaTeX errors:
! LaTeX Error: File `tufte-handout.cls' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: cls)

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {etex}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mev-vignette.tex' failed.
BibTeX errors:
The top-level auxiliary file: mev-vignette.aux
I couldn't open style file apalike2.bst
---line 44 of file mev-vignette.aux
 : \bibstyle{apalike2
 :                   }
I'm skipping whatever remains of this command
I found no style file---while reading file mev-vignette.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘qusage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [52s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  argument x is not a symmetric matrix
  1: MFKnockoffs.filter(X_perm, y, knockoffs = MFKnockoffs.create.fixed) at testthat/test_filter.R:31
  2: knockoffs(X)
  3: MFKnockoffs.create.fixed(x, y = y)
  4: create_sdp(X, randomize)
  5: MFKnockoffs.knocks.solve_sdp(G)
  6: matrixcalc::is.positive.definite(Sigma_k)
  7: stop("argument x is not a symmetric matrix")
  
  testthat results ================================================================
  OK: 54 SKIPPED: 1 FAILED: 1
  1. Error: MFKnockoffs.filter for fixed design is invariant under permutations of the columns of the design matrix. (@test_filter.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: MGLM
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.15 \usepackage
                {rotating}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘biomaRt’

Package suggested but not available for checking: ‘grasp2db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mhde_article.tex' failed.
LaTeX errors:
! LaTeX Error: File `tabulary.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette1.tex' failed.
LaTeX errors:
! LaTeX Error: File `todonotes.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.65 \IfFileExists
                  {upquote.sty}{\usepackage{upquote}}{}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Loading required package: survival
Loading required package: texreg
Version:  1.36.23
Date:     2017-03-03
Author:   Philip Leifeld (University of Glasgow)

Please cite the JSS article in your publications -- see citation("texreg").
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mhurdle.tex' failed.
LaTeX errors:
! LaTeX Error: File `threeparttable.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {amssymb, amsfonts}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'paper.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.61 \usepackage
                {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘MigClim/libs/MigClim.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’, ‘src_cell.o’, ‘validate.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘gWidgets2RGtk2’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `blindtext.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.14 \usepackage
                [bf]{caption2}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘sybilSBML’ ‘glpkAPI’
Error in re-building vignettes:
  ...
This is vegan 2.4-3
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'MiRKAT.tex' failed.
LaTeX errors:
! LaTeX Error: File `tabu.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
     # Call miRNAss with default parameters
     p = miRNAss(x,y)
     
     # Calculate some performance measures
     SE = mean(p[ celegans$CLASS & y==0] > 0)
     SP = mean(p[!celegans$CLASS & y==0] < 0)
     cat("Sensitivity: ", SE, "\nSpecificity: ", SP, "\n")
     

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'miRNAss.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \renewcommand
                 \Affilfont{\itshape\small}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘globaltest’ ‘GlobalAncova’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘BRugs’

Package suggested but not available for checking: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Error in re-building vignettes:
  ...
Loading required package: survival
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mixor.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.65 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘MixSIAR-Ex.R’ failed
The error most likely occurred in:

> ### Name: mixsiar_gui
> ### Title: Run the GUI version of MixSIAR
> ### Aliases: mixsiar_gui
> 
> ### ** Examples
> 
> mixsiar_gui()
Error in mixsiar_gui() : 
  *** gWidgetsRGtk2 package not able to be loaded. ***
        If 'library('gWidgetsRGtk2')' does not work, MixSIAR GUI will not run.
        On Windows/Linux, try 'install.packages('gWidgetsRGtk2')'.
        On Mac, close R, download and install GTK+ from:
        http://r.research.att.com/#other. Then install latest X11 application
        (xQuartz) from http://xquartz.macosforge.org/landing/.

        If installing GTK+ continues to be problematic, consider using the
        script version of MixSIAR. See manual for help and examples.
Execution halted
Error in re-building vignettes:
  ...
Warning in xy.coords(x, y, xlabel, ylabel, log) :
  1 y value <= 0 omitted from logarithmic plot
species, w\\_inf, w\\_mat, beta, sigma, r\\_max, k\\_vbError in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mizer_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.45 \numberwithin
                  {equation}{section}	% Equation numbers relative to section...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error in file(con, "r") : cannot open the connection
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'FOCUS_Z.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.55 \input
           {header}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages unavailable to check Rd xrefs: ‘genefilter’, ‘limma’
Package required but not available: ‘rsgcc’

Packages suggested but not available for checking:
  ‘GeneSelector’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mldr.tex' failed.
LaTeX errors:
! LaTeX Error: File `stmaryrd.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.70 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in split.default(x = seq_len(nrow(x)), f = f, drop = drop, ...) :
  data length is not a multiple of split variable
Warning in split.default(x = seq_len(nrow(x)), f = f, drop = drop, ...) :
  data length is not a multiple of split variable
Warning in split.default(x = seq_len(nrow(x)), f = f, drop = drop, ...) :
  data length is not a multiple of split variable
Warning in lmList(normexam ~ standLRT + sex | school, Exam, subset = type ==  :
  Fitting failed for 1 group(s), probably because a factor only had one level
refitting model(s) with ML (instead of REML)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'StarData.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Formula
Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Exercises.tex' failed.
LaTeX errors:
! LaTeX Error: File `ucs.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \RequirePackage
                   [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘Rfast’ ‘rknn’
Running ‘run-base.R’ [387s/543s]
Running the tests in ‘tests/run-base.R’ failed.
Last 13 lines of output:
         test.i = test.i, measures = measures, weights = weights, rdesc = rin$desc, model = model, 
         extract = extract, show.info = show.info)
  7: train(learner, task, subset = train.i, weights = weights[train.i])
  8: requireLearnerPackages(learner)
  9: requirePackages(learner$package, why = stri_paste("learner", learner$id, sep = " "), 
         default.method = "load")
  10: stopf("For %s please install the following packages: %s", why, ps)
  
  testthat results ================================================================
  OK: 2711 SKIPPED: 2 FAILED: 2
  1. Error: NoFeaturesModel works with FilterWrapper (@test_base_NoFeaturesModel.R#30) 
  2. Error: predict.threshold (@test_base_predict.R#129) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

Re-fitting to get Hessian


Re-fitting to get Hessian


Re-fitting to get Hessian

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mlt.tex' failed.
LaTeX errors:
! LaTeX Error: File `accents.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.27 \usepackage
                {color}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mmap.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.8 \hypersetup
               {colorlinks,%^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: magic
Loading required package: abind
Loading required package: partitions
Loading required package: emulator
Loading required package: mvtnorm
Loading required package: Oarray
Warning: glm.fit: fitted rates numerically 0 occurred
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Gianfranco.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'MNP.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.29 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
Loading required package: rgdal
rgdal: version: 1.2-6, (SVN revision 651)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
 Path to GDAL shared files: /Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/rgdal/gdal
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: /Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/rgdal/proj
 Linking to sp version: 1.2-4 
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ExploreModelMap.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.3 \setlength
              {\parskip}{0.7ex plus0.1ex minus0.1ex}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'modelObj.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: def)

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘Test.R’ [2s/10s]
Running the tests in ‘tests/Test.R’ failed.
Last 13 lines of output:
  +   Dates <- GetDates(SubsetExample$lat, SubsetExample$long, Product)[1:2]
  + 
  +   GetSubset(Lat = SubsetExample$lat, Long = SubsetExample$long, Product = Product, Band = Band,
  +             StartDate = Dates[1], EndDate = Dates[1], KmAboveBelow = 0, KmLeftRight = 0)
  + 
  +   MODISSubsets(LoadDat = SubsetExample, Product = "MCD12Q1", Bands = c("Land_Cover_Type_1"),
  +                Size = c(1,1), StartDate = TRUE)
  + 
  +   MODISSummaries(LoadDat = SubsetExample, Product = "MCD12Q1", Band = "Land_Cover_Type_1",
  +                  ValidRange = c(0,254), NoDataFill = 255, ScaleFactor = 1, StartDate = TRUE)
  + }
  Error in Product == GetProducts() : 
    comparison of these types is not implemented
  Calls: GetBands
  Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'UsingMODISTools.tex' failed.
LaTeX errors:
! LaTeX Error: File `hyphenat.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [noae]{Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-17. For overview type 'help("mgcv-package")'.
Loading required package: splines
Warning: max number of iterations attained
Warning: max number of iterations attained
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'modTempEff.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.70 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
    cm

Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-17. For overview type 'help("mgcv-package")'.
Warning in matrix(l, nrow = 1) %*% solve(V1) %*% matrix(l, ncol = 1)/sigma2 :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mombf.tex' failed.
LaTeX errors:
! LaTeX Error: File `epsf.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.15 \usepackage
                {lscape}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.7Mb
    libs   2.4Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: splines
Loading required package: splines2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'momentuHMM.tex' failed.
LaTeX errors:
! LaTeX Error: File `adjcalc.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.24 \def
         \adjbox@fam{adjbox}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘fftw’ ‘RODBC’
Packages unavailable to check Rd xrefs: ‘seewave’, ‘RODBC’
Error in re-building vignettes:
  ...
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr

Attaching package: 'monitoR'

The following object is masked from 'package:tuneR':

    readMP3

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'monitoR_QuickStart.tex' failed.
LaTeX errors:
! LaTeX Error: File `placeins.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.55 \usepackage
                {natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'modelling.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘MortHump.Rnw’
Error in re-building vignettes:
  ...

Using parallel package.
  * Set seed with set.rseed().
  * Disable this message with options(`mosaic:parallelMessage` = FALSE)

Using parallel package.
  * Set seed with set.rseed().
  * Disable this message with options(`mosaic:parallelMessage` = FALSE)

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Resampling.tex' failed.
LaTeX errors:
! LaTeX Error: File `xstring.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 \RequirePackage
                   {xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'moult.tex' failed.
LaTeX errors:
! LaTeX Error: File `pst-node.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.6 \usepackage
               {listings}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘CGHcall’ ‘aroma.affymetrix’ ‘aroma.cn’ ‘aroma.core’ ‘aroma.light’
File ‘mph/libs/mph.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘mph.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘mph.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  ‘asreml’ ‘happy.hbrem’ ‘Heatplus’ ‘VPdtw’
'library' or 'require' calls to packages already attached by Depends:
  ‘gdata’ ‘seriation’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Heatplus’ ‘VPdtw’ ‘aod’ ‘asreml’ ‘happy.hbrem’ ‘lattice’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘gdata’ ‘seriation’ ‘wgaim’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘qtl:::readMWril’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘qtl:::adjust.rf.ri’ ‘qtl:::plot.scanone’ ‘qtl:::ripple.perm1’
  ‘qtl:::ripple.perm2’ ‘qtl:::testchr’
  See the note in ?`:::` about the use of this operator.
Foreign function calls to a different package:
  .C("R_reorgRIgenoprob", ..., PACKAGE = "qtl")
  .C(cfunc, ..., PACKAGE = "qtl")
  .C(func, ..., PACKAGE = "qtl")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Package unavailable to check Rd xrefs: ‘Heatplus’
Running examples in ‘mpMap-Ex.R’ failed
The error most likely occurred in:

> ### Name: findqtl2
> ### Title: Detect a second QTL in a QTL profile from (composite) interval
> ###   mapping
> ### Aliases: findqtl2
> 
> ### ** Examples
> 
> sim.map <- sim.map(len=rep(100, 2), n.mar=11, include.x=FALSE, eq.spacing=TRUE)
> sim.ped <- sim.mpped(4, 1, 500, 6, 1)
> sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow=TRUE), seed=1)
> mpp.dat <- mpprob(sim.dat, program="qtl", step=2)
[1] "No chromosomes specified, will default to all"
 --Read the following data:
	 500  individuals
	 20  markers
	 2  phenotypes
> mpq.dat <- mpIM(object=mpp.dat, ncov=0, responsename="pheno")
 --Read the following data:
	 500  individuals
	 20  markers
	 2  phenotypes
Loading required package: aod
------Analyzing Chr  1 ----------
------Analyzing Chr  2 ----------
> mpq2 <- findqtl2(mpq.dat, drop=2)
Loading required package: VPdtw
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘VPdtw’
Error in dilation(cpv2, dwindow) : could not find function "dilation"
Calls: findqtl2
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mptinr_introduction.tex' failed.
LaTeX errors:
! LaTeX Error: File `threeparttable.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.65 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘rgdal’ ‘devtools’
Running examples in ‘mptools-Ex.R’ failed
The error most likely occurred in:

> ### Name: mp2sp
> ### Title: Create a SpatialPointsDataFrame describing Metapop population
> ###   centroids
> ### Aliases: mp2sp
> ### Keywords: spatial
> 
> ### ** Examples
> 
> mp <- system.file('example.mp', package='mptools')
> r <- system.file('example_001.tif', package='mptools')
> coords <- mp2xy(mp, r, 9.975)
Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",  : 
  Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Calls: mp2xy ... <Anonymous> -> <Anonymous> -> .local -> .rasterObjectFromFile
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Extracting simulation results from file:
/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/mptools.Rcheck/mptools/example.mp
Extracting population metadata from file:
/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/mptools.Rcheck/mptools/example.mp
Quitting from lines 136-140 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Execution halted
Found the following significant warnings:
  Warning: Pointer at (1) in pointer assignment might outlive the pointer target [-Wtarget-lifetime]
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/mra.Rcheck/00install.out’ for details.
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘Bromaghin_etal_2013_OJE.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'MRCV-vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.100 \usepackage
                 {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘geojsonio’ ‘rgdal’ ‘rgeos’ ‘rmapshaper’
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2Extras’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mRMRe.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘AnnotationDbi’

Packages suggested but not available for checking:
  ‘GO.db’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘Biostrings’
Packages required but not available: ‘mzR’ ‘xcms’

Depends: includes the non-default packages:
  ‘amap’ ‘clValid’ ‘cluster’ ‘fpc’ ‘mzR’ ‘xcms’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MSeasy’

Package suggested but not available for checking: ‘xcms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: xgettext: command not found
sh: msgmerge: command not found
sh: msgmerge: command not found
sh: msgfmt: command not found
sh: msgconv: command not found
Quitting from lines 136-138 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
running msgconv on 'R-en@quot' UTF-8 localization failed
Execution halted
Running examples in ‘mssqlR-Ex.R’ failed
Package required but not available: ‘graph’

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: survival
Warning in coxph(Surv(time, status) ~ ccr5 * factor(trans) + strata(trans),  :
  X matrix deemed to be singular; variable 2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {fullpage}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘cartography’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 43-53 (MTA_Scenario.Rmd) 
Error: processing vignette 'MTA_Scenario.Rmd' failed with diagnostics:
there is no package called 'cartography'
Execution halted
Error in re-building vignettes:
  ...

Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'chfls1.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: def)

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘pgirmess’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SIRtrans.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.71 \usepackage
                {mathtools}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘pcaMethods’ ‘gridGraphics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 54.4Mb
  sub-directories of 1Mb or more:
    libs  54.2Mb
Package required but not available: ‘gridGraphics’

Package suggested but not available for checking: ‘ComplexHeatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: abind

Attaching package: ‘multipol’

The following object is masked from ‘package:base’:

    single

Loading required package: polynom
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'multipol.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'multisensi-vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `epic.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.57 \usepackage
                {graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: glmnet
Loading required package: foreach
Loaded glmnet 2.0-5

Loading required package: ggplot2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'MultiVarSel.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

Attaching package: ‘multivator’

The following objects are masked from ‘package:base’:

    levels, rbind

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cias.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘mutoss’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘mutoss-Ex.R’ failed
The error most likely occurred in:

> ### Name: Qvalue
> ### Title: Storey's (2001) q-value Procedure...
> ### Aliases: Qvalue
> 
> ### ** Examples
> pval <- c(runif(50), runif(50, 0, 0.01))
> result <- Qvalue(pval)
Loading required package: qvalue
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘qvalue’
Package qvalue is required - should we install it?
Error in requireLibrary("qvalue") : 
  Required package qvalue should not be installed
Calls: Qvalue -> requireLibrary
Execution halted
Package required but not available: ‘rattle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette_mvord.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {verbatim}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'article.ltx' failed with diagnostics:
Running 'texi2dvi' on 'article.ltx' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 \usepackage
                [noend]{algpseudocode}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Packages required but not available:
  ‘autothresholdr’ ‘BiocParallel’ ‘EBImage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘vsn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘NanoStringNorm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required and available but unsuitable version: ‘rstanarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Errors in running code in vignettes:
when running code in ‘test-vignette.ipynbmeta’
  ...

  When tangling ‘test-vignette.ipynbmeta’:
Error: Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'test-vignette.ipynbmeta' failed with diagnostics:
Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Running ‘doRUnit.R’ [14s/21s]
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
  Number of failures: 1 
  
   
  1 Test Suite : 
  nCal unit testing - 3 test functions, 2 errors, 1 failure
  ERROR in test.5PL: Error in 0:(ncol(single.fit$coefficients) - 1) : argument of length 0
  FAILURE in test.bcrm: Error in checkEqualsNumeric(mean(fits$median.coef), 4.01789, tolerance = tolerance.jags) : 
    'is.NA' value mismatch: 0 in current 1 in target
  
  ERROR in test.ncal: Error in 0:(ncol(single.fit$coefficients) - 1) : argument of length 0
  Error: 
  
  unit testing failed (#test failures: 1, #R errors: 2)
  
  Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in loadNamespace(name) : there is no package called 'rjags'
Error in loadNamespace(name) : there is no package called 'rjags'
Error in loadNamespace(name) : there is no package called 'rjags'
Quitting from lines 100-102 (nCal-vignette.Rnw) 
Error: processing vignette 'nCal-vignette.Rnw' failed with diagnostics:
argument of length 0
Execution halted
Package suggested but not available for checking: ‘BiocInstaller’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'quick-start.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.59 \usepackage
                [colorlinks=true, urlcolor=blue, pdfborder={0 0 0}]{hyperref...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  computing positions for slice 4
  computing positions for slice 5
  computing positions for slice 6
  computing positions for slice 7
  computing positions for slice 8
  computing positions for slice 9
  computing positions for slice 10
  computing positions for slice 11
rendering splines for each vertex ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ndtv.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.6 \usepackage
               {color}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: neldermead
Loading required package: optimbase
Loading required package: Matrix
Loading required package: optimsimplex
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'neldermead_manual.tex' failed.
LaTeX errors:
! LaTeX Error: File `ucs.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [latin1]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

Warning in coxdetails$hazard/exp(apply(coxdetails$x, 2, mean) %*% beta) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in ((C[exposureindex, ] - C[nexposures + 1, ]) %*% covariatesurvs) *  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'NestedCohort.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {psfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘AnnotationDbi’ ‘graph’ ‘samr’

Package suggested but not available for checking: ‘KEGG.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.5Mb
Package suggested but not available for checking: ‘hasseDiagram’
Package unavailable to check Rd xrefs: ‘hasseDiagram’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   4.0Mb
File ‘NetSim/libs/NetSim.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘utils/Random.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘utils/Random.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required but not available: ‘WGCNA’ ‘minet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

trying URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/Sampson.zip'
Content type 'application/zip' length 2182 bytes
==================================================
downloaded 2182 bytes

Warning in get.vertex.attribute.active(net, "happiness", onset = 2.5, terminus = 4.5) :
  Multiple attribute values matched query spell for attribute happiness.active on some vertices. Only earliest value used

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'networkDynamic.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.6 \usepackage
               {color}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘graph’ ‘KEGGgraph’

Packages suggested but not available for checking:
  ‘BiocStyle’ ‘graphite’ ‘NFPdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ngram-guide.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.217 \usepackage
                 {fancyhdr}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 36.0Mb
  sub-directories of 1Mb or more:
    CppCode       13.8Mb
    R              3.2Mb
    classic-bugs   1.5Mb
    include        5.5Mb
    libs          10.7Mb
Package required but not available: ‘Rsamtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Running ‘test-all.R’ [26s/27s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  Error in library(devtools) : there is no package called 'devtools'
  Calls: <Anonymous> ... with_reporter -> force -> source_file -> eval -> eval -> library
  testthat results ================================================================
  OK: 198 SKIPPED: 0 FAILED: 2
  1. Error: Nlsy79Gen2 (@test-column-utilities.R#89) 
  2. Error: RenameNlsyColumn (@test-column-utilities.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
plot.isp: no visible global function definition for ‘median’
plot.isp: no visible global function definition for ‘plot’
plot.isp: no visible global function definition for ‘lines’
plot.nmcd: no visible global function definition for ‘median’
plot.nmcd: no visible global function definition for ‘plot’
plot.nmcd: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines median plot
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "median")
to your NAMESPACE file.
Packages suggested but not available for checking:
  ‘RcppOctave’ ‘doMPI’ ‘devtools’ ‘Biobase’
.wrapResult: no visible global function definition for ‘exprs’
algorithm,NMFStrategyOctave: no visible global function definition for
  ‘fstop’
evar,ANY: no visible binding for global variable ‘Biobase’
nmf,matrix-numeric-NMFStrategy : run.all: no visible binding for global
  variable ‘n’
nmf,matrix-numeric-NMFStrategy : run.all: no visible binding for global
  variable ‘RNGobj’
nmfModel,formula-ANY : merge_pdata: no visible global function
  definition for ‘pData’
nmfModel,formula-ANY: no visible global function definition for ‘exprs’
rss,matrix: no visible binding for global variable ‘Biobase’
Undefined global functions or variables:
  Biobase RNGobj exprs fstop n pData
Packages unavailable to check Rd xrefs: ‘RcppOctave’, ‘Biobase’
Error in .requirePackage(package) : 
    unable to find required package 'Biobase'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'NMF-unitTests.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.58 \setmargrb
               {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: NMOF
found several files...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DEnss.tex' failed.
LaTeX errors:
! LaTeX Error: File `framed.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.15 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Apr 03, 2017 6:54:41 AM com.github.fommil.netlib.ARPACK <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeSystemARPACK
Apr 03, 2017 6:54:41 AM com.github.fommil.netlib.ARPACK <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeRefARPACK
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'NoiseFiltersR.tex' failed.
LaTeX errors:
! LaTeX Error: File `stmaryrd.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.73 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'nonrandom.tex' failed.
LaTeX errors:
! LaTeX Error: File `sfmath.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.16 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'nopaco.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: def)

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

 You can now run (pdf)latex on ‘noweb.tex’ 
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'noweb.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'nplr.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.55 \setlength
               {\parskip}{0.7ex plus0.1ex minus0.1ex}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
In addition: Warning messages:
1: In nlm(f = .sce, p = .initPars(x, y, 5), x = x, yobs = y, .weight,  :
  NA/Inf replaced by maximum positive value
2: In nlm(f = .sce, p = .initPars(x, y, 5), x = x, yobs = y, .weight,  :
  NA/Inf replaced by maximum positive value
3: In nlm(f = .sce, p = .initPars(x, y, 5), x = x, yobs = y, .weight,  :
  NA/Inf replaced by maximum positive value
4: In nlm(f = .sce, p = .initPars(x, y, 5), x = x, yobs = y, .weight,  :
  NA/Inf replaced by maximum positive value
Execution halted
Error in re-building vignettes:
  ...
Nonparametric Kernel Methods for Mixed Datatypes (version 0.60-3)
[vignette("np_faq",package="np") provides answers to frequently asked questions]
[vignette("np",package="np") an overview]
[vignette("entropy_np",package="np") an overview of entropy-based methods]
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'entropy_np.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: def)

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘aroma.core’ ‘aroma.affymetrix’

Depends: includes the non-default packages:
  ‘R.methodsS3’ ‘MASS’ ‘matrixStats’ ‘R.oo’ ‘R.utils’ ‘aroma.core’
  ‘aroma.affymetrix’ ‘DNAcopy’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘PMA’
Running examples in ‘nscancor-Ex.R’ failed
The error most likely occurred in:

> ### Name: mcancor
> ### Title: Non-Negative and Sparse Multi-Domain CCA
> ### Aliases: mcancor
> 
> ### ** Examples
> 
> library(glmnet)
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-5

> data(breastdata, package="PMA")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘PMA’
Calls: data -> find.package
Execution halted
Packages required but not available: ‘EBImage’ ‘bioimagetools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error: processing vignette 'NUCOMBog.ltx' failed with diagnostics:
Running 'texi2dvi' on 'NUCOMBog.ltx' failed.
LaTeX errors:
! LaTeX Error: File `framed.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.29 \makeatletter
                  ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Error in re-building vignettes:
  ...
Loading required package: xml2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'oaih.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.8 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
File ‘obliclus/libs/obliclus.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Unexported object imported by a ':::' call: ‘tree:::tree.matrix’
  See the note in ?`:::` about the use of this operator.
File ‘oblique.tree/libs/oblique.tree.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: lattice
Loading required package: XML

Attaching package: ‘XML’

The following object is masked from ‘package:tools’:

    toHTML

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'odfWeave.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {algorithm2e}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 74.8Mb
  sub-directories of 1Mb or more:
    libs  74.4Mb
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Actual value: "c++ exception (unknown reason)"
  
  
  2. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#21) 
  error$message does not match "The length value".
  Actual value: "c++ exception (unknown reason)"
  
  
  testthat results ================================================================
  OK: 34 SKIPPED: 0 FAILED: 2
  1. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#20) 
  2. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘ROI.plugin.glpk’
Running examples in ‘ompr.roi-Ex.R’ failed
The error most likely occurred in:

> ### Name: with_ROI
> ### Title: Configures a solver based on 'ROI'
> ### Aliases: with_ROI
> 
> ### ** Examples
> 
> library(magrittr)
> library(ompr)
> library(ROI)
ROI: R Optimization Infrastructure
Registered solver plugins: nlminb, ecos, ipop, lpsolve, nloptr, quadprog, scs.
Default solver: auto.
> library(ROI.plugin.glpk)
Error in library(ROI.plugin.glpk) : 
  there is no package called ‘ROI.plugin.glpk’
Execution halted
Running ‘testthat.R’ [12s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > library(ROI)
  ROI: R Optimization Infrastructure
  Registered solver plugins: nlminb, ecos, ipop, lpsolve, nloptr, quadprog, scs.
  Default solver: auto.
  > library(ROI.plugin.glpk)
  Error in library(ROI.plugin.glpk) : 
    there is no package called 'ROI.plugin.glpk'
  Execution halted
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
comp.freq: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
dev.new(): using pdf(file="Rplots3.pdf")
dev.new(): using pdf(file="Rplots4.pdf")
dev.new(): using pdf(file="Rplots5.pdf")
dev.new(): using pdf(file="Rplots6.pdf")
dev.new(): using pdf(file="Rplots7.pdf")
dev.new(): using pdf(file="Rplots8.pdf")
dev.new(): using pdf(file="Rplots9.pdf")
dev.new(): using pdf(file="Rplots10.pdf")
dev.new(): using pdf(file="Rplots11.pdf")
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'OneTwoSamples.tex' failed.
LaTeX errors:
! LaTeX Error: File `varwidth.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.69 \RequirePackage{varwidth}[2009/03/30]
                                          ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  "phi" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "box" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "r" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "theta" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "phi" is not a graphical parameter
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'onionpaper.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: minpack.lm
Waiting for profiling to be done...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'onls.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘ontologyPlot’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 80-92 (intro-to-ontologyX.Rmd) 
Error: processing vignette 'intro-to-ontologyX.Rmd' failed with diagnostics:
there is no package called 'ontologyPlot'
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/OpenCL.Rcheck/00install.out’ for details.
installed size is 110.2Mb
  sub-directories of 1Mb or more:
    libs    101.9Mb
    models    4.6Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: OpenMx
> ### Title: OpenMx: An package for Structural Equation Modeling and Matrix
> ###   Algebra Optimization
> ### Aliases: OpenMx OpenMx-package
> 
> ### ** Examples
> 
> library(OpenMx)
> data(demoOneFactor)
> # ===============================
> # = Make and run a 1-factor CFA =
> # ===============================
> 
> latents  = c("G") # the latent factor
> manifests = names(demoOneFactor) # manifest variables to be modeled
> # ====================
> # = Make the MxModel =
> # ====================
> m1 <- mxModel("One Factor", type = "RAM", 
+ 	manifestVars = manifests, latentVars = latents, 
+ 	mxPath(from = latents, to = manifests),
+ 	mxPath(from = manifests, arrows = 2),
+ 	mxPath(from = latents, arrows = 2, free = FALSE, values = 1.0),
+ 	mxData(cov(demoOneFactor), type = "cov", numObs = 500)
+ )
> 
> # ===============================
> # = mxRun it and get a summary! =
> # ===============================
> 
> m1 = mxRun(m1)
Running One Factor with 10 parameters
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  c++ exception (unknown reason)
Calls: mxRun -> runHelper -> .Call
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshota5057ab2ba73.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshota5057ab2ba73.png': No such file or directory
Quitting from lines 22-24 (openwindfarm-vignette.Rmd) 
Error: processing vignette 'openwindfarm-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘Biobase’ ‘annotate’ ‘GO.db’ ‘org.At.tair.db’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'optimbase_manual.tex' failed.
LaTeX errors:
! LaTeX Error: File `ucs.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [latin1]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Loading required package: clinfun
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'OptInterim.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.17 \usepackage
                {algorithm2e}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
sh: +RTS: command not found
Error: processing vignette 'optparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
Package required but not available: ‘ROracle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Biobase’
Error in .requirePackage(package) : 
  unable to find required package ‘Biobase’
Calls: <Anonymous> ... withCallingHandlers -> is -> getClassDef -> .requirePackage
Execution halted
Errors in running code in vignettes:
when running code in ‘ordinalgmifs.Rnw’
  ...
Loading required package: survival

> data(hccframe)

> cumulative.logit <- ordinal.gmifs(group ~ 1, x = hccframe[, 
+     -1], data = hccframe)

Execution halted

... incomplete output.  Crash?
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clm_intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithmic.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.14 \usepackage
                [amsmath,thmmarks,standard,thref]{ntheorem}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘IsoGene’ ‘Biobase’
Error in re-building vignettes:
  ...
Loading required package: orgutils
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'orgutils_examples.tex' failed.
LaTeX errors:
! LaTeX Error: File `libertine.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.6 \usepackage
               [scaled=0.8]{DejaVuSansMono}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘genefilter’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘osi-Ex.R’ failed
The error most likely occurred in:

> ### Name: extract_id
> ### Title: Extract components from OSI metadata
> ### Aliases: extract_id extract_keywords extract_name extract_superseded
> ###   extractors
> 
> ### ** Examples
> 
> 
> #Get the names of all licenses
> all_license_metadata <- license_list()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Peer certificate cannot be authenticated with given CA certificates
Calls: license_list ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  8: curl::curl_fetch_memory(url, handle = handle)
  
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 8
  1. Error: All licenses can be retrieved (@test_connectors.R#6) 
  2. Error: Keyword retrieval works (@test_connectors.R#14) 
  3. Error: ID retrieval works (@test_connectors.R#22) 
  4. Error: Content retrieval works (@test_connectors.R#29) 
  5. Error: licenses IDs can be retrieved (@test_extractors.R#4) 
  6. Error: licenses names can be retrieved (@test_extractors.R#11) 
  7. Error: licenses superseded states can be retrieved (@test_extractors.R#18) 
  8. Error: licenses keywords can be retrieved (@test_extractors.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   3.6Mb
Package required but not available: ‘Rglpk’

Package suggested but not available for checking: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'overlap.tex' failed.
LaTeX errors:
! LaTeX Error: File `placeins.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 \usepackage
                [usenames,dvipsnames,svgnames]{xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘genealogicalSorting’ ‘phybase’ ‘Rmpi’
Error in re-building vignettes:
  ...
Warning: Removed 575 rows containing non-finite values
(stat_density).
Warning: Removed 2 rows containing missing values (geom_vline).
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: Removed 575 rows containing non-finite values
(stat_density).
Warning: Removed 2 rows containing missing values (geom_vline).
Warning: Removed 370 rows containing missing values (geom_point).
Warning: Removed 370 rows containing missing values (geom_point).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'P2C2M_Vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {listings}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DEU_PISA2012_description.tex' failed.
LaTeX errors:
! LaTeX Error: File `apacite.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {tabularx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: GCD
This is paleofire v1.1.9 | GCD v3.0.5
trying URL 'http://blarquez.com/public/data/data_cageo.zip'
Content type 'application/zip' length 14857 bytes (14 KB)
==================================================
downloaded 14 KB

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'paleofire-paper.tex' failed.
LaTeX errors:
! LaTeX Error: File `elsarticle.cls' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: cls)

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘GO.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pan-tr.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {amsmath,epsfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Factors are dropped from the summary
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Factors are dropped from the summary
Factors are dropped from the summary
Factors are dropped from the summary
Factors are dropped from the summary
Non-factors are dropped from the summary
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'papeR_with_latex.tex' failed.
LaTeX errors:
! LaTeX Error: File `capt-of.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.55 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Loading required package: highlight
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'parallelDist.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.383 \setmargrb
                {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘pcalg’ ‘Rgraphviz’
Running examples in ‘ParallelPC-Ex.R’ failed
The error most likely occurred in:

> ### Name: IDA_parallel
> ### Title: Estimate Total Causal Effects using the IDA_parallel Algorithm
> ### Aliases: IDA_parallel
> 
> ### ** Examples
> 
> ##########################################
> ## Using IDA_parallel without mem.efficeient
> ##########################################
> library(bnlearn)

Attaching package: ‘bnlearn’

The following object is masked from ‘package:stats’:

    sigma

> library(pcalg)
Error in library(pcalg) : there is no package called ‘pcalg’
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'parfm.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.12 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Linking to GEOS 3.6.1, GDAL 2.1.3, proj.4 4.9.3

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Downloading MP data
Downloading constituency data
Warning: Column `party_id` joining character vector and factor, coercing into character vector
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot131e51ff86.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot131e51ff86.png': No such file or directory
Quitting from lines 67-112 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘Rglpk’

Package suggested but not available for checking: ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘parmigene/libs/parmigene.so’:
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: survival
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'partDSAvig.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: partitions
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'partitionspaper.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'partsm.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.47 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Vignette 'Japanese.Rnw' requires 'uplatex' and 'dvipdfmx'
Error: processing vignette 'Japanese.Rnw' failed with diagnostics:
Failed to locate the ‘weave’ output file (by engine ‘patchDVI::JSweave’) for vignette with name ‘Japanese’. The following files exist in directory ‘.’: ‘Japanese.Rnw’, ‘patchDVI.Rnw’, ‘patchDVI.bib’, ‘sample.Rnw.txt’
Execution halted
Packages suggested but not available for checking: ‘hu6800.db’ ‘golubEsets’

Depends: includes the non-default packages:
  ‘svmpath’ ‘kernlab’ ‘affy’ ‘Biobase’ ‘ROCR’ ‘igraph’ ‘lpSolve’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Errors in running code in vignettes:
when running code in ‘pathClass.rnw’
  ...

    union

Loading required package: lpSolve

> library(golubEsets)

  When sourcing ‘pathClass.R’:
Error: there is no package called ‘golubEsets’
Execution halted
Error in re-building vignettes:
  ...

    lowess

Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:BiocGenerics’:

    normalize, union

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Loading required package: lpSolve

Error: processing vignette 'pathClass.rnw' failed with diagnostics:
 chunk 2 (label = loadALLpackage) 
Error in library(golubEsets) : there is no package called ‘golubEsets’
Execution halted
Error in re-building vignettes:
  ...
Warning in readLines(con) :
  incomplete final line found on 'patternplot-intro.Rmd'
Quitting from lines 11-14 (patternplot-intro.Rmd) 
Error: processing vignette 'patternplot-intro.Rmd' failed with diagnostics:
there is no package called 'Cairo'
Execution halted
Packages required but not available: ‘pbdMPI’ ‘pbdSLAP’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘pbdMPI’ ‘pbdBASE’ ‘pbdDMAT’

Package which this enhances but not available for checking: ‘pmclust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘pbdMPI’ ‘pbdBASE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdPROF’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/pbdMPI.Rcheck/00install.out’ for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/pbdPROF.Rcheck/00install.out’ for details.
Packages which this enhances but not available for checking:
  ‘pbdMPI’ ‘pbdCS’
Error in re-building vignettes:
  ...
Loading required package: pbkrtest
Loading required package: lme4
Loading required package: Matrix
refitting model(s) with ML (instead of REML)
refitting model(s) with ML (instead of REML)
   [[ suppressing 10 column names '1', '2', '3' ... ]]
   [[ suppressing 10 column names '1', '2', '3' ... ]]
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pbkrtest-introduction.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [noae]{Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    examples   1.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/pcaL1.Rcheck/00install.out’ for details.
Package required but not available: ‘safe’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘strvalidator’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
large z may result in inaccurate quantiles
Loading required package: polynom
Loading required package: reshape2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'PDQutils.tex' failed.
LaTeX errors:
! LaTeX Error: File `paralist.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.98 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘pedantics/libs/pedantics.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘pedantics.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: ‘georob’ ‘spsurvey’
Packages unavailable to check Rd xrefs: ‘spsurvey’, ‘georob’
Running examples in ‘pedometrics-Ex.R’ failed
The error most likely occurred in:

> ### Name: vgmICP
> ### Title: Initial covariance parameters (ICP)
> ### Aliases: vgmICP
> 
> ### ** Examples
> 
> data(meuse, package = "sp")
> icp <- vgmICP(z = log(meuse$copper), coords = meuse[, 1:2])
Error: Package(s) needed for this function to work but notinstalled: georob
Execution halted
Package suggested but not available for checking: ‘globaltest’
Errors in running code in vignettes:
when running code in ‘penalized.Rnw’
  ...

> fit <- penalized(response, X, lambda1 = 2, lambda2 = 2, 
+     fusedl = chr)


> library(globaltest)

  When sourcing ‘penalized.R’:
Error: there is no package called ‘globaltest’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: survival
Welcome to penalized. For extended examples, see vignette("penalized").

Error: processing vignette 'penalized.Rnw' failed with diagnostics:
 chunk 31 (label = globaltest) 
Error in library(globaltest) : there is no package called ‘globaltest’
Execution halted
Error in re-building vignettes:
  ...
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Definition.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {verbatim}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘biomaRt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Paper_Analysis.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {tikz}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

Warning in z + c(-1, 1) * sigma * qnorm((1 + conf.level)/2) :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in z + c(-1, 1) * sigma * qnorm((1 + conf.level)/2) :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'PerformanceAnalyticsChartsPresentation-Meielisalp-2007.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.28 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/permGPU.Rcheck/00install.out’ for details.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

infoImage: no visible global function definition for ‘quantile’
markPoisson: no visible global function definition for ‘runif’
markPoisson: no visible global function definition for ‘flush.console’
phantom : model: missing arguments not allowed in calls to ‘c’
readData: no visible global function definition for ‘read.table’
readData: no visible global function definition for ‘read.image’
readSifData: no visible global function definition for ‘flush.console’
viewData: no visible global function definition for ‘gray’
viewData: no visible global function definition for ‘dev.cur’
viewData: no visible global function definition for ‘dev.set’
viewData: no visible global function definition for ‘X11’
viewData: no visible global function definition for ‘par’
viewData: no visible global function definition for ‘image’
viewData: no visible global function definition for ‘title’
writeData: no visible global function definition for ‘write.table’
writeData: no visible global function definition for ‘make.image’
writeData: no visible global function definition for ‘write.image’
Undefined global functions or variables:
  X11 dev.cur dev.set flush.console gray image make.image par quantile
  read.image read.table runif title write.image write.table
Consider adding
  importFrom("grDevices", "X11", "dev.cur", "dev.set", "gray")
  importFrom("graphics", "image", "par", "title")
  importFrom("stats", "quantile", "runif")
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
File ‘PET/libs/PET.so’:
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘misc.o’
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘art.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘art.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pgam/libs/pgam.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘pgam.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: gsl
Loading required package: R2Cuba
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pgs_user.tex' failed.
LaTeX errors:
! LaTeX Error: File `path.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {listings}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘seqLogo’ ‘Biostrings’
Error in re-building vignettes:
  ...
Loading required package: ape
Loading required package: seqLogo
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘seqLogo’
Loading required package: seqLogo
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘seqLogo’
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Ancestral.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./Ancestral-figLOGO.pdf): PDF inclusion: required
 page does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘PhaseType/libs/PhaseType.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘LJMA_arms.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘RankProd’
Package unavailable to check Rd xrefs: ‘RankProd’
File ‘phmm/libs/phmm.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘arms.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: lattice
Loading required package: Matrix
Warning in lmer(m ~ -1 + t + z1 + z2 + (z1 + z2 | cluster) + offset(log(N)),  :
  calling lmer with 'family' is deprecated; please use glmer() instead
Warning in (function (fn, par, lower = rep.int(-Inf, n), upper = rep.int(Inf,  :
  failure to converge in 10000 evaluations
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0102246 (tol = 0.001, component 1)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'phmm_poisson_df.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: def)

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Read 18 items
Parsed with column specification:
cols(
  W = col_double(),
  D = col_double(),
  S = col_double(),
  P = col_double()
)
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=Vikki,%2000790%20Helsinki,%20Finland&sensor=false
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'user-guide.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbding.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.66 \usepackage
                {xspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
Package required but not available: ‘LBE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-53 (LongPhyloinfer.Rmd) 
Error: processing vignette 'LongPhyloinfer.Rmd' failed with diagnostics:
INLA needed for this function to work. Use install.packages("INLA", repos="https://www.math.ntnu.no/inla/R/stable").
Execution halted
Error in re-building vignettes:
  ...
Attaching package: ‘R.oo’

The following objects are masked from ‘package:methods’:

    getClasses, getMethods

The following objects are masked from ‘package:base’:

    attach, detach, gc, load, save

Loading required package: ape
Loading required package: compoisson
Loading required package: MASS
Loading required package: ggplot2
Warning in setEquDist.GeneralSubstitution(this, value, force = TRUE) :
  The provided probabilities have been rescaled in order to sum to one!

Warning in insertSequence.Sequence(sequence, insert, insert.pos, process = process) :
  The length of the sequence to be inserted is zero! Nothing to do here!

Warning in insertSequence.Sequence(sequence, insert, insert.pos, process = process) :
  The length of the sequence to be inserted is zero! Nothing to do here!


Execution halted
Package required but not available: ‘qvalue’

Package suggested but not available for checking: ‘OCplus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘RPostgreSQL’ ‘topicmodels’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pivotalr.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.98 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotc6164697968e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotc6164697968e.png': No such file or directory
Quitting from lines 61-64 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘devtools’ ‘ReportingTools’
Package unavailable to check Rd xrefs: ‘devtools’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pkgmaker-unitTests.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.58 \setmargrb
               {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘rggobi’

Depends: includes the non-default packages:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘lattice’ ‘rggobi’ ‘ggplot2’
  ‘proto’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘gmp’
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    libs  23.6Mb
Error in re-building vignettes:
  ...
Warning in rug(subTics) : some values will be clipped
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'plan.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {boxedminipage}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘GenomicRanges’ ‘VariantAnnotation’ ‘Rsamtools’ ‘rtracklayer’
  ‘SummarizedExperiment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘RGtk2’

Package suggested but not available for checking: ‘latticist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘edgeR’ ‘DESeq’
Error in re-building vignettes:
  ...
Saving an object of class 'gstatModel'...
Subsetting observations to fit the prediction domain in 2D...
Generating predictions using the trend model (RK method)...
Running 5-fold cross validation using 'krige.cv'...
Creating an object of class "SpatialPredictions"
KML file opened for writing...
Reprojecting to +proj=longlat +datum=WGS84 ...
Writing to KML...
Closing  fmd_ST.kml
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'jss1079.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.53 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘mvabund’
Error in re-building vignettes:
  ...

Attaching package: ‘pls’

The following object is masked from ‘package:stats’:

    loadings

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pls-manual.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.6 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘survcomp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘pbdMPI’ ‘pbdBASE’ ‘pbdDMAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...


Attaching package: 'gridExtra'

The following object is masked from 'package:dplyr':

    combine

Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda

Execution halted
Package required but not available: ‘gWidgetsRGtk2’

Package which this enhances but not available for checking: ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘polmineR.Rcpp’ ‘europarl.en’ ‘rcqp’
Packages required but not available: ‘impute’ ‘pcaMethods’ ‘imputeLCMD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
as.popgraph: no visible global function definition for ‘is’
centroid_distance: no visible global function definition for ‘is’
centroid_variance: no visible global function definition for ‘is’
centroid_variance: no visible global function definition for ‘cov’
decorate_graph: no visible global function definition for ‘is’
overlay_popgraph: no visible global function definition for ‘is’
overlay_popgraph: no visible global function definition for ‘lines’
overlay_popgraph: no visible global function definition for ‘points’
overlay_popgraph: no visible global function definition for ‘text’
permute_popgraph: no visible global function definition for ‘is’
popgraph: no visible global function definition for ‘is’
popgraph: no visible global function definition for ‘qchisq’
popgraph: no visible global function definition for ‘prcomp’
popgraph: no visible global function definition for ‘var’
read.popgraph: no visible global function definition for ‘read.table’
test_congruence: no visible global function definition for ‘cor.test’
to_data.frame: no visible global function definition for ‘is’
to_pgraph: no visible global function definition for ‘is’
write_popgraph: no visible global function definition for ‘is’
write_popgraph : <anonymous>: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  cor.test cov is lines points prcomp qchisq read.table text var
  write.csv
Consider adding
  importFrom("graphics", "lines", "points", "text")
  importFrom("methods", "is")
  importFrom("stats", "cor.test", "cov", "prcomp", "qchisq", "var")
  importFrom("utils", "read.table", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘Popgraph.tex’
Package has no Sweave vignette sources and no VignetteBuilder field.
Error in re-building vignettes:
  ...
Loading required package: boot
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'popKorn.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘VariantAnnotation’
Errors in running code in vignettes:
when running code in ‘poplite.Rnw’
  ...
8             8         8    18      0  1.6844357  0.53539884          2     F
9             9         9    20      1  0.9113913 -0.55527835          2     F
10           10        10    12      1  0.2374303  1.77950291          1     M
# ... with more rows

> library(VariantAnnotation)

  When sourcing ‘poplite.R’:
Error: there is no package called ‘VariantAnnotation’
Execution halted
Error in re-building vignettes:
  ...

    select

The following object is masked from ‘package:stats’:

    filter

Error in makeSchemaFromData(dna, "dna") : 
  ERROR: The names of the supplied data.frame need to be modified for the database see correct.df.names
Starting clinical
Warning: RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data).
Starting samples
Starting dna
Error in filter_.Database(.data, .dots = lazyeval::lazy_dots(...)) : 
  ERROR: Cannot uniquely map columns to table, try using: tableX.columnY
Starting gender
Starting clinical
Starting samples
Starting dna

Error: processing vignette 'poplite.Rnw' failed with diagnostics:
 chunk 15 
Error in library(VariantAnnotation) : 
  there is no package called ‘VariantAnnotation’
Execution halted
Error in re-building vignettes:
  ...
Warning in replayPlot(x) : "border" is not a graphical parameter
Warning in replayPlot(x) : "fill" is not a graphical parameter
Warning in replayPlot(x) : "border" is not a graphical parameter
Warning in replayPlot(x) : "fill" is not a graphical parameter
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Warning in infinite_vals_replacement(D, warning) :
  Infinite values detected.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'algo.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.64 \usepackage
                {mathtools}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

The following object is masked from ‘package:utils’:

    object.size

The following object is masked from ‘package:base’:

    startsWith

Calculating life expectancy at birth ...
... done
Calculating net number of migrants ...
... done
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'burkina-faso-females.tex' failed.
BibTeX errors:
The top-level auxiliary file: burkina-faso-females.aux
I couldn't open style file apa.bst
---line 19 of file burkina-faso-females.aux
 : \bibstyle{apa
 :              }
I'm skipping whatever remains of this command
I found no style file---while reading file burkina-faso-females.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘Rglpk’ ‘ROI.plugin.glpk’ ‘ROI.plugin.symphony’
Errors in running code in vignettes:
when running code in ‘ROI_vignette.Rnw’
  ...

> suppressMessages(library(ROI))

> suppressMessages(library(ROI.plugin.quadprog))

> suppressMessages(library(ROI.plugin.glpk))

  When sourcing ‘ROI_vignette.R’:
Error: there is no package called ‘ROI.plugin.glpk’
Execution halted
when running code in ‘custom_moments_objectives.Rnw’
  ...
+     r .... [TRUNCATED] 

> opt.sd <- optimize.portfolio(R, SD.portf, optimize_method = "ROI", 
+     momentFUN = "sigma.robust")
Loading required package: MASS

  When sourcing ‘custom_moments_objectives.R’:
Error: No solution found: Error in UseMethod("as.constraint") : 
  no applicable method for 'as.constraint' applied to an object of class "c('matrix', 'list')"
Execution halted
when running code in ‘portfolio_vignette.Rnw’
  ...

> maxret <- add.objective(portfolio = init, type = "return", 
+     name = "mean")

> opt_maxret <- optimize.portfolio(R = R, portfolio = maxret, 
+     optimize_method = "ROI", trace = TRUE)

  When sourcing ‘portfolio_vignette.R’:
Error: paste0("package:", plugin) %in% search() || requireNamespace(plugin,  .... is not TRUE
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DesignThoughts.tex' failed.
LaTeX errors:
! LaTeX Error: File `footmisc.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {ctable}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'PortfolioEffectEstim.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.15 \usepackage
                {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'PortfolioEffectHFT.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.15 \usepackage
                {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.7Mb
Error in re-building vignettes:
  ...
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in analyseMCMCs(object$fitMCMC$chains, stat = NULL, statName = "loglik",  :
  For  loglik calling coda::effectiveSize resulted in an error: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 
  0 (non-NA) cases

Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in analyseMCMCs(object$fitMCMC$chains, stat = NULL, statName = "AIC",  :
  For  AIC calling coda::effectiveSize resulted in an error: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 
  0 (non-NA) cases

Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in analyseMCMCs(object$fitMCMC$chains, stat = NULL, statName = "AICc",  :
  For  AICc calling coda::effectiveSize resulted in an error: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 
  0 (non-NA) cases

Quitting from lines 419-430 (UserGuide.Rmd) 
Error: processing vignette 'UserGuide.Rmd' failed with diagnostics:
package 'Rmpfr' not found
Execution halted
Found the following significant warnings:
  powell.c:700:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  powell.c:724:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/powell.Rcheck/00install.out’ for details.
File ‘powell/libs/powell.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘powell.o’
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘powell.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required but not available: ‘AnnotationDbi’ ‘GOSemSim’ ‘GO.db’

Packages which this enhances but not available for checking:
  ‘KEGG.db’ ‘org.Hs.eg.db’ ‘org.Sc.sgd.db’ ‘org.Ag.eg.db’
  ‘org.Pt.eg.db’ ‘org.Rn.eg.db’ ‘org.Ss.eg.db’ ‘org.At.tair.db’
  ‘org.Bt.eg.db’ ‘org.Ce.eg.db’ ‘org.Cf.eg.db’ ‘org.Dm.eg.db’
  ‘org.Dr.eg.db’ ‘org.EcK12.eg.db’ ‘org.EcSakai.eg.db’ ‘org.Gg.eg.db’
  ‘org.Mm.eg.db’ ‘org.Mmu.eg.db’ ‘org.Pf.plasmo.db’ ‘org.Xl.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘PerfMeas’
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Packages suggested but not available for checking: ‘rosm’ ‘rgdal’
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'charfunc.tex' failed.
LaTeX errors:
! LaTeX Error: File `esint.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.12 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'profdpm.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithmic.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.58 \newcommand
                {\bz}{\boldsymbol{z}}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    extdata  10.9Mb
    libs      1.0Mb
Running examples in ‘proftools-Ex.R’ failed
The error most likely occurred in:

> ### Name: filterProfileData
> ### Title: Filter Profile Data
> ### Aliases: filterProfileData
> ### Keywords: programming utilities
> 
> ### ** Examples
> 
> pd <- readProfileData(system.file("samples", "glmEx.out", package="proftools"))
> plotProfileCallGraph(pd)
Error in loadNamespace(name) : there is no package called ‘graph’
Calls: plotProfileCallGraph ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Quitting from lines 221-222 (proftools.Rnw) 
Error: processing vignette 'proftools.Rnw' failed with diagnostics:
there is no package called 'graph'
Execution halted
Packages suggested but not available for checking:
  ‘qtbase’ ‘RGtk2’ ‘cairoDevice’ ‘gWidgetsRGtk2’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 71-76 (ProliferativeIndexVignette.Rmd) 
Error: processing vignette 'ProliferativeIndexVignette.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Error in re-building vignettes:
  ...
  In `d' `NA' elements were replaced with string "NA"
Warning in `[<-.factor`(`*tmp*`, thisvar, value = "NA") :
  invalid factor level, NA generated
Warning in `[<-.factor`(`*tmp*`, thisvar, value = "NA") :
  invalid factor level, NA generated
Warning in location(g3, species = c("human"), vertex.size = 3, vertex.label.cex = 0.5,  :
  There are some 'NA' values in graph attribute 'category'!
Warning in if (layout %in% c("reingold.tilford", "circle", "random", "fruchterman.reingold",  :
  the condition has length > 1 and only the first element will be used
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \usepackage
               {caption}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [59s/59s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Initial log joint probability = -15.5191
  Optimization terminated normally: 
    Convergence detected: relative gradient magnitude is below tolerance
  Initial log joint probability = -15.5191
  Optimization terminated normally: 
    Convergence detected: relative gradient magnitude is below tolerance
  Initial log joint probability = -15.5191
  Optimization terminated normally: 
    Convergence detected: relative gradient magnitude is below tolerance
  testthat results ================================================================
  OK: 316 SKIPPED: 0 FAILED: 1
  1. Error: logistic_floor (@test_prophet.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘ALDEx2’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: RcppArmadillo
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'prospectr-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.65 \usepackage
                [cm, headings]{fullpage} % for larger margins^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘Biostrings’ ‘GOSemSim’ ‘org.Hs.eg.db’
Package required but not available: ‘aroma.light’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fftw’
Error in re-building vignettes:
  ...
Loading required package: Formula
Loading required package: ggplot2

Attaching package: ‘Hmisc’

The following objects are masked from ‘package:base’:

    format.pval, round.POSIXt, trunc.POSIXt, units

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'multiple.tex' failed.
LaTeX errors:
! LaTeX Error: File `framed.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.8 \definecolor
                {shadecolor}{rgb}{0.9, 0.9, 0.9}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘printr’
Errors in running code in vignettes:
when running code in ‘overview.Rnw’
  ...

> if (!require("GPArotation")) {
+     stop("GPArotation must be installed to do rotations")
+ } else {
+     f3t <- fa(Thurstone, 3, n.obs = 213)
+   .... [TRUNCATED] 

  When sourcing ‘overview.R’:
Error: could not find function "fa"
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `footmisc.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.48 \let
         \proglang=\textsf^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
Missing or unexported object: ‘purrr::as_mapper’
Package required but not available: ‘Rmpfr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: survival
PwrGSD 2.000
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'GrpSeqBnds-vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `harvard.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cleaning_and_debugging.tex' failed.
LaTeX errors:
! LaTeX Error: File `animate.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.68 \usepackage
                {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'QGglmmHowTo.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.16 \usepackage
                {fancyhdr}		%En-tête personnalisés (voir \fancyhead)^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘GenomicFeatures’ ‘Rsamtools’ ‘exomePeak’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/qtbase.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: qtl
Loading required package: lattice
Loading required package: corpcor
Loading required package: mnormt
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cmst.tex' failed.
LaTeX errors:
! LaTeX Error: File `epsf.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \usepackage
               {epsfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘graph’ ‘pcalg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    contrib   3.7Mb
    doc       2.9Mb
    libs      1.2Mb
Error in re-building vignettes:
  ...
Warning in fixXgeno.f2(cross, alleles) :
   --Assuming that all individuals are female.

Warning in checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata,  :
  Dropping 4 individuals with missing phenotypes.

Warning in checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata,  :
  Dropping 4 individuals with missing phenotypes.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bcsft.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \marginparwidth
                    0pt^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘qtbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
  implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, i, value = <S4 object of class "taguchiFactor">) :
  implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, i, value = <S4 object of class "taguchiFactor">) :
  implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, i, value = <S4 object of class "taguchiFactor">) :
  implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, i, value = <S4 object of class "taguchiFactor">) :
  implicit list embedding of S4 objects is deprecated
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'qualityTools.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.23 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Running ‘testthat.R’ [213s/195s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         grow_dtm = FALSE, skip_grams_window = 3L))) at testthat/test-fcm.R:13
  2: eval(code, test_env)
  
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  testthat results ================================================================
  OK: 1491 SKIPPED: 6 FAILED: 2
  1. Error: test stm converter: under extreme situations  (@test-convert.R#119) 
  2. Error: compare the output feature co-occurrence matrix to that of the text2vec package (@test-fcm.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Removed 16 rows containing missing values (geom_point).
Warning: Removed 16 rows containing missing values (geom_point).
Quitting from lines 146-147 (Use_case.Rmd) 
Error: processing vignette 'Use_case.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
File ‘QUIC/libs/QUIC.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Quipu_tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.31 \sectionfont
                 {\sffamily\bfseries\color{BiocBlue}\sectionrule{0pt}{0pt}{-...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
conf.statement: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  pbeta
Consider adding
  importFrom("stats", "pbeta")
to your NAMESPACE file.
Running ‘loadlibs.r’ [0s/1s]
  Running ‘test.r’ [1s/1s]
Running the tests in ‘tests/test.r’ failed.
Last 13 lines of output:
  > source('loadlibs.r')
  > loadlibs(forcelocal=TRUE)
  
  Attaching package: 'combinat'
  
  The following object is masked from 'package:utils':
  
      combn
  
  make: *** No rule to make target `../src/core.o', needed by `../src/Quor.so'.  Stop.
  Error in dyn.load(file.path(package.loc, "src", "Quor.so")) : 
    unable to load shared object '/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Quor.Rcheck/tests/../src/Quor.so':
    dlopen(/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Quor.Rcheck/tests/../src/Quor.so, 6): image not found
  Calls: loadlibs -> dyn.load
  Execution halted
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'QZ-guide.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.72 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
FancyPies: no visible global function definition for ‘rainbow’
FancyPies: no visible global function definition for ‘plot’
FancyPies: no visible global function definition for ‘polygon’
Hist2GE: no visible global function definition for ‘dist’
Pies2GE: no visible global function definition for ‘rainbow’
Plots2GE: no visible global function definition for ‘aggregate’
Plots2GE: no visible global function definition for ‘x11’
Plots2GE: no visible global function definition for ‘title’
Plots2GE: no visible global function definition for ‘png’
Plots2GE: no visible global function definition for ‘dev.off’
PolyLines2GE: no visible global function definition for ‘rainbow’
Shapes2GE: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  aggregate dev.off dist plot png polygon rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow", "x11")
  importFrom("graphics", "plot", "polygon", "title")
  importFrom("stats", "aggregate", "dist")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'R2OpenBUGS.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.20 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages required but not available:
  ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘RGtk2Extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'R2WinBUGS.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.20 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 21-23 (TextureAnalysis.Rmd) 
Error: processing vignette 'TextureAnalysis.Rmd' failed with diagnostics:
there is no package called 'devtools'
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
Packages required but not available: ‘gRbase’ ‘RBGL’ ‘graph’

Package suggested but not available for checking: ‘KEGGgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘gRbase’ ‘rags2ridges’ ‘graph’ ‘marray’ ‘RBGL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: MASS
Loading required package: pcaPP
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rainbow.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.3Mb
Package suggested but not available for checking: ‘Heatplus’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   3.7Mb
Error in re-building vignettes:
  ...
  Solution may be nonunique
Warning in rq.fit.br(wx, wy, tau = tau, ...) :
  Solution may be nonunique
Warning in rq.fit.br(wx, wy, tau = tau, ...) :
  Solution may be nonunique
Warning in rq.fit.br(wx, wy, tau = tau, ...) :
  Solution may be nonunique
Warning in rq.fit.br(wx, wy, tau = tau, ...) :
  Solution may be nonunique
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.23 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'random-essay.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \setpapersize
                 {USletter}                 % use USletter paper^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: rngWELL
This is randtoolbox. For overview, type 'help("randtoolbox")'.
Warning in coll.test(runif, 2^7, 2^10, 1, echo = FALSE) :
  p-values will be approximate in the presence of low expected collision number.
Warning in coll.test(congruRand, 2^8, 2^14, 1, echo = FALSE) :
  p-values will be approximate in the presence of low expected collision number.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'fullpres.tex' failed.
LaTeX errors:
! LaTeX Error: File `footmisc.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.80 \usepackage
                {perpage}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘rgeos’ ‘rgdal’
Package suggested but not available for checking: ‘kohonen’
Error in re-building vignettes:
  ...
Loading required package: cluster
Loading required package: mclust
Package 'mclust' version 5.3
Type 'citation("mclust")' for citing this R package in publications.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RankAggreg.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.28 \usepackage
                [mathcal]{euscript}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rankcluster.tex' failed.
LaTeX errors:
! LaTeX Error: File `elsarticle.cls' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: cls)

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘graph’ ‘RBGL’ ‘NetPreProc’ ‘PerfMeas’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Pacific Biological Station, Nanaimo

All available PBS packages can be found at
http://code.google.com/p/pbs-software/

To see demos, type '.PBSfigs()'.
-----------------------------------------------------------


Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RapidPolygonLookup.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {graphicx,color,alltt}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘Biostrings’ ‘Rsamtools’ ‘GenomicRanges’ ‘GenomicAlignments’

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RAppArmor.Rcheck/00install.out’ for details.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   8.5Mb
Packages suggested but not available for checking: ‘rgdal’ ‘ncdf4’
Package unavailable to check Rd xrefs: ‘rgdal’
Error in re-building vignettes:
  ...
Loading required package: sp
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Raster.tex' failed.
LaTeX errors:
! LaTeX Error: File `hanging.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  non-integer #successes in a binomial glm!
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  dots in figure paths replaced with _ ("figure/panel_a")
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  dots in figure paths replaced with _ ("figure/panel_b")
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  dots in figure paths replaced with _ ("figure/hist_cdf")
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RDperm.tex' failed.
LaTeX errors:
! LaTeX Error: File `standalone.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.27 \usepackage
                {import} % To source LaTeX code^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘rattle’
Packages required but not available: ‘RGtk2’ ‘cairoDevice’

Packages suggested but not available for checking:
  ‘gWidgetsRGtk2’ ‘playwith’ ‘rggobi’ ‘RGtk2Extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in text.default(xlim[1], 2, transcript, adj = 0, cex = 1.2) :
  font width unknown for character 0x9
Warning in text.default(xlim[1], 2, transcript, adj = 0, cex = 1.2) :
  font width unknown for character 0x9
Warning in text.default(xlim[1], 2, transcript, adj = 0, cex = 1.2) :
  font metrics unknown for character 0x9
Warning in text.default(xlim[1], 2, transcript, adj = 0, cex = 1.2) :
  font metrics unknown for character 0x9
[getGenePositions.ucscGenome] Adding 'start_codon' and 'stop_codon' positions.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rbamtools.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.25 \usepackage
                {hyperref}                       % Index links, should be lo...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required and available but unsuitable version: ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp

Attaching package: 'dplyr'

The following objects are masked from 'package:raster':

    intersect, select, union

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 16-24 (BGM_Spatial.Rmd) 
Error: processing vignette 'BGM_Spatial.Rmd' failed with diagnostics:
there is no package called 'rgdal'
Execution halted
Packages required but not available: ‘fmcsR’ ‘ChemmineR’ ‘KEGGREST’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   3.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Package suggested but not available for checking: ‘downscale’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.8Mb
Packages suggested but not available for checking: ‘git2r’ ‘devtools’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 336-337 (RClone_qmsevpops.Rmd) 
Error: processing vignette 'RClone_qmsevpops.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Rclusterpp
Loading required package: Rcpp
Loading required package: RcppEigen
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rclusterpp.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \lstset
           {language=C++,basicstyle=\footnotesize\ttfamily}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘fabia’ ‘iBBiG’ ‘superbiclust’ ‘BcDiag’ ‘rqubic’ ‘BicARE’

Depends: includes the non-default packages:
  ‘biclust’ ‘fabia’ ‘iBBiG’ ‘superbiclust’ ‘BcDiag’ ‘rqubic’ ‘BicARE’
  ‘s4vd’ ‘BiBitR’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages in Depends field not imported from:
  ‘Rcmdr’ ‘seeg’ ‘sgeostat’ ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error in re-building vignettes:
  ...
Loading required package: splines
Loading required package: RcmdrMisc
Loading required package: car
Loading required package: sandwich
Loading required package: effects

Attaching package: ‘effects’

The following object is masked from ‘package:car’:

    Prestige

The Commander GUI is launched only in interactive sessions
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Getting-Started-with-the-Rcmdr.tex' failed.
BibTeX errors:
The top-level auxiliary file: Getting-Started-with-the-Rcmdr.aux
I couldn't open style file apa.bst
---line 3 of file Getting-Started-with-the-Rcmdr.aux
 : \bibstyle{apa
 :              }
I'm skipping whatever remains of this command
I found no style file---while reading file Getting-Started-with-the-Rcmdr.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [56s/89s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  7: asNamespace(ns)
  8: getNamespace(ns)
  9: tryCatch(loadNamespace(name), error = function(e) stop(e))
  10: tryCatchList(expr, classes, parentenv, handlers)
  11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  12: value[[3L]](cond)
  
  testthat results ================================================================
  OK: 742 SKIPPED: 32 FAILED: 3
  1. Error: loadCMIP5 handles spatial mismatches between ensembles (@test_loadCMIP5.R#104) 
  2. Error: loadCMIP5 handles FUN correctly (@test_loadCMIP5.R#193) 
  3. Error: loadEnsemble handles no files found (@test_loadEnsemble.R#35) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rcplex.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RcppAPT.Rcheck/00install.out’ for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    include   4.9Mb
    libs      1.4Mb
Error in re-building vignettes:
  ...
Error in asSpMat(lm) : lgCMatrix is not supported.
Error in asSpMat(L) : lgTMatrix is not supported.
dimnames(.) <- NULL:  translated to 
dimnames(.) <- list(NULL,NULL)  <==>  unname(.)
Error in asSpMat(nm) : ngCMatrix is not supported.
Error in asSpMat(ngt) : ngTMatrix is not supported.
Error in asSpMat(nM) : ntTMatrix is not supported.
Error in asSpMat(nsc) : nsCMatrix is not supported.
Error in asSpMat(ldi) : ldiMatrix is not supported.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppArmadillo-unitTests.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \setmargrb
              {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following warnings:
  ../inst/include/blaze/math/smp/openmp/Functions.h:98:1: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RcppBlaze.Rcheck/00install.out’ for details.
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.6Mb
Error in re-building vignettes:
  ...
Loading required package: RcppClassic
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppClassic-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.382 \setmargrb
                {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppCNPy-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.384 ^^M
         
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 30.8Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     22.6Mb
Running ‘doRUnit.R’ [82s/83s]
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
  Error executing .setUp before test.gsl.vector.view : Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
    Error 1 occurred building shared library.
  .setUp (before test.gsl.vector.wrappers): ERROR !! 
  Error executing .setUp before test.gsl.vector.wrappers : Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
    Error 1 occurred building shared library.
  > 
  > ## Return success or failure to R CMD CHECK
  > if (getErrors(tests)$nFail > 0) {
  +    stop("TEST FAILED!")
  + }
  > if (getErrors(tests)$nErr > 0) {
  +    stop("TEST HAD ERRORS!")
  + }
  Error: TEST HAD ERRORS!
  Execution halted
Errors in running code in vignettes:
when running code in ‘RcppGSL-unitTests.Rnw’
  ...

> if (err$nFail > 0) stop(sprintf("unit test problems: %d failures", 
+     err$nFail))

> if (err$nErr > 0) stop(sprintf("unit test problems: %d errors", 
+     err$nErr))

  When sourcing ‘RcppGSL-unitTests.R’:
Error: unit test problems: 14 errors
Execution halted
Error in re-building vignettes:
  ...
Loading required package: inline
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppGSL-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.393 \setmargrb
                {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      21.7Mb
    libs      7.9Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppMLPACK-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {epstopdf}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      5.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RcppOctave.Rcheck/00install.out’ for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    include   8.8Mb
    libs      2.1Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    include   6.2Mb
    libs      4.0Mb
Error in re-building vignettes:
  ...
Loading required package: inline

Attaching package: ‘inline’

The following object is masked from ‘package:Rcpp’:

    registerPlugin

Loading required package: highlight
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rcpp-FAQ.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.383 \setmargrb
                {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RcppRedis.Rcheck/00install.out’ for details.
installed size is 76.8Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
    lib      48.9Mb
    libs     23.4Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppZiggurat.tex' failed.
LaTeX errors:
! LaTeX Error: File `mathdesign.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.399 ^^M
         
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rcqp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rcriticor.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rcrypt.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rDEA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RDieHarder.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: rDNAse
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rDNAse.tex' failed.
LaTeX errors:
! LaTeX Error: File `tablefootnote.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.6 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: gbRd
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Inserting_bibtex_references.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {graphicx,color,alltt}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot9ce16a2399ae.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot9ce16a2399ae.png': No such file or directory
Quitting from lines 22-26 (mapDWD.Rmd) 
Error: processing vignette 'mapDWD.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   6.0Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'readJDX.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.68 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘Rmosek’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs  10.9Mb
Package required but not available: ‘isva’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'registry.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {amsfonts,hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘interval’ ‘Icens’
Package unavailable to check Rd xrefs: ‘interval’
Packages suggested but not available for checking:
  ‘Rgraphviz’ ‘Rglpk’ ‘Rsymphony’

Package which this enhances but not available for checking: ‘Rcplex’
Running examples in ‘relations-Ex.R’ failed
The error most likely occurred in:

> ### Name: choice
> ### Title: Relation-Based Choices
> ### Aliases: relation_choice
> ### Keywords: math
> 
> ### ** Examples
> 
> data("SVM_Benchmarking_Classification")
> ## Determine the three best classification learners in the above sense.
> relation_choice(SVM_Benchmarking_Classification, k = 3)
Error in loadNamespace(name) : there is no package called ‘Rglpk’
Calls: relation_choice ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Errors in running code in vignettes:
when running code in ‘relations.Rnw’
  ...

> data("Felines")

> relations <- as.relation_ensemble(Felines)

> E <- relation_consensus(relations, "symdiff/E")

  When sourcing ‘relations.R’:
Error: there is no package called ‘Rglpk’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Rgraphviz’
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Rgraphviz’

Error: processing vignette 'relations.Rnw' failed with diagnostics:
 chunk 26 (label = consensus1b) 
Error in loadNamespace(name) : there is no package called ‘Rglpk’
Execution halted
Error in re-building vignettes:
  ...
  Hat-values numerically 1 are replaced by 1 - 1e-8
Warning in hglm.default(y = Y, X = X, Z = Z, RandC = RandC, maxit = 200,  :
  Residuals numerically 0 are replaced by 1e-8
Warning in hglm.default(y = Y, X = X, Z = Z, RandC = RandC, maxit = 200,  :
  Hat-values numerically 1 are replaced by 1 - 1e-8
Warning in hglm.default(y = Y, X = X, Z = Z, RandC = RandC, maxit = 200,  :
  Residuals numerically 0 are replaced by 1e-8
Warning in hglm.default(y = Y, X = X, Z = Z, RandC = RandC, maxit = 200,  :
  Hat-values numerically 1 are replaced by 1 - 1e-8
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RepeatABEL_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `framed.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {marginnote}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [23s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 25 SKIPPED: 0 FAILED: 27
  1. Error: can't see environment of caller (@test-env.R#5) 
  2. Error: reprex doesn't write into environment of caller (@test-env.R#11) 
  3. Error: I understand exactly what I'm putting in reprex env (@test-env.R#22) 
  4. Error: reprex: clipboard input works (@test-input.R#12) 
  5. Error: reprex: expression input works (@test-input.R#17) 
  6. Error: reprex: character input works (@test-input.R#23) 
  7. Error: reprex: file input works (@test-input.R#31) 
  8. Error: reprex: file input in a subdirectory works (@test-input.R#40) 
  9. Error: Circular use is detected before render (@test-input.R#47) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘Guide_restorepoint.Rmd’, ‘Guide_restorepoint.html’,
    ‘Guide_restorepoint.md’
Package has no Sweave vignette sources and no VignetteBuilder field.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RESTguide.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.63 \usepackage
                {float}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘gWidgets2RGtk2’ ‘cairoDevice’ ‘RGtk2’
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
Package suggested but not available for checking: ‘BiocParallel’
Package required but not available: ‘PKI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is 79.7Mb
  sub-directories of 1Mb or more:
    libs      77.2Mb
    pictures   1.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rgeolocate.Rcheck/00install.out’ for details.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rglpk.Rcheck/00install.out’ for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    fonts   1.5Mb
    libs    3.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rgnuplot.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
(./tufte-handout.cls
Document Class: tufte-handout 2009/12/11 v3.5.0 Tufte-handout class
(./tufte-common.def
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2016basic/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2016basic/texmf-dist/tex/generic/xkeyval/keyval.tex))))

! LaTeX Error: File `xifthen.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

Enter file name: 
! Emergency stop.
<read *> 
         
l.14 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on rgp_introduction.log.
make: *** [pdf] Error 1
Error in buildVignettes(dir = "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rgp.Rcheck/vign_test/rgp") : 
  running 'make' failed
Execution halted
Packages suggested but not available for checking:
  ‘graph’ ‘gWidgetsRGtk2’ ‘hyperdraw’ ‘hypergraph’ ‘playwith’ ‘pmg’
  ‘rgdal’ ‘rggobi’ ‘Rgraphviz’ ‘SVGAnnotation’
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    extra   9.4Mb
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RGtk2.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rhosp.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {amsfonts,amsmath,amssymb,amsthm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rhpc.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘httr’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘installr’
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: ‘rggobi’ ‘fftw’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: xlsx
Loading required package: rJava
Loading required package: xlsxjars
Loading required package: ggplot2
Loading required package: stringr
Loading required package: shiny
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RJafroc.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.120 \usepackage
                 {float}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Note: information on .o files is not available
File ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘chopsticks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rkafka.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: def)

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following apparent object files/libraries:
  src/l64/c.o src/m64/c.o src/w32/c.o src/w64/c.o
Object files/libraries should not be included in a source package.
Found the following executable file:
  src/w32/c.o
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  ‘genefilter’ ‘golubEsets’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'data.handling.tex' failed.
LaTeX errors:
! LaTeX Error: File `gensymb.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 \usepackage
               [noae]{Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'Rlda.ltx' failed with diagnostics:
Running 'texi2dvi' on 'Rlda.ltx' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {calrsfs}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rLindo.Rcheck/00install.out’ for details.
Mallows: no visible global function definition for ‘runif’
Mallows: no visible global function definition for ‘x11’
Mallows: no visible global function definition for ‘plot’
Mallows: no visible global function definition for ‘dev.off’
UpdateLambda: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RMark.Rcheck/00install.out’ for details.
File ‘RMC/libs/RMC.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'The_rmgarch_models.tex' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [round]{natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Running examples in ‘RMongo-Ex.R’ failed
The error most likely occurred in:

> ### Name: dbAggregate-methods
> ### Title: Performing a MongoDB aggregate query
> ### Aliases: dbAggregate dbAggregate-methods
> ###   dbAggregate,RMongo,character,character-method
> 
> ### ** Examples
> 
>   mongo <- mongoDbConnect("test")
>   # insert two records
>   dbInsertDocument(mongo, "test_data", '{"foo": "bar", "size": 5 }')
Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
  com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
Calls: dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck -> .Call
Execution halted
Running ‘RMongo-Ex.R’ [3s/3s]
Running the tests in ‘tests/RMongo-Ex.R’ failed.
Last 13 lines of output:
  +   dbRemoveQuery(mongo, "test_data", '{}')
  +   dbDisconnect(mongo)
  +   
  +   # print(length(output))
  +   print(as.character(output[1]))
  + 
  +   checkEquals("{ \"_id\" : \"bar\"}", as.character(output[1]))
  +   # checkEquals("bar", as.character(output[1]))
  + }
  > 
  > test.dbInsertDocument()
  Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
    com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
  Calls: test.dbInsertDocument ... dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck -> .Call
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rmosek.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rMouse.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

The following objects are masked from ‘package:stats’:

    dbinom, dnorm, dpois, pnorm

The following objects are masked from ‘package:base’:

    cbind, pmax, pmin, rbind

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Maechler_useR_2011-abstr.tex' failed.
LaTeX errors:
! LaTeX Error: File `hanging.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.3 \usepackage
               [pdftex]{graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rmpi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Integer division truncated to constant ‘768614336404’ at (1) [-Winteger-division]
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rmumps.Rcheck/00install.out’ for details.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Packages suggested but not available for checking: ‘topGO’ ‘DESeq’
Packages unavailable to check Rd xrefs: ‘DESeq’, ‘topGO’
Package suggested but not available for checking: ‘RnavGraph’
Package required but not available: ‘graph’

Packages suggested but not available for checking:
  ‘PairViz’ ‘RDRToolbox’ ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rgeos’ ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Running examples in ‘RndTexExams-Ex.R’ failed
The error most likely occurred in:

> ### Name: rte.build.rdn.test
> ### Title: Build random tests from LaTeX file
> ### Aliases: rte.build.rdn.test
> 
> ### ** Examples
> 
> # define some options
> latex.dir.out = 'latexOut' # Name of folder where latex files are going (will create if not exists)
> pdf.dir.out = 'PdfOut'     # Name of folder where resulting pdf files are going
> f.out <- 'MyRandomTest_'   # Name of pdfs (MyRandomTest_1.pdf, MyRandomTest_2.pdf, ... )
> n.test <- 1                # Number of tests to build
> n.question <- 2            # Number of questions in each test
> 
> # Get latex example from package
> f.in <- system.file("extdata", "MyRandomTest_examdesign.tex", package = "RndTexExams")
> 
> # Break latex file into a R list
> list.out <- rte.analyze.tex.file(f.in,
+                                  latex.dir.out = latex.dir.out,
+                                  pdf.dir.out = pdf.dir.out)

rte: Changing LaTeX file into dataframe... Done> 
> # Build pdfs
> result.out <- rte.build.rdn.test(list.in = list.out,
+                                  f.out = f.out,
+                                  n.test = n.test,
+                                  n.question = n.question,
+                                  latex.dir.out = latex.dir.out,
+                                  pdf.dir.out = pdf.dir.out)

rte: Checking for error in inputs... Done
rte: pdflatex flavor: texlive
rte: Type of OS: Darwin
rte: Latex compile function: texi2pdf
rte: Type of exam template: examdesign
rte: Number of mchoice questions: 4
rte: Building Test #1...Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'latexOut/MyRandomTest_1.tex' failed.
Messages:
/usr/local/bin/texi2dvi: pdflatex exited with bad status, quitting.
Calls: rte.build.rdn.test -> rte.compile.latex -> <Anonymous> -> texi2dvi
Execution halted
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  rte: Changing LaTeX file into dataframe... Done
  rte: Checking for error in inputs... Done
  rte: pdflatex flavor: texlive
  rte: Type of OS: Darwin
  rte: Latex compile function: texi2pdf
  rte: Type of exam template: examdesign
  rte: Number of mchoice questions: 4
  rte: Building Test #1...Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
    Running 'texi2dvi' on 'latexOut/MyRandomTest_1.tex' failed.
  Messages:
  /usr/local/bin/texi2dvi: pdflatex exited with bad status, quitting.
  Calls: test_check ... rte.build.rdn.test -> rte.compile.latex -> <Anonymous> -> texi2dvi
  testthat results ================================================================
  OK: 1 SKIPPED: 0 FAILED: 0
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 121-147 (rte-vignette_creating_exams.Rmd) 
Error: processing vignette 'rte-vignette_creating_exams.Rmd' failed with diagnostics:
Running 'texi2dvi' on 'latexOut/MyRandomTest_1.tex' failed.
Messages:
/usr/local/bin/texi2dvi: pdflatex exited with bad status, quitting.
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rngtools-unitTests.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.58 \setmargrb
               {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 93.2Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     91.1Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Warning in warn_if_args_exist(list(...)) :
  Extra arguments: 'colour', 'alpha', 'shape' are being ignored.  If these are meant to be aesthetics, submit them using the 'mapping' variable within ggpairs with ggplot2::aes or ggplot2::aes_string.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'robCompositions-overview.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘beadarray’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: rgenoud
##  rgenoud (Version 5.7-12.4, Build Date: 2015-07-19)
##  See http://sekhon.berkeley.edu/rgenoud for additional documentation.
##  Please cite software as:
##   Walter Mebane, Jr. and Jasjeet S. Sekhon. 2011.
##   ``Genetic Optimization Using Derivatives: The rgenoud package for R.''
##   Journal of Statistical Software, 42(11): 1-26. 
##

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RobPer_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {thumbpdf,lmodern}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘SSOAP’
Error in re-building vignettes:
  ...
Loading required package: robustbase
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'fastMcd-kmini.tex' failed.
BibTeX errors:
The top-level auxiliary file: fastMcd-kmini.aux
I couldn't open style file chicago.bst
---line 43 of file fastMcd-kmini.aux
 : \bibstyle{chicago
 :                  }
I'm skipping whatever remains of this command
I found no style file---while reading file fastMcd-kmini.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
cluster_em_outlier: no visible global function definition for ‘qchisq’
jth_dsty: no visible global function definition for ‘mahalanobis’
k_means: no visible global function definition for ‘kmeans’
mix_rcm: no visible global function definition for ‘median’
Undefined global functions or variables:
  kmeans mahalanobis median qchisq
Consider adding
  importFrom("stats", "kmeans", "mahalanobis", "median", "qchisq")
to your NAMESPACE file.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
Running examples in ‘robustrank-Ex.R’ failed
The error most likely occurred in:

> ### Name: sim.partially.matched
> ### Title: Simulate Paired, Independent, or Partially Matched Two-Sample
> ###   Data
> ### Aliases: r2sample sim.partially.matched
> 
> ### ** Examples
> 
> dat=sim.partially.matched(m=10,n.x=5,n.y=4,distr="normal",
+     params=c("loc.2"=0,"rho"=0,"scale.2"=1),seed=1)
> X=dat$X; Y=dat$Y; Yprime=dat$Yprime    
> 
> dat=sim.partially.matched(m=10,n.x=5,n.y=4,distr="logistic",
+     params=c("loc.2"=0,"rho"=0,"scale.2"=1),seed=1)
Error in loadNamespace(name) : there is no package called ‘copula’
Calls: sim.partially.matched ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Running examples in ‘robustX-Ex.R’ failed
The error most likely occurred in:

> ### Name: rbwheel
> ### Title: Multivariate Barrow Wheel Distribution Random Vectors
> ### Aliases: rbwheel
> ### Keywords: distribution robust
> 
> ### ** Examples
> 
> set.seed(17)
> rX8 <- rbwheel(1000,8, fullResult = TRUE, scaleAfter=FALSE)
> with(rX8, stopifnot(all.equal(X, X0 %*% A,    tol = 1e-15),
+                     all.equal(X0, X %*% t(A), tol = 1e-15)))
> ##--> here, don't need to keep X0 (nor A, since that is Qrot(p))
> 
> ## for n = 100,  you  don't see "it", but may guess .. :
> n <- 100
> pairs(r <- rbwheel(n,6))
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> ## for n = 500, you *do* see it :
> n <- 500
> pairs(r <- rbwheel(n,6))
> ## show explicitly
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> ## but increasing sig2 does help:
> pairs(r <- rbwheel(n,6, sig2 = .2))
> 
> ## show explicitly
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> set.seed(12)
> pairs(X <- rbwheel(n, 7, spherize=TRUE))
> colSums(X) # already centered
[1] -3.129441e-15  6.151329e-15 -8.555656e-15  2.352285e-15  2.428613e-16
[6]  3.505876e-15 -3.537101e-15
> 
> if(require("ICS")) {
+   # ICS: Compare M-estimate [Max.Lik. of t_{df = 2}] with high-breakdown :
+   stopifnot(require("MASS"))
+   X.paM <- ics(X, S1 = cov, S2 = function(.) cov.trob(., nu=2)$cov, stdKurt = FALSE)
+   X.paM.<- ics(X, S1 = cov, S2 = function(.) tM(., df=2)$V, stdKurt = FALSE)
+   X.paR <- ics(X, S1 = cov, S2 = function(.) covMcd(.)$cov, stdKurt = FALSE)
+   plot(X.paM) # not at all clear
+   plot(X.paM.)# ditto
+   plot(X.paR)# very clear
+ }
Loading required package: ICS
Loading required package: mvtnorm
Loading required package: MASS
Error in covMcd(.) : could not find function "covMcd"
Calls: ics -> do.call -> S2
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rchaeology.tex' failed.
LaTeX errors:
! LaTeX Error: File `breakurl.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.21 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘test_netlib.R’ [18s/30s]
Running the tests in ‘tests/test_netlib.R’ failed.
Last 13 lines of output:
  wood1p    1.442902e+00
  woodw     1.304476e+00
  > afiro <- netlib("afiro")
  > 
  > if ( length(ROI_applicable_solvers(afiro)) ) {
  + 	## solve a problem
  + 	sol <- ROI_solve(afiro)
  + 	sol
  + 	stopifnot( equal(sol$objval, 
  + 		       as.numeric(netlib("metainfo")["afiro", "optimal_value"])) )
  + }
  Error in SOLVE(x, ROI_translate(control, solver)) : 
    the directions "<", "<=", ">" and ">=" can only be used in combination with the "free" cone! The constraints c(3, 4, 7, 8, 9, 10, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) are inequality constraints but don`t belong to the "free" cone.
  Calls: ROI_solve -> SOLVE
  Execution halted
Package required but not available: ‘clpAPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ROI.plugin.glpk’ ‘ROI.plugin.symphony’

Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
Packages suggested but not available for checking: ‘proj4’ ‘rgdal’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 21-27 (rollply.Rmd) 
Error: processing vignette 'rollply.Rmd' failed with diagnostics:
there is no package called 'proj4'
Execution halted
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/ROracle.Rcheck/00install.out’ for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.8Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rotations-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [9s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  7: getExportedValue(pkg, name)
  8: asNamespace(ns)
  9: getNamespace(ns)
  10: tryCatch(loadNamespace(name), error = function(e) stop(e))
  11: tryCatchList(expr, classes, parentenv, handlers)
  12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  13: value[[3L]](cond)
  
  ?testthat results ================================================================
  OK: 484 SKIPPED: 0 FAILED: 2
  1. Error: can document eager data (@test-rd-data.R#7) 
  2. Error: can document lazy data (@test-rd-data.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rpanel.Rcheck/00install.out’ for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rpg.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘seqLogo’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Error in re-building vignettes:
  ...
Loading required package: rphast
Compacting sufficient statistics ...
Fitting tree model to alignment using REV ...
numpar = 13
Done.  log(likelihood) = -5370.320518 numeval=625
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette1.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.13 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘TNRSVignette.pdf’, ‘rPlantVignette.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rpms_2017_02_10.tex' failed.
LaTeX errors:
! LaTeX Error: File `tikz-qtree.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.14 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rpoppler.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RPPanalyzer.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {caption}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RProtoBuf.Rcheck/00install.out’ for details.
'library' or 'require' calls to packages already attached by Depends:
  ‘RSAGA’ ‘shapefiles’
  Please remove these calls from your code.
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’

Package which this enhances but not available for checking: ‘rjpod’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RQuantLib.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error: processing vignette 'RSP_refcard.tex.rsp' failed with diagnostics:
Running 'texi2dvi' on 'RSP_refcard.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.34 \titlespacing
                  {\section}{0pt}{2.0ex}{0.5ex}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
File ‘RSAgeo/libs/RSAgeo.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘RSAc.o’, ‘lib.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RSAc.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RSAP.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Quitting from lines 305-308 (article.Rnw) 
Error: processing vignette 'article.Rnw' failed with diagnostics:
Please run "rscala::scalaInstall()" or install Scala manually.
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RSclient.Rcheck/00install.out’ for details.
File ‘rscproxy/libs/rscproxy.so’:
  Found non-API calls to R: ‘R_DefParams’, ‘R_ReplDLLinit’,
    ‘R_SetParams’, ‘R_set_command_line_arguments’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘ptr_R_Busy’, ‘ptr_R_ReadConsole’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required but not available: ‘RBGL’ ‘graph’

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSclient’
Note: information on .o files is not available
File ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’

Package suggested but not available for checking: ‘ctc’

Depends: includes the non-default packages:
  ‘biwt’ ‘cairoDevice’ ‘fBasics’ ‘gplots’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘minerva’ ‘parmigene’ ‘stringr’ ‘snowfall’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: squeue: command not found
Quitting from lines 84-86 (rslurm.Rmd) 
Error: processing vignette 'rslurm.Rmd' failed with diagnostics:
slr_job has not been submitted
Execution halted
Package required but not available: ‘graph’

Package required and available but unsuitable version: ‘S4Vectors’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 43.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  42.0Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 65.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  61.9Mb
Running examples in ‘rstanarm-Ex.R’ failed
The error most likely occurred in:

> ### Name: pp_check.stanreg
> ### Title: Graphical posterior predictive checks
> ### Aliases: pp_check pp_check.stanreg
> 
> ### ** Examples
> 
> fit <- stan_glmer(mpg ~ wt + am + (1|cyl), data = mtcars, 
+                   iter = 400, chains = 2) # just to keep example quick
Error in new_CppObject_xp(fields$.module, fields$.pointer, ...) : 
  c++ exception (unknown reason)
trying deprecated constructor; please alert package maintainer

SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).

Gradient evaluation took 0.000102 seconds
1000 transitions using 10 leapfrog steps per transition would take 1.02 seconds.
Adjust your expectations accordingly!


Iteration:   1 / 400 [  0%]  (Warmup)
[1] "Error in sampler$call_sampler(args_list[[i]]) : "
[2] "  c++ exception (unknown reason)"                
error occurred during calling the sampler; sampling not done
Error in check_stanfit(stanfit) : 
  Invalid stanfit object produced please report bug
Calls: stan_glmer -> stan_glm.fit -> check_stanfit
Execution halted
Running ‘testthat.R’ [11s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Calls: test_check ... withCallingHandlers -> stan_glm -> stan_glm.fit -> check_stanfit
  testthat results ================================================================
  OK: 15 SKIPPED: 0 FAILED: 9
  1. Error: loo & waic throw error for non mcmc models (@test_loo.R#65) 
  2. Error: loo errors if model has weights (@test_loo.R#72) 
  3. Error: loo with k_threshold works for edge case(s) (@test_loo.R#118) 
  4. Error: kfold throws error for non mcmc models (@test_loo.R#132) 
  5. Error: kfold throws error if model has weights (@test_loo.R#144) 
  6. Error: kfold works on some examples (@test_loo.R#155) 
  7. Error: compare_models throws correct errors (@test_loo.R#181) 
  8. Error: compare_models works (@test_loo.R#222) 
  9. Error: kfold_and_reloo_data works (@test_loo.R#287) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 207.7Mb
  sub-directories of 1Mb or more:
    libs  205.5Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Error in re-building vignettes:
  ...

Attaching package: ‘rstpm2’

The following object is masked from ‘package:survival’:

    colon

Warning in log(-log(as.vector(S))) : NaNs produced
Warning in log(-log(as.vector(S))) : NaNs produced
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Introduction.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rsymphony.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: rtfbs
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.13 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Rcpp

Attaching package: ‘rtkore’

The following object is masked from ‘package:Rcpp’:

    LdFlags

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rtkpp-Arrays.tex' failed.
LaTeX errors:
! LaTeX Error: File `mdframed.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.46 \usepackage
                {xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Ruchardet.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘devtools’
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RVowpalWabbit.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: RWeka
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RWeka.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Errors in running code in vignettes:
when running code in ‘rworldmapFAQ.Rnw’
  ...
> mtext("Source: Andy South, The R Journal Vol. 3/1, June 2011", 
+     side = 1, line = -1)

> par(mai = c(0, 0, 0.2, 0), xaxs = "i", yaxs = "i")

> library(rgdal)

  When sourcing ‘rworldmapFAQ.R’:
Error: there is no package called ‘rgdal’
Execution halted
Error in re-building vignettes:
  ...
0 codes from your data failed to match with a country code in the map
94 codes from the map weren't represented in your data
Warning in classInt::classIntervals(sPDF[["EPI"]], n = 5, style = "jenks") :
  var has missing values, omitted in finding classes
149 codes from your data successfully matched countries in the map
0 codes from your data failed to match with a country code in the map
94 codes from the map weren't represented in your data
Warning in classInt::classIntervals(sPDF[["EPI"]], n = 5, style = "jenks") :
  var has missing values, omitted in finding classes
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rworldmap.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.37 \usepackage
                [colorlinks=true,urlcolor=blue]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs    4.8Mb
    yacas   1.3Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Ryacas.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
`stat_bin()` using `bins = 30`. Pick better value with
`binwidth`.
large z may result in inaccurate quantiles
`stat_bin()` using `bins = 30`. Pick better value with
`binwidth`.
large z may result in inaccurate quantiles
`stat_bin()` using `bins = 30`. Pick better value with
`binwidth`.
large z may result in inaccurate quantiles
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sadists.tex' failed.
LaTeX errors:
! LaTeX Error: File `paralist.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.91 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: bbmle
Loading required package: stats4
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sads_intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `framed.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {xspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Warning in sqrt(diag(vc)) : NaNs produced
Warning in sqrt(diag(vc)) : NaNs produced
Warning in sqrt(diag(vc)) : NaNs produced
Warning in sqrt(diag(vc)) : NaNs produced
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'selection.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  Population size       = 10
  Number of Generations = 40
  Elitism               = 2
  Mutation Chance       = 0.05


Warning in sink() : no sink to remove

 *** Sample size :  409.6178
 *** Number of strata :  203
---------------------------
...written output to outstrata.txt
Warning in sink() : no sink to remove
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SamplingStrataVignette.tex' failed.
BibTeX errors:
The top-level auxiliary file: SamplingStrataVignette.aux
I couldn't open style file chicago.bst
---line 23 of file SamplingStrataVignette.aux
 : \bibstyle{chicago
 :                  }
I'm skipping whatever remains of this command
I found no style file---while reading file SamplingStrataVignette.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘sampSurf-Ex.R’ failed
The error most likely occurred in:

> ### Name: izGridMirage
> ### Title: Generate Objects of Class "'mirageInclusionZoneGrid'"
> ### Aliases: izGridMirage
> ### Keywords: ~kwd1 ~kwd2
> 
> ### ** Examples
>  
> tr = Tract(c(x=20,y=20), cellSize=1)
> mtr = mirageTract(tr)
> st = standingTree(centerOffset=c(x=16,y=16))
> ag = angleGauge(4)     #4=baf
> hps.iz = horizontalPointIZ(st, angleGauge=ag)
> hps.izg = izGridMirage(hps.iz, mtr, truncateOverlap=FALSE)
Loading required package: rgeos
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rgeos’
Error in gIntersects(North, p.iz) : could not find function "gIntersects"
Calls: izGridMirage -> izGridMirage -> .local
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'GettingStarted.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘GO.db’ ‘GOstats’ ‘networkTomography’ ‘org.Sc.sgd.db’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sas7bdat.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.20     \usepackage
                    {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'saves.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.14 \usepackage
                [^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'scaRabee.tex' failed.
LaTeX errors:
! LaTeX Error: File `ucs.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [latin1]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'scglrVignettes.tex' failed.
LaTeX errors:
! LaTeX Error: File `diagbox.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.64 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TechnicalDocument.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
SciencesPo 1.4.1
Warning in is.na(names(TABLE)) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(names(TABLE)) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
Quitting from lines 754-756 (Indices.Rmd) 
Error: processing vignette 'Indices.Rmd' failed with diagnostics:
there is no package called 'devtools'
Execution halted
Error in re-building vignettes:
  ...

Warning in i[, 2]/crossdist(start, end) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in i[, 2]/crossdist(start, end) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sclero_tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `placeins.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {marginnote}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘BiocParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘oligoClasses’
Package suggested but not available for checking: ‘rgbif’
Error in re-building vignettes:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sdcMicro
--------
This is sdcMicro v5.0.3.
For references, please have a look at citation('sdcMicro')
Note: since version 5.0.0, the graphical user-interface is a shiny-app that can be started with sdcApp().
Please submit suggestions and bugs at: https://github.com/sdcTools/sdcMicro/issues
--------
Loading required package: xtable
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sdc_guidelines.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {color,xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following executable file:
  inst/external/env/bio14.bil
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: sp
[1] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio1.bil" 
[2] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio11.bil"
[3] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio12.bil"
[4] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio14.bil"
[5] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio16.bil"
[6] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio5.bil" 
[7] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio7.bil" 
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sdmvspecies.tex' failed.
LaTeX errors:
! LaTeX Error: File `hanging.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'doptimal.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {algpseudocode}% http://ctan.org/pkg/algorithmicx^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'seas.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [colorlinks = true]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Preparing the data.
Fitting model for 04035.
Computing the best seasonal wave.
Final model survreg results saved to myfit3_survregCall.txt.
Plots saved to myfit304035.pdf.
Fitting model for 04041.
Computing the best seasonal wave.
Final model survreg results saved to myfit3_survregCall.txt.
Plots saved to myfit304041.pdf.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \hypersetup
               {^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages in Depends field not imported from:
  ‘car’ ‘sgeostat’ ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/seewave.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Attaching package: ‘Ecfun’

The following object is masked from ‘package:base’:

    sign


Attaching package: ‘Ecdat’

The following object is masked from ‘package:datasets’:

    Orange

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SeleMix-vignette.tex' failed.
BibTeX errors:
The top-level auxiliary file: SeleMix-vignette.aux
I couldn't open style file chicago.bst
---line 30 of file SeleMix-vignette.aux
 : \bibstyle{chicago
 :                  }
I'm skipping whatever remains of this command
I found no style file---while reading file SeleMix-vignette.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'SemiCompRisks.ltx' failed with diagnostics:
Running 'texi2dvi' on 'SemiCompRisks.ltx' failed.
LaTeX errors:
! LaTeX Error: File `ntheorem.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \newtheorem
               {theorem}{Theorem}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Error in re-building vignettes:
  ...
      see ?specifyEquations
Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:tools':

    toHTML

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'semPLS-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               [english]{babel}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘bugBO.R’ [4s/6s]
  Running ‘bugKEEPdprime.R’ [4s/6s]
  Running ‘testBugResiduals.R’ [79s/123s]
  Running ‘testDprimes.R’ [66s/103s]
  Running ‘testKEEPeffs.R’ [168s/265s]
  Running ‘testMAM.R’ [12m/18m]
Running the tests in ‘tests/testMAM.R’ failed.
Last 13 lines of output:
    |========================================================              |  80%
  
    |                                                                            
    |=============================================================         |  87%
  
    |                                                                            
    |=================================================================     |  93%
  
  Warning messages:
  1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
    unable to evaluate scaled gradient
  2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
    Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
  
  Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'methodology.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithmic.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'seqDesignInstructions.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [round,authoryear]{natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘Biostrings’ ‘qvalue’ ‘widgetTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘Biostrings’ ‘rggobi’ ‘gWidgetsRGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs   5.0Mb
Package required but not available: ‘copynumber’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error: processing vignette 'vignette.ltx' failed with diagnostics:
Running 'texi2dvi' on 'vignette.ltx' failed.
LaTeX errors:
! LaTeX Error: File `beramono.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \usepackage
               [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 102.8Mb
  sub-directories of 1Mb or more:
    doc      4.9Mb
    libs    94.2Mb
    sqlite   1.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Package suggested but not available for checking: ‘SGP’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sgt.tex' failed.
LaTeX errors:
! LaTeX Error: File `todonotes.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {booktabs}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Searching for a suitable Scala installation.
  * FAILURE: 'scala.home' argument is NULL
  * FAILURE: 'rscala.scala.home' (<UNSET>) global option
  * FAILURE: SCALA_HOME () environment variable
  * FAILURE: 'scala' in the shell's search path

Cannot find a suitable Scala installation.

Scala is not distributed with the rscala package.  Individuals can install
Scala using "rscala::scalaInstall()" which places Scala in "~/.rscala" in the
user's home directory.  System administrators should install Scala globally as
described here: http://www.scala-lang.org/download/install.html.  In short,
simply download the archive, unpack it, and add the "scala" script to the path.
Note that Scala itself requires Java.  The rscala package tries various
techniques to find a suitable Scala installation, including searching the path.
Details on the search are available using "rscala::scalaInfo(verbose=TRUE)".

Error in get(f, envir = code_env) : 
  Please run "rscala::scalaInstall()" or install Scala manually.
Execution halted
Searching for a suitable Scala installation.
  * FAILURE: 'scala.home' argument is NULL
  * FAILURE: 'rscala.scala.home' (<UNSET>) global option
  * FAILURE: SCALA_HOME () environment variable
  * FAILURE: 'scala' in the shell's search path

Cannot find a suitable Scala installation.

Scala is not distributed with the rscala package.  Individuals can install
Scala using "rscala::scalaInstall()" which places Scala in "~/.rscala" in the
user's home directory.  System administrators should install Scala globally as
described here: http://www.scala-lang.org/download/install.html.  In short,
simply download the archive, unpack it, and add the "scala" script to the path.
Note that Scala itself requires Java.  The rscala package tries various
techniques to find a suitable Scala installation, including searching the path.
Details on the search are available using "rscala::scalaInfo(verbose=TRUE)".

Error in get(f, envir = code_env) : 
  Please run "rscala::scalaInstall()" or install Scala manually.
Calls: <Anonymous> -> lapply -> FUN -> get
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Searching for a suitable Scala installation.
  * FAILURE: 'scala.home' argument is NULL
  * FAILURE: 'rscala.scala.home' (<UNSET>) global option
  * FAILURE: SCALA_HOME () environment variable
  * FAILURE: 'scala' in the shell's search path

Cannot find a suitable Scala installation.

Scala is not distributed with the rscala package.  Individuals can install
Scala using "rscala::scalaInstall()" which places Scala in "~/.rscala" in the
user's home directory.  System administrators should install Scala globally as
described here: http://www.scala-lang.org/download/install.html.  In short,
simply download the archive, unpack it, and add the "scala" script to the path.
Note that Scala itself requires Java.  The rscala package tries various
techniques to find a suitable Scala installation, including searching the path.
Details on the search are available using "rscala::scalaInfo(verbose=TRUE)".


Searching for a suitable Scala installation.
  * FAILURE: 'scala.home' argument is NULL
  * FAILURE: 'rscala.scala.home' (<UNSET>) global option
  * FAILURE: SCALA_HOME () environment variable
  * FAILURE: 'scala' in the shell's search path

Cannot find a suitable Scala installation.

Scala is not distributed with the rscala package.  Individuals can install
Scala using "rscala::scalaInstall()" which places Scala in "~/.rscala" in the
user's home directory.  System administrators should install Scala globally as
described here: http://www.scala-lang.org/download/install.html.  In short,
simply download the archive, unpack it, and add the "scala" script to the path.
Note that Scala itself requires Java.  The rscala package tries various
techniques to find a suitable Scala installation, including searching the path.
Details on the search are available using "rscala::scalaInfo(verbose=TRUE)".

Error in get(n, envir = env) : 
  Please run "rscala::scalaInstall()" or install Scala manually.
Calls: <Anonymous> ... withCallingHandlers -> do.call -> <Anonymous> -> get
Execution halted
Searching for a suitable Scala installation.
  * FAILURE: 'scala.home' argument is NULL
  * FAILURE: 'rscala.scala.home' (<UNSET>) global option
  * FAILURE: SCALA_HOME () environment variable
  * FAILURE: 'scala' in the shell's search path

Cannot find a suitable Scala installation.

Scala is not distributed with the rscala package.  Individuals can install
Scala using "rscala::scalaInstall()" which places Scala in "~/.rscala" in the
user's home directory.  System administrators should install Scala globally as
described here: http://www.scala-lang.org/download/install.html.  In short,
simply download the archive, unpack it, and add the "scala" script to the path.
Note that Scala itself requires Java.  The rscala package tries various
techniques to find a suitable Scala installation, including searching the path.
Details on the search are available using "rscala::scalaInfo(verbose=TRUE)".

Error in get(f, envir = ns_env) : 
  Please run "rscala::scalaInstall()" or install Scala manually.
Calls: <Anonymous> -> Filter -> unlist -> lapply -> FUN -> get
Execution halted
Error in re-building vignettes:
  ...
The following object is masked from 'package:quantmod':

    summary

The following object is masked from 'package:base':

    summary

Loading required package: sandwich
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SharpeRatio.tex' failed.
LaTeX errors:
! LaTeX Error: File `paralist.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.72 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    www   6.4Mb
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  The following object is masked from 'package:rstan':
  
      traceplot
  
  Error in new_CppObject_xp(fields$.module, fields$.pointer, ...) : 
    c++ exception (unknown reason)
  trying deprecated constructor; please alert package maintainer
  error occurred during calling the sampler; sampling not done
  Error in check_stanfit(stanfit) : 
    Invalid stanfit object produced please report bug
  Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Error in re-building vignettes:
  ...

Warning in c(t(v1) %*% v2y, t(v1) %*% v2x)/(2 * (t(y) %*% v2x)) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in c(t(v1) %*% v2y, t(v1) %*% v2x)/(2 * (t(y) %*% v2x)) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'shotGroups.tex' failed.
LaTeX errors:
! LaTeX Error: File `apacite.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.80 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘edgeR’
Errors in running code in vignettes:
when running code in ‘SIBER.Rnw’
  ...

> SIBER(y = log(Dat[1, ] + 1), model = "NL")
      mu1       mu2    sigma1    sigma2       pi1     delta        BI 
6.2297063 6.8917722 0.3672838 0.3672838 0.1016360 1.8026005 0.5446901 

> library(edgeR)

  When sourcing ‘SIBER.R’:
Error: there is no package called ‘edgeR’
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'SIBER.Rnw' failed with diagnostics:
 chunk 8 
Error in library(edgeR) : there is no package called ‘edgeR’
Execution halted
Packages required but not available: ‘pcalg’ ‘RBGL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘test-all.R’ [150s/233s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  RUNIT TEST PROTOCOL -- Mon Apr  3 05:33:43 2017 
  *********************************************** 
  Number of test functions: 28 
  Number of errors: 1 
  Number of failures: 0 
  
   
  1 Test Suite : 
  simcausal unit testing - 28 test functions, 1 error, 0 failures
  ERROR in test.MV: Error in loadNamespace(name) : there is no package called 'rCopula'
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 1)
  
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: Formula

Attaching package: 'Hmisc'

The following objects are masked from 'package:base':

    format.pval, round.POSIXt, trunc.POSIXt, units

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'simcausal_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `footmisc.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.61 \usepackage
                [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘doMPI’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SimInf.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {algorithmic}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Packages required but not available:
  ‘Biostrings’ ‘BSgenome’ ‘GenomeInfoDb’ ‘GenomicRanges’

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘gRbase’ ‘graph’ ‘qpgraph’

Packages suggested but not available for checking: ‘clipper’ ‘topologyGSA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Biostrings’ ‘ShortRead’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ontologyPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: raster
Loading required package: sp

Attaching package: ‘SiMRiv’

The following object is masked from ‘package:stats’:

    simulate

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SiMRiv.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               [pdfborder={0 0 0}, colorlinks=true, urlcolor=blue, linkcolor...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘Rmpi’ ‘copula’
Running ‘doExtras.R’ [1s/1s]
  Comparing ‘doExtras.Rout’ to ‘doExtras.Rout.save’ ... OK
  Running ‘getArray-swap.R’ [1s/2s]
  Running ‘tst-wrongs.R’ [16s/53s]
  Running ‘tstTGforecasts.R’ [5s/18s]
  Running ‘tstVaRsuperadd.R’ [1s/1s]
Running the tests in ‘tests/tstVaRsuperadd.R’ failed.
Last 13 lines of output:
  > ## manually
  > require(copula) # for the following call of doOne()
  Loading required package: copula
  
  > nonGr <- get.nonGrids(varList)$nonGrids
  
  > dd <- doOne(n= min(nonGr$n, 100), d=4, family="Clayton", tau=0.5,
  +             qmargin=nonGr$qmargin, alpha=nonGr$alpha)
  Error in onacopulaL("Clayton", list(th = iTau(archmCopula("clayton"),  : 
    could not find function "onacopulaL"
  Calls: demo -> source -> withVisible -> eval -> eval -> doOne
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'copula'
  Execution halted
Package unavailable to check Rd xrefs: ‘copula’
Error in re-building vignettes:
  ...
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Shutting down cluster.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Execution halted
Packages unavailable to check Rd xrefs: ‘Rgraphviz’, ‘graph’
Packages required and available but unsuitable versions:
  ‘ggeffects’ ‘sjstats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘sjstats-Ex.R’ failed
The error most likely occurred in:

> ### Name: hdi
> ### Title: Compute high density intervals (HDI) for MCMC samples
> ### Aliases: hdi
> 
> ### ** Examples
> 
> library(rstanarm)
Loading required package: Rcpp
rstanarm (Version 2.15.2, packaged: 2017-04-19 09:04:44 UTC)
- Do not expect the default priors to remain the same in future rstanarm versions.
Thus, R scripts should specify priors explicitly, even if they are just the defaults.
- For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores())

Attaching package: ‘rstanarm’

The following object is masked from ‘package:sjstats’:

    se

> fit <- stan_glm(mpg ~ wt + am, data = mtcars, chains = 1)
Error in new_CppObject_xp(fields$.module, fields$.pointer, ...) : 
  c++ exception (unknown reason)
trying deprecated constructor; please alert package maintainer

SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).

Gradient evaluation took 0.00038 seconds
1000 transitions using 10 leapfrog steps per transition would take 3.8 seconds.
Adjust your expectations accordingly!


Iteration:    1 / 2000 [  0%]  (Warmup)
[1] "Error in sampler$call_sampler(args_list[[i]]) : "
[2] "  c++ exception (unknown reason)"                
error occurred during calling the sampler; sampling not done
Error in check_stanfit(stanfit) : 
  Invalid stanfit object produced please report bug
Calls: stan_glm -> stan_glm.fit -> check_stanfit
Execution halted
Package required but not available: ‘strataG’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.6Mb
Error in re-building vignettes:
  ...

    D, IQR, binom.test, cor, cov, fivenum, median, prop.test,
    quantile, sd, t.test, var

The following objects are masked from 'package:base':

    max, mean, min, prod, range, sample, sum

Loading required package: Sleuth2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'chapter01-HortonMosaic.tex' failed.
LaTeX errors:
! LaTeX Error: File `xstring.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \RequirePackage
                   {xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

    D, IQR, binom.test, cor, cov, fivenum, median, prop.test,
    quantile, sd, t.test, var

The following objects are masked from 'package:base':

    max, mean, min, prod, range, sample, sum

Loading required package: Sleuth3
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'chapter01-HortonMosaic.tex' failed.
LaTeX errors:
! LaTeX Error: File `xstring.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \RequirePackage
                   {xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘hitandrun’
Package unavailable to check Rd xrefs: ‘hitandrun’
Error in re-building vignettes:
  ...
See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/judge-plot1-1-eps-converted-to.pdf' no
t found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/shepard-plot1-1-eps-converted-to.pdf' 
not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/perm-plot1-1-eps-converted-to.pdf' not
 found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/spp-plot1-1-eps-converted-to.pdf' not 
found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! P
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘rhdf5’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘sva’ ‘isva’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'smm.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.21 \usepackage
                {diagbox}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pairwiseSNHT.tex' failed.
LaTeX errors:
! LaTeX Error: File `breakurl.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.61 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘GenomicRanges’ ‘Biostrings’ ‘Rsamtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rgdal’ ‘RODBC’ ‘rgeos’
Package suggested but not available for checking: ‘meteoForecast’
Error in re-building vignettes:
  ...
Warning in FUN(X[[i]], ...) :
  swe:Quantity given without unit of measurement: Salinity

Attaching package: ‘xtable’

The following object is masked from ‘package:maptools’:

    label

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sos4R.tex' failed.
LaTeX errors:
! LaTeX Error: File `csquotes.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.19 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘rgdal’ ‘rgeos’ ‘RPostgreSQL’
Running examples in ‘spacetime-Ex.R’ failed
The error most likely occurred in:

> ### Name: stConstruct
> ### Title: create ST* objects from long or wide tables
> ### Aliases: stConstruct
> ### Keywords: manip
> 
> ### ** Examples
> 
> # example 0: construction of STFDF from long table:
> library(maps)
> states.m = map('state', plot=FALSE, fill=TRUE)
> IDs <- sapply(strsplit(states.m$names, ":"), function(x) x[1])
>  
> library(maptools)
Loading required package: sp
Checking rgeos availability: FALSE
 	Note: when rgeos is not available, polygon geometry 	computations in maptools depend on gpclib,
 	which has a restricted licence. It is disabled by default;
 	to enable gpclib, type gpclibPermit()
> states = map2SpatialPolygons(states.m, IDs=IDs)
> 
> library(plm)
Loading required package: Formula
Warning: S3 methods ‘print.sparseSummary’, ‘print.diagSummary’, ‘c.abIndex’, ‘as.array.Matrix’, ‘as.array.sparseVector’, ‘as.matrix.Matrix’, ‘as.matrix.sparseVector’, ‘as.vector.Matrix’, ‘as.vector.sparseVector’ were declared in NAMESPACE but not found
Error: package or namespace load failed for ‘plm’ in library.dynam(lib, package, package.lib):
 shared object ‘Matrix.so’ not found
Execution halted
Running ‘basic.R’ [3s/5s]
  Comparing ‘basic.Rout’ to ‘basic.Rout.save’ ... OK
  Running ‘over.R’ [4s/7s]
  Comparing ‘over.Rout’ to ‘over.Rout.save’ ... OK
  Running ‘raster.R’ [5s/9s]
  Comparing ‘raster.Rout’ to ‘raster.Rout.save’ ... OK
  Running ‘rw.R’ [5s/8s]
  Comparing ‘rw.Rout’ to ‘rw.Rout.save’ ...38,40c38,43
< Warning message:
< In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
<   there is no package called 'rgeos'
---
> rgeos version: 0.3-19, (SVN revision 524)
>  GEOS runtime version: 3.5.0-CAPI-1.9.0 r4084 
>  Linking to sp version: 1.2-3 
>  Polygon checking: TRUE 
> 
> [1] TRUE
  Running ‘stconstruct.R’ [2s/4s]
Running the tests in ‘tests/stconstruct.R’ failed.
Last 13 lines of output:
  >     
  > library(maptools)
  Checking rgeos availability: FALSE
   	Note: when rgeos is not available, polygon geometry 	computations in maptools depend on gpclib,
   	which has a restricted licence. It is disabled by default;
   	to enable gpclib, type gpclibPermit()
  > states = map2SpatialPolygons(states.m, IDs=IDs)
  > 
  > library(plm)
  Loading required package: Formula
  Error: package or namespace load failed for 'plm' in library.dynam(lib, package, package.lib):
   shared object 'Matrix.so' not found
  In addition: Warning message:
  S3 methods 'print.sparseSummary', 'print.diagSummary', 'c.abIndex', 'as.array.Matrix', 'as.array.sparseVector', 'as.matrix.Matrix', 'as.matrix.sparseVector', 'as.vector.Matrix', 'as.vector.sparseVector' were declared in NAMESPACE but not found 
  Execution halted
Errors in running code in vignettes:
when running code in ‘jss816.Rnw’
  ...
+     tz = "GMT")

> library(plm)
Loading required package: Formula
Warning: S3 methods 'print.sparseSummary', 'print.diagSummary', 'c.abIndex', 'as.array.Matrix', 'as.array.sparseVector', 'as.matrix.Matrix', 'as.matrix.sparseVector', 'as.vector.Matrix', 'as.vector.sparseVector' were declared in NAMESPACE but not found

  When sourcing 'jss816.R':
Error: package or namespace load failed for 'plm' in library.dynam(lib, package, package.lib):
 shared object 'Matrix.so' not found
Execution halted
Error in re-building vignettes:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: quickPlot
Loading required package: reproducible

Attaching package: 'SpaDES.core'

The following objects are masked from 'package:stats':

    end, start

Quitting from lines 357-361 (ii-modules.Rmd) 
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    libs  30.5Mb
span: no visible global function definition for ‘complete.cases’
spanr: no visible global function definition for ‘model.frame’
spanr: no visible global function definition for ‘complete.cases’
spanr.hull: no visible global function definition for ‘par’
spanr.hull: no visible global function definition for ‘plot.new’
spanr.hull: no visible global function definition for ‘plot.window’
spanr.hull: no visible global function definition for ‘axis’
spanr.hull: no visible global function definition for ‘title’
spanr.hull: no visible global function definition for ‘points’
spanr.hull: no visible global function definition for ‘lines’
spanr.hull: no visible global function definition for ‘abline’
spanr.hull: no visible global function definition for ‘text’
spanr.hull: no visible global function definition for ‘segments’
spanr.hull: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box complete.cases lines model.frame par plot.new
  plot.window points segments text title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "lines", "par",
             "plot.new", "plot.window", "points", "segments", "text",
             "title")
  importFrom("stats", "complete.cases", "model.frame")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotdcab656233c5.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotdcab656233c5.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages required and available but unsuitable versions:
  ‘sparsebnUtils’ ‘ccdrAlgorithm’

Package suggested but not available for checking: ‘graph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘graph’ ‘RCy3’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sparsebnUtils)
  > 
  > test_check("sparsebnUtils")
  Error in loadNamespace(name) : there is no package called 'graph'
  Calls: test_check ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sparseHessianFD.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.27 \usepackage
                {algorithmic}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sparseMVN.tex' failed.
LaTeX errors:
! LaTeX Error: File `placeins.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.30 \usepackage
                {array}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in optim(unlist(start), obj.fun, hessian = FALSE, control = control,  :
  unknown names in control: cov11
Warning in Dev * c :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SpatialExtremesGuide.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.2 \usepackage
               {amsmath,amsfonts,amsthm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Matrix
Replacing existing trend.
Replacing existing trend.
Replacing existing trend.
Replacing existing trend.
Smooth interpolated at 279 time(s).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ST_tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `hyphenat.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 \usepackage
                [unicode,linktocpage=true,bookmarksnumbered=true]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    R      4.8Mb
    data   3.4Mb
    doc    4.6Mb
    help   5.2Mb
    libs   1.6Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  11.5Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'spBayesSurv.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.109 \usepackage
                 {enumerate}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘MassSpecWavelet’

Package suggested but not available for checking: ‘speaq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MassSpecWavelet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘xcms’ ‘MAIT’ ‘genefilter’ ‘impute’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
lambda.global: no visible global function definition for ‘mad’
lambda.global: no visible global function definition for ‘quantile’
lambda.global: no visible global function definition for ‘qnorm’
lambda.global: no visible global function definition for ‘pnorm’
ls.comp: no visible global function definition for ‘lsfit’
modterritory: no visible global function definition for ‘median’
newgotterritory: no visible global function definition for ‘median’
newterritory: no visible global function definition for ‘median’
ridge.comp: no visible global function definition for ‘lsfit’
ridge.diacomp: no visible global function definition for ‘ls.diag’
sw.plot: no visible global function definition for ‘par’
sw.plot: no visible global function definition for ‘plot’
sw.plot: no visible global function definition for ‘points’
sw.plot: no visible global function definition for ‘image’
sw.plot: no visible global function definition for ‘axis’
sw.plot: no visible global function definition for ‘legend’
sw.plot: no visible global function definition for ‘box’
sw.plot: no visible global function definition for ‘title’
thresh.level: no visible global function definition for ‘na.omit’
thresh.level: no visible global function definition for ‘mad’
thresh.level: no visible global function definition for ‘qnorm’
thresh.level: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  axis box image legend ls.diag lsfit mad median na.omit par plot pnorm
  points qnorm quantile title
Consider adding
  importFrom("graphics", "axis", "box", "image", "legend", "par", "plot",
             "points", "title")
  importFrom("stats", "ls.diag", "lsfit", "mad", "median", "na.omit",
             "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  predictions outside fitted range for lin(glucose).
Warning in (function (xnew)  :
  predictions outside fitted range for sm(glucose).
Warning in bsplines(mf[[i]], knots = args$knots[[i]]$knots, boundary.knots = args$knots[[i]]$boundary.knots,  :
  Some 'x' values are beyond 'boundary.knots'; Linear extrapolation used.
Warning in (function (xnew)  :
  predictions outside fitted range for lin(glucose).
Warning in (function (xnew)  :
  predictions outside fitted range for sm(glucose).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'UsingSpikeSlabGAM.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithmic.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {algorithm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘kirby21.fmri’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 35-44 (fmri_processing_spm12r.Rmd) 
Error: processing vignette 'fmri_processing_spm12r.Rmd' failed with diagnostics:
there is no package called 'kirby21.fmri'
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   4.8Mb
Error in re-building vignettes:
  ...
Loading required package: spray

Attaching package: ‘spray’

The following objects are masked from ‘package:base’:

    pmax, pmin

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'spray.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘CMA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘Biostrings’ ‘ShortRead’ ‘golubEsets’ ‘RankProd’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sprint.Rcheck/00install.out’ for details.
.dpssToEigenvalues: no visible global function definition for ‘mvfft’
smooth.construct.sp.smooth.spec: no visible global function definition
  for ‘str’
Undefined global functions or variables:
  mvfft str
Consider adding
  importFrom("stats", "mvfft")
  importFrom("utils", "str")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: sp

Version 3.3 of the spsurvey package was loaded successfully.

Warning in grts(design = Paneldsgn, DesignID = "UNEQUAL", type.frame = "area",  :
  
Oversample size is not proportional to category sample sizes for stratum
"None".

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CDF_Analysis.tex' failed.
LaTeX errors:
! LaTeX Error: File `chicago.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \bibliographystyle
                      {chicago}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  11.3Mb
Error in re-building vignettes:
  ...
    backsolve, forwardsolve

Loading required package: maps
--------------------------------------------------------------
 Analysis of Geostatistical Data
 For an Introduction to geoR go to http://www.leg.ufpr.br/geoR
 geoR version 1.7-5.2 (built on 2016-05-02) is now loaded
--------------------------------------------------------------

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'spTest-vig.tex' failed.
LaTeX errors:
! LaTeX Error: File `tabu.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages which this enhances but not available for checking:
  ‘RPostgreSQL’ ‘RODBC’
Errors in running code in vignettes:
when running code in ‘SQUAREM.Rnw’
  ...
+     Ap <- pvec * tA
+     pnew <- colMeans(t(Ap)/colSums(Ap))
+     pnew * (pnew > 0)
+ }

> library(interval)

  When sourcing ‘SQUAREM.R’:
Error: there is no package called ‘interval’
Execution halted
Error in re-building vignettes:
  ...
URL:                http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html
Repository:         CRAN
NeedsCompilation:   no
Packaged:           2016-08-18 16:13:21 UTC; rvaradh1
Date/Publication:   2016-08-18 23:27:39
Built:              R 3.4.0; ; 2017-04-22 00:14:02 UTC; unix

Index:

fpiter                  Fixed-Point Iteration Scheme
squarem                 Squared Extrapolation Methods for Accelerating
                        Slowly-Convergent Fixed-Point Iterations

Further information is available in the following vignettes in
directory
‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/SQUAREM.Rcheck/SQUAREM/doc’:

SQUAREM: SQUAREM Tutorial (source, pdf)

Loading required package: setRNG

Error: processing vignette 'SQUAREM.Rnw' failed with diagnostics:
 chunk 27 (label = libinterval) 
Error in library(interval) : there is no package called ‘interval’
Execution halted
draw.srd: no visible global function definition for ‘complete.cases’
draw.srd: no visible global function definition for ‘runif’
draw.srd: no visible global function definition for ‘arrows’
draw.srd: no visible global function definition for ‘text’
draw.srd: no visible global function definition for ‘segments’
draw.srd.enc: no visible global function definition for ‘par’
draw.srd.enc: no visible global function definition for ‘plot.new’
draw.srd.enc: no visible global function definition for ‘plot.window’
draw.srd.enc: no visible global function definition for ‘rgb’
draw.srd.enc: no visible global function definition for ‘polygon’
draw.srd.enc: no visible global function definition for ‘pchisq’
draw.srd.enc: no visible global function definition for ‘text’
draw.srd.enc: no visible global function definition for ‘title’
draw.srd.enc: no visible global function definition for ‘arrows’
drawcell: no visible global function definition for ‘polygon’
drawcell: no visible global function definition for ‘segments’
rotate.srd: no visible global function definition for ‘devAskNewPage’
srd: no visible global function definition for ‘devAskNewPage’
Undefined global functions or variables:
  arrows complete.cases devAskNewPage par pchisq plot.new plot.window
  polygon rgb runif segments text title
Consider adding
  importFrom("grDevices", "devAskNewPage", "rgb")
  importFrom("graphics", "arrows", "par", "plot.new", "plot.window",
             "polygon", "segments", "text", "title")
  importFrom("stats", "complete.cases", "pchisq", "runif")
to your NAMESPACE file.
Running examples in ‘SRRS-Ex.R’ failed
The error most likely occurred in:

> ### Name: SRRS-package
> ### Title: The Stepwise Response Refinement Screener (SRRS)
> ### Aliases: SRRS-package
> 
> ### ** Examples
> 
> SRRS()
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: SRRS -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error in re-building vignettes:
  ...
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Loading required package: spdep
Loading required package: sp
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ssfavignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘edgeR’ ‘qvalue’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘NetPreProc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SSsimple.tex' failed.
LaTeX errors:
! LaTeX Error: File `supertabular.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    include   8.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
Packages suggested but not available for checking:
  ‘easyNCDF’ ‘s2dverification’
Unavailable namespace imported from by a ':::' call: ‘s2dverification’
  See the note in ?`:::` about the use of this operator.
Package unavailable to check Rd xrefs: ‘s2dverification’
Packages required but not available:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘RSCABS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘stepPlr/libs/stepPlr.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘cg_descent.o’
  Found ‘__gfortran_stop_string’, possibly from ‘stop’ (Fortran)
    Object: ‘cg_descent.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Successfully loaded stepR package version 2.0-1.
Several new functions are added in version 2.0-0. Some older functions are deprecated (still working) and may be defunct in a later version. Please read the documentation for more details.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'StepR.tex' failed.
LaTeX errors:
! LaTeX Error: File `floatrow.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.56 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘stepwise-Ex.R’ failed
The error most likely occurred in:

> ### Name: maxchi
> ### Title: Stepwise detection of recombination breakpoints using MaxChi
> ### Aliases: maxchi
> ### Keywords: htest
> 
> ### ** Examples
>  demo(maxchi) 


	demo(maxchi)
	---- ~~~~~~

> inputFile<- system.file("extdata", "simulinfile.txt", package = "stepwise")

> breaks<-c(531,616,810)

> WinHalfWidth<-30

> permReps<-10

> a<-maxchi(inputFile, breaks, WinHalfWidth, permReps)
bos.cat2: no visible global function definition for ‘resid’
bos.cat2: no visible global function definition for ‘lm’
plot.rt: no visible global function definition for ‘plot’
plot.rt: no visible global function definition for ‘text’
plot.rt: no visible global function definition for ‘rect’
plot.rt: no visible global function definition for ‘title’
plot.rt: no visible global function definition for ‘par’
stdata: no visible binding for global variable ‘var’
stima: no visible global function definition for ‘fitted’
stima: no visible global function definition for ‘lm’
stima: no visible global function definition for ‘anova’
stima: no visible global function definition for ‘predict’
stima: no visible global function definition for ‘cor’
stima: no visible global function definition for ‘as.formula’
stima: no visible global function definition for ‘step’
Undefined global functions or variables:
  anova as.formula cor fitted lm par plot predict rect resid step text
  title var
Consider adding
  importFrom("graphics", "par", "plot", "rect", "text", "title")
  importFrom("stats", "anova", "as.formula", "cor", "fitted", "lm",
             "predict", "resid", "step", "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
stm v1.3.0 (2017-09-08) successfully loaded. See ?stm for help.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'stmVignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `placeins.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.59 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/tools/bm.sty)

! LaTeX Error: File `tablefootnote.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

Enter file name: 
! Emergency stop.
<read *> 
         
l.22 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on article.log.
make: *** [article.pdf] Error 1
Error in buildVignettes(dir = "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/stochvol.Rcheck/vign_test/stochvol") : 
  running 'make' failed
Execution halted
Packages suggested but not available for checking: ‘rgeos’ ‘tigris’
Error in re-building vignettes:
  ...

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

The following object is masked from 'package:dplyr':

    combine

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=georgia&zoom=5&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=georgia&sensor=false
Warning: Removed 703 rows containing missing values (geom_point).
Warning: Removed 89 rows containing missing values (geom_point).
Warning: Removed 1 rows containing missing values (geom_path).
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 98-100 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
there is no package called 'tigris'
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
Running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {rotating}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
'library' or 'require' calls in package code:
  ‘rgl’ ‘rpanel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages required but not available: ‘Rglpk’ ‘MultAlloc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘limma’ ‘samr’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.9Mb
Running ‘test-all.R’ [167s/242s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  RUNIT TEST PROTOCOL -- Mon Apr  3 00:44:25 2017 
  *********************************************** 
  Number of test functions: 18 
  Number of errors: 1 
  Number of failures: 0 
  
   
  1 Test Suite : 
  stremr unit testing - 18 test functions, 1 error, 0 failures
  ERROR in test.speedglm.allestimators10Kdata: Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 1)
  
  Execution halted
Packages required but not available:
  ‘AnnotationDbi’ ‘GO.db’ ‘biomaRt’ ‘org.Hs.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 31.3Mb
  sub-directories of 1Mb or more:
    libs  30.7Mb
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

Loading required package: sandwich
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'strucchange-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {graphicx,color,alltt}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘phyloseq’
Error in .requirePackage(package) : 
    unable to find required package 'phyloseq'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  Execution halted
Packages required but not available: ‘gWidgets2RGtk2’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘KFKSDS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RBGL’ ‘graph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'VignetteSubrank.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 \usepackage
               [pdftex]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘genefilter’ ‘sva’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'copulas.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {amsmath, natbib, hyperref, doi}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.3Mb
Error in re-building vignettes:
  ...
Type gamlssNews() to see new features/changes/bug fixes.

Doing computations: FALSE
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Doing computations: FALSE
Loading required namespace: spdep
Note: range of maximum neighbour order by region is 3-5
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'hhh4_spacetime.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.53 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 66.8Mb
  sub-directories of 1Mb or more:
    libs  66.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
Package unavailable to check Rd xrefs: ‘survJamda’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'plots.tex' failed.
LaTeX errors:
! LaTeX Error: File `morefloats.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.67 \usepackage
                [section]{placeins}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘survrec/libs/survrec.so’:
  Found ‘__gfortran_rand’, possibly from ‘rand’ (Fortran)
    Object: ‘bootstrap.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: SurvRegCensCov
Loading required package: survival
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'weibull.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {amsmath, amsthm, amssymb}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘svmpath/libs/svmpath.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'svUnit.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: def)

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/SWATmodel.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘cplexAPI’ ‘glpkAPI’
Running examples in ‘sybilcycleFreeFlux-Ex.R’ failed
The error most likely occurred in:

> ### Name: cfFBA
> ### Title: cycle free flux
> ### Aliases: cfFBA lrFBA
> ### Keywords: cycle free flux loopless FBA
> 
> ### ** Examples
> 
> ##---- Should be DIRECTLY executable !! ----
> ##-- ==>  Define data, use random,
> ##--	or do  help(data=index)  for the standard data sets.
> data(iAF1260)
> model=iAF1260
> fba=optimizeProb(model)
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’
Error in checkDefaultMethod(solver, method, pType) : 
  package ‘glpkAPI’ not found
Calls: optimizeProb -> optimizeProb -> .local -> sysBiolAlg
Execution halted
Packages suggested but not available for checking:
  ‘glpkAPI’ ‘cplexAPI’ ‘clpAPI’
Package unavailable to check Rd xrefs: ‘glpkAPI’
Running examples in ‘sybil-Ex.R’ failed
The error most likely occurred in:

> ### Name: SYBIL_SETTINGS
> ### Title: Set and Get sybil Parameters
> ### Aliases: SYBIL_SETTINGS SOLVER METHOD TOLERANCE MAXIMUM ALGORITHM
> ###   OPT_DIRECTION USE_NAMES PATH_TO_MODEL SOLVER_CTRL_PARM
> ### Keywords: optimize
> 
> ### ** Examples
> 
>   ## show all current parameters
>   SYBIL_SETTINGS()
$MODELORG_VERSION
[1] "2.0"

$SOLVER
[1] "glpkAPI"

$METHOD
[1] "simplex"

$TOLERANCE
[1] 1e-06

$MAXIMUM
[1] 1000

$ALGORITHM
[1] "fba"

$OPT_DIRECTION
[1] "max"

$USE_NAMES
[1] FALSE

$PATH_TO_MODEL
[1] "."

$SOLVER_CTRL_PARM
  NA
1 NA

>   
>   ## show current setting for "SOLVER"
>   SYBIL_SETTINGS("SOLVER")
[1] "glpkAPI"
> 
>   ## change current solver to glpkAPI
>   SYBIL_SETTINGS("SOLVER", "glpkAPI")
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’
Error in checkDefaultMethod(solver = value, method = "", probType = "",  : 
  package ‘glpkAPI’ not found
Calls: SYBIL_SETTINGS -> checkDefaultMethod
Execution halted
Errors in running code in vignettes:
when running code in ‘sybil.Rnw’
  ...
number of exchange reactions: 20

> optL <- optimizeProb(Ec_core, algorithm = "fba", retOptSol = FALSE)
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’

  When sourcing ‘sybil.R’:
Error: package ‘glpkAPI’ not found
Execution halted
Error in re-building vignettes:
  ...
sybil::fluxVar          Flux Variability Analysis


Type '?PKG::FOO' to inspect entries 'PKG::FOO', or 'TYPE?PKG::FOO' for
entries like 'PKG::FOO-TYPE'.




reading model description, ... OK
reading metabolite list ... OK
parsing reaction list ... OK
GPR mapping ... OK
sub systems ... OK
prepare modelorg object ... OK
validating object ... OK
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’

Error: processing vignette 'sybil.Rnw' failed with diagnostics:
 chunk 13 
Error in checkDefaultMethod(solver, method, pType) : 
  package ‘glpkAPI’ not found
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sybilSBML.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sylly_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: def)

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘mpoly’
Running examples in ‘symmoments-Ex.R’ failed
The error most likely occurred in:

> ### Name: convert.mpoly
> ### Title: Convert between mpoly and list representations of multivariate
> ###   polynomials
> ### Aliases: ' convert.mpoly '
> 
> ### ** Examples
> 
> # create an mpoly object here
> 
> # convert from mpoly to list representation
> library(mpoly)
Error in library(mpoly) : there is no package called ‘mpoly’
Execution halted
Errors in running code in vignettes:
when running code in ‘symmoments.rnw’
  ...
[4,]    1    1    1    2

> evaluate(m1234, c(4, 2, 1, 1, 3, 1, 1, 2, 1, 2))
[1] 3480

> library(mpoly)

  When sourcing ‘symmoments.R’:
Error: there is no package called ‘mpoly’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Loading required package: cubature
Loading required package: combinat

Attaching package: ‘combinat’

The following object is masked from ‘package:utils’:

    combn

Loading required package: multipol
Loading required package: abind

Attaching package: ‘multipol’

The following object is masked from ‘package:base’:

    single


Error: processing vignette 'symmoments.rnw' failed with diagnostics:
 chunk 13 (label = noncentral3a) 
Error in library(mpoly) : there is no package called ‘mpoly’
Execution halted
Packages suggested but not available for checking: ‘tigris’ ‘rgdal’
Packages suggested but not available for checking: ‘GISTools’ ‘rgeos’
Running examples in ‘tbart-Ex.R’ failed
The error most likely occurred in:

> ### Name: allocate
> ### Title: Teitz-Bart algorithm applied to Spatial* and Spatial*DataFrame
> ###   objects
> ### Aliases: allocate
> 
> ### ** Examples
> 
> data(meuse)
> coordinates(meuse) <- ~x+y
> allocate(meuse,p=5)
  [1]   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9  23
 [19]  23  23  23  23  23   9   9   9  23  23  23   9  23  23  23  23  23  23
 [37]  23  23  23  23  23 132 132 132 132 132 132 132 132 132 132 132 132 132
 [55] 132 132 132 132 132 132 132 113 113 113 113 113 113 113 113  77  77  77
 [73]  77  77  77  77  77  77  77  77  77 113 113   9 113 113  77  77  77  77
 [91]  77  77  77  77  77  77  77  77  77  77  77 113 113 113 113 132 113 113
[109] 113 113 113 113 113 113 113 113 113 113 132 132 132 132 132 132 132 132
[127] 132 132   9  23 113 132  23 132 113 113 113  77  77  77  77  77  77  77
[145]  77  77  77  77  77  77  77  77  77  77 113
> 
> 
> 
> require(RColorBrewer)
Loading required package: RColorBrewer
> require(GISTools)
Loading required package: GISTools
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GISTools’
> data(georgia)
Warning in data(georgia) : data set ‘georgia’ not found
> allocations.list <- allocate(georgia2,p=5)
Error in allocate(georgia2, p = 5) : object 'georgia2' not found
Execution halted
Package required but not available: ‘CNTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘edgeR’ ‘DESeq2’
Errors in running code in vignettes:
when running code in ‘tcpl_Overview.Rnw’
  ...
Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null.
Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null.
OMP: Error #13: Assertion failure at kmp_runtime.cpp(6480).
OMP: Hint: Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/.
OMP: Error #13: Assertion failure at kmp_runtime.cpp(6480).
OMP: Hint: Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/.

  When sourcing ‘tcpl_Overview.R’:
Error: argument to 'which' is not logical
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  34.7Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {dsfont,bm,color,multirow}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'tdthap-paper.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {amsmath,epsfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs       6.8Mb
    tessdata  31.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.5Mb
    libs   3.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/textTinyR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: textutils

Attaching package: 'textutils'

The following object is masked from 'package:tools':

    toHTML

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'btable.tex' failed.
LaTeX errors:
! LaTeX Error: File `libertine.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.6 \usepackage
               [scaled=0.8]{DejaVuSansMono}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Tides
Warning in gapsts(dry$time, dtMax, unit = unit, shiftbegin = TRUE) :
  First data point is beginning of gap. To shift t0, dt is estimated from next continuous series
Warning in gapsts(dry$time, dtMax, unit = unit, shiftbegin = TRUE) :
  First data point is beginning of gap. To shift t0, dt is estimated from next continuous series
Warning in gapsts(dry$time, dtMax, unit = unit, shiftbegin = TRUE) :
  First data point is beginning of gap. To shift t0, dt is estimated from next continuous series
Warning in gapsts(dry$time, dtMax, unit = unit, shiftbegin = TRUE) :
  First data point is beginning of gap. To shift t0, dt is estimated from next continuous series
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Tides.tex' failed.
BibTeX errors:
The top-level auxiliary file: Tides.aux
I couldn't open style file apalike2.bst
---line 14 of file Tides.aux
 : \bibstyle{apalike2
 :                   }
I'm skipping whatever remains of this command
I found no style file---while reading file Tides.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘tikzDevice-Ex.R’ failed
The error most likely occurred in:

> ### Name: getLatexStrWidth
> ### Title: Obtain Font Metrics from LaTeX
> ### Aliases: getLatexCharMetrics getLatexStrWidth
> ### Keywords: character metrics string
> 
> ### ** Examples
> 
> 
>    getLatexStrWidth('{\\\\tiny Hello \\\\LaTeX!}')
Error in getMetricsFromLatex(TeXMetrics, verbose = verbose) : 
TeX was unable to calculate metrics for the following string
or character:

	{\\tiny Hello \\LaTeX!}

Common reasons for failure include:
  * The string contains a character which is special to LaTeX unless
    escaped properly, such as % or $.
  * The string makes use of LaTeX commands provided by a package and
    the tikzDevice was not told to load the package.

The contents of the LaTeX log of the aborted run have been printed above,
it may contain additional details as to why the metric calculation failed.
Calls: getLatexStrWidth -> getMetricsFromLatex
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Quitting from lines 73-92 (tikzDevice.Rnw) 
Error: processing vignette 'tikzDevice.Rnw' failed with diagnostics:

TeX was unable to calculate metrics for the following string
or character:

	m

Common reasons for failure include:
  * The string contains a character which is special to LaTeX unless
    escaped properly, such as % or $.
  * The string makes use of LaTeX commands provided by a package and
    the tikzDevice was not told to load the package.

The contents of the LaTeX log of the aborted run have been printed above,
it may contain additional details as to why the metric calculation failed.
Execution halted
Errors in running code in vignettes:
when running code in ‘tileHMM.Rnw’
  ...

> h3k27.data <- as.matrix(simChIP[, 7:14])

> h3k27.data <- log(h3k27.data, 2)

> h3k27.norm <- preprocessCore::normalize.quantiles(h3k27.data)

  When sourcing ‘tileHMM.R’:
Error: there is no package called ‘preprocessCore’
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'tileHMM.Rnw' failed with diagnostics:
 chunk 3 
Error in loadNamespace(name) : 
  there is no package called ‘preprocessCore’
Execution halted
'library' or 'require' call to ‘ggplot2’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘microbenchmark’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
determine_replications: no visible global function definition for
  ‘microbenchmark’
do_timeit: no visible global function definition for ‘Rprof’
do_timeit: no visible global function definition for ‘summaryRprof’
mean.timeit: no visible global function definition for ‘aggregate’
plot.timeit: no visible global function definition for ‘ggplot’
plot.timeit: no visible global function definition for ‘aes’
plot.timeit: no visible global function definition for ‘geom_boxplot’
plot.timeit: no visible global function definition for ‘geom_point’
plot.timeit: no visible global function definition for ‘xlab’
plot.timeit: no visible global function definition for ‘ylab’
plot.timeit: no visible global function definition for ‘ggtitle’
plot.timeit: no visible global function definition for ‘coord_flip’
timeit: no visible binding for global variable ‘median’
Undefined global functions or variables:
  Rprof aes aggregate coord_flip geom_boxplot geom_point ggplot ggtitle
  median microbenchmark summaryRprof xlab ylab
Consider adding
  importFrom("stats", "aggregate", "median")
  importFrom("utils", "Rprof", "summaryRprof")
to your NAMESPACE file.
Running ‘simple.R’ [1s/1s]
Running the tests in ‘tests/simple.R’ failed.
Complete output:
  > 
  > ## run in the R session temp.dir. which gets cleaned
  > setwd(tempdir())                        
  > 
  > ## process html -- should work everywhere
  > file.copy(system.file("examples", "simpleHtml.Rmd", package="tint"), "simpleHtml.Rmd")
  [1] TRUE
  > rmarkdown::render("simpleHtml.Rmd")
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Execution halted
.my.tkdev: no visible global function definition for ‘X11’
tkpersp : draw: no visible global function definition for ‘par’
tkpersp : draw: no visible global function definition for ‘persp’
Undefined global functions or variables:
  X11 par persp
Consider adding
  importFrom("grDevices", "X11")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
Running examples in ‘tmcn-Ex.R’ failed
The error most likely occurred in:

> ### Name: revUTF8
> ### Title: Revert UTF-8 string to Chinese character.
> ### Aliases: revUTF8
> 
> ### ** Examples
> 
> revUTF8("1<U+4E8C>3<U+56DB>5")
Error in as.hexmode(str2) : 'x' cannot be coerced to class "hexmode"
Calls: revUTF8 -> intToUtf8 -> as.hexmode
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'tmle-npvi.tex' failed.
LaTeX errors:
! LaTeX Error: File `manfnt.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.59 \usepackage
                [textwidth=15cm, textheight=23cm]{geometry}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘limma’ ‘org.Hs.eg.db’
Running examples in ‘tmod-Ex.R’ failed
The error most likely occurred in:

> ### Name: tmodLimmaTest
> ### Title: Run tmod enrichment tests directly on a limma object
> ### Aliases: tmodLimmaTest
> 
> ### ** Examples
> 
> library(limma)
Error in library(limma) : there is no package called ‘limma’
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 47-57 (tmod.rmd) 
Error: processing vignette 'tmod.rmd' failed with diagnostics:
there is no package called 'limma'
Execution halted
Packages suggested but not available for checking:
  ‘Rcampdf’ ‘Rgraphviz’ ‘Rpoppler’ ‘tm.lexicon.GeneralInquirer’
Packages unavailable to check Rd xrefs: ‘graph’, ‘Rpoppler’
Running examples in ‘tm-Ex.R’ failed
The error most likely occurred in:

> ### Name: readPDF
> ### Title: Read In a PDF Document
> ### Aliases: readPDF
> ### Keywords: file
> 
> ### ** Examples
> 
> uri <- sprintf("file://%s", system.file(file.path("doc", "tm.pdf"), package = "tm"))
> if(all(file.exists(Sys.which(c("pdfinfo", "pdftotext"))))) {
+     pdf <- readPDF(control = list(text = "-layout"))(elem = list(uri = uri),
+                                                      language = "en",
+                                                      id = "id1")
+     content(pdf)[1:13]
+ }
> VCorpus(URISource(uri, mode = ""),
+         readerControl = list(reader = readPDF(engine = "ghostscript")))
sh: : command not found
Error in system2(gs_cmd, c("-dNODISPLAY -q", sprintf("-sFile=%s", shQuote(file)),  : 
  error in running command
Calls: VCorpus ... mapply -> <Anonymous> -> <Anonymous> -> pdf_info -> system2
Execution halted
Packages required but not available: ‘DESeq’ ‘edgeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘RGtk2’ ‘gWidgetsRGtk2’
Packages required but not available: ‘graph’ ‘gRbase’ ‘qpgraph’

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘rggobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘tpr/libs/tpr.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Expanding_TR8.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'traitr.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.15 \usepackage
                {amsmath}            % for amslatex stuff^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘rgdal’ ‘rgeos’ ‘OpenStreetMap’
Package unavailable to check Rd xrefs: ‘rgeos’
Running ‘tracks.R’ [2s/3s]
Running the tests in ‘tests/tracks.R’ failed.
Complete output:
  > Sys.setenv(TZ = "Europe/Berlin")
  > # Load required libraries.
  > 
  > library(sp)
  > library(spacetime)
  > library(trajectories)
  > library(rgdal)
  Error in library(rgdal) : there is no package called 'rgdal'
  Execution halted
Error in re-building vignettes:
  ...
 [>] max. distance: 139.84
 [>] neighborhood radius: 13.98
 [>] 4 representative(s) selected, coverage=39% (threshold=35%)
 [>] 148 distinct sequence(s)
 [>] number of objects (sum of weights): 99.22
 [>] max. distance: 139.84
 [>] neighborhood radius: 13.98
 [>] 5 representative(s) selected, coverage=38% (threshold=35%)
 [>] 89 distinct sequence(s)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TraMineR-state-sequence.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.77 \usepackage
                {afterpage}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in add.known.TRAMPknowns(x$knowns, x$samples, sample.fk, ...) :
  Mutiple peaks per enzyme/primer combination for sample 221, taking largest peaks only
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TRAMPRdemo.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `wrapfig.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {rotating}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: trapezoid
Loading required package: plyr
Loading required package: ggplot2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'trapezoid.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs  26.7Mb
Package required but not available: ‘phyloseq’

Package suggested but not available for checking: ‘adaptiveGPCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘treeHFM-Ex.R’ failed
The error most likely occurred in:

> ### Name: DrawViterbiTree
> ### Title: Arranges a Viterbi tree
> ### Aliases: DrawViterbiTree
> ### Keywords: misc
> 
> ### ** Examples
> 
> ## Fit a continous treeHFM ## 
> nHStates = 2;
> ########create observation sequences########
> obs1 <- rbind(runif(10,0,1),runif(10,0,1))
> obs2 <- rbind(runif(8,0,1),runif(8,0,1))
> data=list()
> data[[1]]=obs1
> data[[2]]=obs2
> ######### create guesses for gaussian covariance matrix and means #########
> mc2 <- Mclust(t(cbind(obs1,obs2)), G=2)
> muInit=mc2$parameters$mean;
> SigmaInit=mc2$parameters$variance$sigma
> #########create tree topology####################################
> nodeIndices1=cbind(c(0,1,2,3,3,4,5,6,7,8),c(1,2,3,4,5,6,7,8,9,10));
> nodeIndices2=cbind(c(0,1,2,3,4,4,5,6),c(1,2,3,4,5,6,7,8));
> dataNodeIndices=list()
> dataNodeIndices[[1]]=nodeIndices1;
> dataNodeIndices[[2]]=nodeIndices2;
> ######### create guesses for prior and transition matrices#########
> prior1=array(1,nHStates);
> priorInit = array(1,nHStates)/nHStates;
> transmatInit = matrix(1,nHStates,nHStates)*(1/nHStates);
> transInitDiv= matrix(1,nHStates,nHStates*nHStates)*(1/(nHStates*nHStates))
> #
> hfm=HFMfit(data,nHStates,dataNodeIndices,priorInit,transmatInit,transInitDiv,'c',
+ SigmaInit=SigmaInit, muInit=muInit);

 *** caught segfault ***
address 0x8, cause 'memory not mapped'

Traceback:
 1: .Call("RWrapperBM", priorInit, transmatInit, transInitDiv, emissionProb,     data, nodeIndices, parents, summationIndices, indicesXD,     type, stateIndicesSingle, nHStates, nDStates, nObs, dimData,     nEStates, SigmaInit, muInit)
 2: HFMfit(data, nHStates, dataNodeIndices, priorInit, transmatInit,     transInitDiv, "c", SigmaInit = SigmaInit, muInit = muInit)
An irrecoverable exception occurred. R is aborting now ...
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 62-71 (trip.Rmd) 
Error: processing vignette 'trip.Rmd' failed with diagnostics:
there is no package called 'rgdal'
Execution halted
Packages required but not available: ‘AnnotationDbi’ ‘GO.db’ ‘topGO’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'qexpfamily.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.35 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages which this enhances but not available for checking:
  ‘TSPostgreSQL’ ‘TSodbc’
Running ‘test_code.r’ [0s/2s]
Running the tests in ‘tests/test_code.r’ failed.
Last 13 lines of output:
  +     scoring(fit)
  +   }
  +   if(interv){
  +     interv_test(fit, tau=floor(n/2), delta=0.8, external=FALSE, est_interv=TRUE, ...)
  +     interv_detect(fit, taus=floor(0.45*n):ceiling(0.55*n), delta=0.8, B=3, ...)
  +     interv_multiple(fit, taus=floor(0.45*n):ceiling(0.55*n), deltas=c(0,1), B=3, final.control_bootstrap=NULL, ...)
  +   }
  +   return(TRUE)
  + }
  > 
  > checkfit(model=list(past_obs=1, past_mean=1), param=list(intercept=2, past_obs=0.4, past_mean=0.3), startestims=TRUE, extended=TRUE)
  Error in tsglm.sim(n = n, param = param, model = model, xreg = xreg, link = link,  : 
    could not find function "tsglm.sim"
  Calls: checkfit
  Execution halted
Error in re-building vignettes:
  ...
The following object is masked from 'package:gamlss.dist':

    DPO

Version 0.4-0 included new data defaults. See ?getSymbols.
Warning in vglm.fitter(x = x, y = y, w = w, offset = offset, Xm2 = Xm2,  :
  iterations terminated because half-step sizes are very small
Warning in vglm.fitter(x = x, y = y, w = w, offset = offset, Xm2 = Xm2,  :
  some quantities such as z, residuals, SEs may be inaccurate due to convergence at a half-step
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {mathabx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘TSPostgreSQL’ ‘TSodbc’ ‘RPostgreSQL’ ‘RODBC’
Packages unavailable to check Rd xrefs: ‘TSPostgreSQL’, ‘TSodbc’, ‘RPostgreSQL’, ‘RODBC’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
Apr 02, 2017 10:18:16 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData
INFO: The sdmx call returned messages in the footer:
 Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]]
Apr 02, 2017 10:18:16 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData
INFO: The sdmx call returned messages in the footer:
 Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]]

  When sourcing ‘Guide.R’:
Error: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxXmlContentException: The query: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT did not match any time series on the provider.
Execution halted
when running code in ‘GuideAppendix.Stex’
  ...

> options(continue = "  ")

> user <- Sys.getenv("MYSQL_USER")

> setup <- RMySQL::dbConnect(RMySQL::MySQL(), dbname = "test")

  When sourcing ‘GuideAppendix.R’:
Error: Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
Execution halted
Package unavailable to check Rd xrefs: ‘TSPostgreSQL’
Error in re-building vignettes:
  ...
Error: processing vignette 'tsdisagg2manual.ltx' failed with diagnostics:
Running 'texi2dvi' on 'tsdisagg2manual.ltx' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.16 \usepackage
                {enumerate}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: knitr
Loading required package: grid
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TurtleGraphics.tex' failed.
LaTeX errors:
! LaTeX Error: File `tocbibind.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.73 \usepackage
                {rotating}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Attaching package: ‘survey’

The following object is masked from ‘package:graphics’:

    dotchart

Loading required package: xtable
Loading required package: latticeExtra
Loading required package: RColorBrewer
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'iptw.tex' failed.
LaTeX errors:
! LaTeX Error: File `srcltx.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘link2GI’
  All declared Imports should be used.
Running examples in ‘uavRmp-Ex.R’ failed
The error most likely occurred in:

> ### Name: makeTP
> ### Title: Flight Track Planning tool
> ### Aliases: makeTP
> 
> ### ** Examples
> 
> ## (1) get example DEM data
> dsmFn <- system.file("extdata", "mrbiko.tif", package = "uavRmp")
> tutorial_flightArea <- system.file("extdata", "positions.csv", package = "uavRmp")
> 
> ## (2) make position flight plan
> makeTP  <-  makeTP(missionTrackList= tutorial_flightArea,
+                    demFn = dsmFn,
+                    uavType = "solo",
+                    followSurfaceRes=5,
+                    launchPos = c(8.679,50.856))
preprocessing DSM data...
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
Warning in gdal_setInstallation(ignore.full_scan = ignore.full_scan, verbose = verbose) :
  No GDAL installation found. Please install 'gdal' before continuing:
	- www.gdal.org (no HDF4 support!)
	- www.trac.osgeo.org/osgeo4w/ (with HDF4 support RECOMMENDED)
	- www.fwtools.maptools.org (with HDF4 support)

Warning in gdal_setInstallation(ignore.full_scan = ignore.full_scan, verbose = verbose) :
  If you think GDAL is installed, please run:
gdal_setInstallation(ignore.full_scan=FALSE)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘crop’ for signature ‘"NULL"’
Calls: makeTP -> makeFlightPathT3 -> <Anonymous> -> <Anonymous>
Execution halted
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    doc         2.2Mb
    dummydata   1.4Mb
    libs       20.1Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Umpire.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.15 \pagestyle
               {myheadings}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'design.tex' failed.
LaTeX errors:
! LaTeX Error: File `apalike.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.6 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘umx-Ex.R’ failed
The error most likely occurred in:

> ### Name: logLik.MxModel
> ### Title: logLik.MxModel
> ### Aliases: logLik.MxModel
> 
> ### ** Examples
> 
> require(umx)
> data(demoOneFactor)
> latents  = c("G")
> manifests = names(demoOneFactor)
> m1 <- mxModel("One Factor", type = "RAM", 
+ 	manifestVars = manifests, latentVars = latents, 
+ 	mxPath(from = latents, to = manifests),
+ 	mxPath(from = manifests, arrows = 2),
+ 	mxPath(from = latents, arrows = 2, free = FALSE, values = 1.0),
+ 	mxData(cov(demoOneFactor), type = "cov", numObs = 500)
+ )
> m1 = umxRun(m1, setLabels = TRUE, setValues = TRUE)
Running One Factor with 10 parameters
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  c++ exception (unknown reason)
Calls: umxRun -> mxRun -> runHelper
Execution halted
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Attaching package: 'umx'
  
  The following object is masked from 'package:stats':
  
      loadings
  
  > 
  > test_check("umx")
  Running One Factor with 10 parameters
  Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
    c++ exception (unknown reason)
  Calls: test_check ... eval -> eval -> umxRun -> mxRun -> runHelper -> .Call
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: reshape
Loading required package: lattice
Loading required package: parallel
Loading required package: Rcpp
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cap-recap.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 126-127 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
lexical error: invalid char in json text.
                                	      <!DOCTYPE html PUBLIC "-//W3C//
                     (right here) ------^
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Warning: 'data' shows efficiency > 1; this looks almost too good to be true
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'usl.tex' failed.
LaTeX errors:
! LaTeX Error: File `mathdesign.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.65 \usepackage
                [scaled=0.85]{beramono}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘uuid/libs/uuid.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  37.1Mb
'library' or 'require' call to ‘foreach’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘foreach’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
constant.post.9mo: no visible global function definition for ‘pexp’
ll.coverage.optim.const.post.9m: no visible global function definition
  for ‘dexp’
make.sample.pop: no visible global function definition for ‘runif’
mcmc.converge: no visible global function definition for ‘par’
mcmc.converge: no visible global function definition for ‘plot’
mcmc.converge: no visible global function definition for ‘points’
mcmc.converge: no visible global function definition for ‘density’
mcmc.converge: no visible global function definition for ‘lines’
mcmc.converge : <anonymous>: no visible global function definition for
  ‘sd’
mcmc.estimate : run.chain: no visible global function definition for
  ‘dexp’
mcmc.estimate : run.chain: no visible global function definition for
  ‘rnorm’
mcmc.estimate : run.chain: no visible global function definition for
  ‘runif’
mcmc.estimate : run.chain: no visible global function definition for
  ‘par’
mcmc.estimate : run.chain: no visible global function definition for
  ‘plot’
mcmc.estimate: no visible global function definition for ‘%dopar%’
mcmc.estimate: no visible global function definition for ‘foreach’
sim.n.vacc.sample.pop : <anonymous>: no visible global function
  definition for ‘runif’
vaccinate.sample.pop: no visible global function definition for ‘runif’
Undefined global functions or variables:
  %dopar% density dexp foreach lines par pexp plot points rnorm runif
  sd
Consider adding
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("stats", "density", "dexp", "pexp", "rnorm", "runif", "sd")
to your NAMESPACE file.
Running ‘coverageTest.r’ [0s/1s]
Running the tests in ‘tests/coverageTest.r’ failed.
Last 13 lines of output:
  > #*  
  > #*  $Id: coverageTest.r 378 2012-01-27 02:35:09Z ken $
  > #*  ----------------------------------------------------------------------------
  > 
  > 
  > # TBD: Add file header
  > # TBD: Do I need some 'library( pkg )' or 'source( file )' calls here???
  > 
  > 
  > # source( "../tests/testUtils.r" )
  > source( getTestPaths("vacem","tests/testUtils.r") )
  Error in getTestPaths("vacem", "tests/testUtils.r") : 
    could not find function "getTestPaths"
  Calls: source
  Execution halted
Packages suggested but not available for checking:
  ‘vaers’ ‘vaersND’ ‘devtools’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/VBmix.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   3.0Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vcrpart.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: def)

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Warning in has_utility("pdfcrop") :
  pdfcrop not installed or not in PATH
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vdg.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.75 \usepackage
                {algorithmic}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'decision-vegan.tex' failed.
LaTeX errors:
! LaTeX Error: File `ucs.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 \usepackage
                [utf8x]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'MedRegExample.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘VeryLargeIntegers-Ex.R’ failed
The error most likely occurred in:

> ### Name: 01. Basics
> ### Title: Very Large Integers Basics
> ### Aliases: '01. Basics' as.vli as.vli.default as.vli.character
> ###   as.vli.numeric asnumeric asnumeric.default asnumeric.vli
> ###   as.integer.vli as.character.vli vli print.vli is.vli
> 
> ### ** Examples
> 
> ## Creating a new vli object
> x <- as.vli("-89027148538375418689123052")
> 
> ## Printing a vli object
> print(x)
Very Large Integer: 
[1] -89027148538375418689123052
> 
> ## Testing the class
> is.vli(x)
[1] TRUE
> 
> ## Coercing into a character object
> as.character(x)
[1] "-89027148538375418689123052"
> 
> ## Accessing to the attributes of the vli object
> x$sign
[1] -1
> x$value
[1]   89  271 4853 8375 4186 8912 3052
> x$length
[1] 26
> 
> ## Punctuation signs are ignored
> as.vli("2345.25")
Very Large Integer: 
[1] 234525
> 
> 
> 
> ### * <FOOTER>
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  23.474 0.247 23.723 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
Error: segfault from C stack overflow
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: raster
Loading required package: sp

Attaching package: 'raster'

The following object is masked from 'package:colorspace':

    RGB

Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer

Attaching package: 'latticeExtra'

The following object is masked from 'package:ggplot2':

    layer

Quitting from lines 204-213 (intro-to-viridis.Rmd) 
Error: processing vignette 'intro-to-viridis.Rmd' failed with diagnostics:
Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Execution halted
Error in re-building vignettes:
  ...

The following object is masked from ‘package:base’:

    backsolve

Loading required package: grid
Warning in structure(ia, dimnames = NULL) :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ConfoundingPotential.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.25 \usepackage
                {keyval}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespaces in Imports field not imported from:
  ‘iterators’ ‘knitr’ ‘testthat’
  All declared Imports should be used.
Missing or unexported object: ‘dplyr::pull’
Package required but not available: ‘GenomicRanges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘waffect/libs/waffect.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 49.4Mb
  sub-directories of 1Mb or more:
    libs  48.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 124-128 (walker.Rmd) 
Error: processing vignette 'walker.Rmd' failed with diagnostics:
argument of length 0
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'walkr.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/wand.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
There are  2000 missing values for 05054000 or 49.78 percent of the data.
The maximum block of missing 05054000 data is 12 days long.
Filled in 2000 values for 05054000
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \hypersetup
               {^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Watersheds.tex' failed.
LaTeX errors:
! LaTeX Error: File `apacite.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.14 \bibliographystyle
                       {apacite}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Content type 'unknown' length 1513796 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'http://www.webgestalt.org/data/goslim/hsapiens_GOSlim_MolecularFunction.table'
Content type 'unknown' length 1122875 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'WebGestaltR.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: def)

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
Package suggested but not available for checking: ‘rgeolocate’
Error in re-building vignettes:
  ...
 [>] 490 sequences in the data set
 [>] min/max sequence length: 70/70
 [>] 490 sequences with 6 distinct states
 [>] creating a 'sm' with a single substitution cost of 1
 [>] creating 6x6 substitution-cost matrix using 1 as constant value
 [>] 490 distinct sequences
 [>] min/max sequence length: 70/70
 [>] computing distances using the HAM metric
 [>] elapsed time: 0.17 secs
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'WeightedClusterPreview.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.78 \usepackage
                {afterpage}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Definition.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {verbatim}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘HotDeckImputation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘impute’ ‘GO.db’ ‘AnnotationDbi’

Packages suggested but not available for checking:
  ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ ‘minet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AnnotationDbi’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'funwithfunload.tex' failed.
LaTeX errors:
! LaTeX Error: File `supertabular.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘genefilter’
Packages suggested but not available for checking:
  ‘devtools’ ‘AnomalyDetection’ ‘BreakoutDetection’
Unexported objects imported by ':::' calls:
  ‘circular:::DensityCircularRad’ ‘circular:::DvonmisesRad’
  ‘circular:::DwrappednormalRad’ ‘circular:::MlevonmisesRad’
  ‘circular:::MlewrappednormalRad’
  See the note in ?`:::` about the use of this operator.
Packages required but not available: ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-54 (Automat.Rmd) 
Error: processing vignette 'Automat.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'wrappedvig.ltx' failed with diagnostics:
Running 'texi2dvi' on 'wrappedvig.ltx' failed.
LaTeX errors:
! Package pdftex.def Error: File `wrappedv1-eps-converted-to.pdf' not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package pdftex.def Error: File `wrappedv2-eps-converted-to.pdf' not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package pdftex.def Error: File `wrappedv3-eps-converted-to.pdf' not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package pdftex.def Error: File `wrappedv4-eps-converted-to.pdf' not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                
Execution halted
Error in re-building vignettes:
  ...
See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/soccer2-plot1-1-eps-converted-to.pdf' 
not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/goggles-plot1-1-eps-converted-to.pdf' 
not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/swim-plot1-1-eps-converted-to.pdf' not
 found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/swim2-plot1-1-eps-converted-to.pdf' no
t found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘wsrf-Ex.R’ failed
The error most likely occurred in:

> ### Name: combine.wsrf
> ### Title: Combine Ensembles of Trees
> ### Aliases: combine combine.wsrf
> 
> ### ** Examples
> 
>   library("wsrf")
> 
>   # Prepare parameters.
>   ds     <- rattle::weather
Error in loadNamespace(name) : there is no package called ‘rattle’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Running ‘wsrftest.R’ [0s/0s]
Running the tests in ‘tests/wsrftest.R’ failed.
Complete output:
  > suppressMessages(library(wsrf))
  > suppressMessages(library(rattle))
  Error in library(rattle) : there is no package called 'rattle'
  Calls: suppressMessages -> withCallingHandlers -> library
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 63-67 (wsrf-guide.Rmd) 
Error: processing vignette 'wsrf-guide.Rmd' failed with diagnostics:
there is no package called 'rattle'
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    bin   4.1Mb
    lib   2.1Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Packages required but not available:
  ‘dnet’ ‘GenomicRanges’ ‘supraHex’ ‘rtracklayer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'XiMpLe_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: def)

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

Loading required package: ggplot2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'XLConnect.tex' failed.
LaTeX errors:
! LaTeX Error: File `couriers.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.12 \usepackage
                [colorlinks]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Xmisc

Attaching package: ‘Xmisc’

The following object is masked from ‘package:base’:

    dir.exists

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Xmisc-ArgumentParser.tex' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'OtherPackagesGallery.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.67 \usepackage
                {hyperref} % hyperref last^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/xtensor.Rcheck/00install.out’ for details.
Packages required but not available: ‘biomaRt’ ‘Rsamtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MBESS’
Running examples in ‘yhat-Ex.R’ failed
The error most likely occurred in:

> ### Name: aps
> ### Title: All Possible Subsets Regression
> ### Aliases: aps
> ### Keywords: models regression
> 
> ### ** Examples
> 
>   ## APS regression predicting miles per gallon based 
>   ## on vehicle weight, type of 
>   ## carborator, & number of engine cylinders
>      apsOut<-aps(mtcars,"mpg",list("wt","carb","cyl"))
> 
>   ## APS regression predicting paragraph comprehension based 
>   ## on thre verbal tests: general info, sentence comprehension,
>   ## & word classification
>  
>   ## Use HS dataset in MBESS 
>      require ("MBESS")
Loading required package: MBESS
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘MBESS’
>      data(HS.data)
Warning in data(HS.data) : data set ‘HS.data’ not found
>   ## APS
>      apsOut<-aps(HS.data,"paragrap",list("general","sentence",
+                                          "wordc"))
Error in is.data.frame(x) : object 'HS.data' not found
Calls: aps -> colnames -> is.data.frame
Execution halted
Packages required but not available: ‘graph’ ‘PairViz’

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'zipfr-tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.13 \setpapersize
                  [portrait]{A4}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/zstdr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: D:/temp/RtmpEdKNhm/R.INSTALL46fe01a1a689e/ACEt/man/ACEt-package.Rd:1: All text must be in a section
See 'd:/Rcompile/CRANpkg/local/3.3/ACEt.Rcheck/00install.out' for details.
prepare_Rd: ACEt-package.Rd:1: All text must be in a section
Authors@R field gives persons with no valid roles:
  Anders Hedenström [fnd]
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/audio.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: replacing previous import 'flexclust::clusters' by 'igraph::clusters' when loading 'AurieLSHGaussian'
See 'd:/Rcompile/CRANpkg/local/3.3/AurieLSHGaussian.Rcheck/00install.out' for details.
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/BayClone2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/bayesCL.Rcheck/00install.out' for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.6Mb
Authors@R field gives persons with no valid roles:
  Bea Hernández [rev] (Bea reviewed the package for ropensci, see https://github.com/ropensci/onboarding/issues/116)
  Elaine McVey [rev] (Elaine reviewed the package for ropensci, see https://github.com/ropensci/onboarding/issues/116)
Running 'testthat.R' [235s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  downloaded 107 bytes
  
  trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
  ...
  downloaded 3574 bytes
  
  testthat results ================================================================
  OK: 59 SKIPPED: 0 FAILED: 4
  1. Failure: install.nongithub (@test_install.R#38) 
  2. Failure: install.nongithub (@test_install.R#42) 
  3. Failure: install.bioinfo (@test_install.R#50) 
  4. Error: download.file.custom (@test_utils.R#104) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/biomartr.Rcheck/00install.out' for details.
installed size is 72.1Mb
  sub-directories of 1Mb or more:
    include   2.7Mb
    lib      69.0Mb
Running examples in 'BrailleR-Ex.R' failed
The error most likely occurred in:

> ### Name: ScatterPlot
> ### Title: Create a standard scatter plot with a few extra elements added
> ###   to the output object
> ### Aliases: FittedLinePlot ScatterPlot plot.scatterplot
> ###   plot.fittedlineplot print.scatterplot print.fittedlineplot
> 
> ### ** Examples
> 
> attach(airquality)
> op = par(mfcol=c(3,2))
> plot(Wind, Ozone, pch=4)
> test1 = ScatterPlot(Wind, Ozone, pch=4)
> test1 #does the plot method work?
> plot(Wind, Ozone)
> abline(coef(lm(Ozone~Wind)), col=4)
> test2 = FittedLinePlot(Wind, Ozone, line.col=4)
Error in as.list(x[setdiff(names(x), ToRemove)]) : 
  attempt to set an attribute on NULL
Calls: FittedLinePlot -> .GrabExtraArgs -> as.list
Execution halted
Running 'test-all.R' [8s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("broom")
  Loading required package: broom
  Error in tbl(lahman_df(), "Batting") : 
    could not find function "lahman_df"
  Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval -> tbl
  testthat results ================================================================
  OK: 621 SKIPPED: 0 FAILED: 0
  Execution halted
Package required but not available: 'OpenCL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/cate.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "causaleffect.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'causaleffect.ltx' failed with diagnostics:
running 'texi2dvi' on 'causaleffect.ltx' failed

LaTeX errors:
tes/causaleffect.ltx:81: LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help
You're in trouble here.  Try typing  <return>  to proceed.
Execution halted
The following files look like leftovers/mistakes:
  'Causata-vignette.log'
Please remove them from your package.
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
regularize.values: possible error in xy.coords(x, y, setLab = FALSE):
  unused argument (setLab = FALSE)
Error in re-building vignettes:
  ...

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:tools':

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'moe430a.db'
Loading required package: RankAggreg
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "clValid.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'clValid.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex.EXE (file ./clValid-022.pdf): PDF inclusion: required p
age does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Execution halted
Conjoint: no visible global function definition for 'dev.new'
Conjoint: no visible global function definition for 'barplot'
caFactorialDesign: no visible global function definition for 'cor'
caModel: no visible global function definition for 'as.formula'
caModel: no visible global function definition for 'lm'
caModel: no visible global function definition for 'summary.lm'
caSegmentation: no visible global function definition for 'kmeans'
caUtilities: no visible global function definition for 'as.formula'
caUtilities: no visible global function definition for 'lm'
caUtilities: no visible global function definition for 'summary.lm'
partutilities: no visible global function definition for 'as.formula'
partutilities: no visible global function definition for 'lm'
partutils: no visible global function definition for 'as.formula'
partutils: no visible global function definition for 'lm'
profsimcode: no visible global function definition for 'as.formula'
profsimcode: no visible global function definition for 'lm'
profsimcode: no visible global function definition for 'model.matrix'
totalutilities: no visible global function definition for 'as.formula'
totalutilities: no visible global function definition for 'lm'
totalutilities: no visible global function definition for
  'model.matrix'
utlsplot: no visible global function definition for 'dev.new'
utlsplot: no visible global function definition for 'barplot'
Undefined global functions or variables:
  as.formula barplot cor dev.new kmeans lm model.matrix summary.lm
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "barplot")
  importFrom("stats", "as.formula", "cor", "kmeans", "lm",
             "model.matrix", "summary.lm")
to your NAMESPACE file.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   6.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cplexAPI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/CTTShiny.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cudaBayesreg.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/DataCombine.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    bin   3.1Mb
    doc   1.7Mb
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    include  18.9Mb
    libs      1.3Mb
Found the following significant warnings:
  Warning: running command 'domino help' had status 127
See 'd:/Rcompile/CRANpkg/local/3.3/domino.Rcheck/00install.out' for details.
Running 'doRUnit.R' [8s]
Running the tests in 'tests/doRUnit.R' failed.
Last 13 lines of output:
  Number of test functions: 3 
  Number of errors: 0 
  Number of failures: 1 
  
   
  1 Test Suite : 
  doSNOW unit testing - 3 test functions, 0 errors, 1 failure
  FAILURE in test.pkgname.test.stress: Error in checkTrue(!is(res, "try-error"), msg = "pkgname stress test failed") : 
    Test not TRUE
  pkgname stress test failed
  Error: 
  
  unit testing failed (#test failures: 1, #R errors: 0)
  
  Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'scales'

The following object is masked from 'package:purrr':

    discard


Attaching package: 'gridExtra'

The following object is masked from 'package:dplyr':

    combine


Attaching package: 'GGally'

The following object is masked from 'package:dplyr':

    nasa

Quitting from lines 337-354 (exploring-election-data.Rmd) 
Error: processing vignette 'exploring-election-data.Rmd' failed with diagnostics:
could not find function "dmap"
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/EMCC.Rcheck/00install.out' for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    xsd   5.4Mb
Error in re-building vignettes:
  ...
'font.add()' is now renamed to 'font_add()'
The old version still works, but consider using the new function in future code
ggtree v1.6.11  For help: https://guangchuangyu.github.io/ggtree

If you use ggtree in published research, please cite:
Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628
Quitting from lines 46-54 (phylomoji.Rmd) 
Error: processing vignette 'phylomoji.Rmd' failed with diagnostics:
argument is not interpretable as logical
Execution halted
Missing or unexported object: 'xcms::profMat'
Packages in Depends field not imported from:
  'boot' 'xts' 'zoo'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/FastRWeb.Rcheck/00install.out' for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data    3.7Mb
    doc     2.9Mb
    tests   2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/gender.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'grid'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'test-all.R' [85s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  8: eval_bare(dot$expr, dot$env)
  9: lapply(seq(1:lags), .lag)
  10: FUN(X[[i]], ...)
  11: as.vector(lag(ts, k))
  12: lag(ts, k)
  13: bad_args("x", "must be a vector, not a ts object, do you want `stats::lag()`?")
  14: glubort(fmt_args(args), ..., .envir = .envir)
  15: .abort(text)
  
  testthat results ================================================================
  OK: 1442 SKIPPED: 9 FAILED: 1
  1. Error: gglagplot (@test-tslib.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'ggmap-Ex.R' failed
The error most likely occurred in:

> ### Name: get_map
> ### Title: Grab a map.
> ### Aliases: get_map
> 
> ### ** Examples
> 
> map <- get_map()
Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=29.763284,-95.363271&zoom=10&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false': HTTP status was '403 Forbidden'
Error in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") : 
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=29.763284,-95.363271&zoom=10&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false'
Calls: get_map -> get_googlemap -> download.file
Execution halted
Authors@R field gives persons with no valid roles:
  Mark S.
        Handcock Developer <handcock@stat.ucla.edu>
  Michael S.
        Rendall Developer <mrendall@rand.org>
Error in re-building vignettes:
  ...
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-10

Warning: from glmnet Fortran code (error code -26); Convergence for 26th lambda value not reached after maxit=100 iterations; solutions for larger lambdas returned
Warning: from glmnet Fortran code (error code -26); Convergence for 26th lambda value not reached after maxit=100 iterations; solutions for larger lambdas returned
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "glmnetcr.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error in find_vignette_product(name, by = "texi2pdf", engine = engine) : 
  Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for vignette with name 'glmnetcr'. The following files exist in directory '.': 'Rplots.pdf', 'glmnetRefs.bib', 'glmnetcr-004.pdf', 'glmnetcr-005.pdf', 'glmnetcr.Rnw', 'glmnetcr.tex'
Calls: buildVignettes -> find_vignette_product
Execution halted
Running examples in 'gmapsdistance-Ex.R' failed
The error most likely occurred in:

> ### Name: gmapsdistance
> ### Title: gmapsdistance
> ### Aliases: gmapsdistance
> 
> ### ** Examples
> 
> # Example 1
> results = gmapsdistance(origin = "Washington+DC", 
+                         destination = "New+York+City+NY", 
+                         mode = "driving")
> results
$Time
[1] 13656

$Distance
[1] 361721

$Status
[1] "OK"

> 
> # Example 2
> results = gmapsdistance(origin = "38.1621328+24.0029257",
+                         destination = "37.9908372+23.7383394",
+                         mode = "walking")
> results
$Time
[1] 30487

$Distance
[1] 39509

$Status
[1] "OK"

> 
> # Example 3
> results = gmapsdistance(origin = c("Seattle+WA", "Miami+FL"), 
+                         destination = c("Chicago+IL", "Philadelphia+PA"), 
+                         mode = "bicycling", 
+                         dep_date = "2017-08-16", 
+                         dep_time = "20:40:00")
Error in UseMethod("xmlChildren") : 
  no applicable method for 'xmlChildren' applied to an object of class "NULL"
Calls: gmapsdistance -> as -> .class1 -> xmlChildren
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/gmum.r.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/goftte.Rcheck/00install.out' for details.
Warning: no function found corresponding to methods exports from 'gpclib' for: 'coerce', 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
read.polyfile: no visible global function definition for 'as'
write.polyfile: no visible global function definition for 'is'
write.polyfile: no visible global function definition for 'as'
[,gpc.poly: no visible global function definition for 'new'
append.poly,gpc.poly-gpc.poly: no visible global function definition
  for 'new'
coerce,data.frame-gpc.poly: no visible global function definition for
  'as'
coerce,list-gpc.poly: no visible global function definition for 'as'
coerce,matrix-gpc.poly: no visible global function definition for 'new'
coerce,numeric-gpc.poly: no visible global function definition for
  'new'
coerce,numeric-gpc.poly.nohole: no visible global function definition
  for 'new'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'as'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'new'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'as'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'new'
tristrip,gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for
  'new'
Undefined global functions or variables:
  as is new
Consider adding
  importFrom("methods", "as", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running the tests in 'tests/bug1.R' failed.
Last 13 lines of output:
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > suppressMessages(library(gpclib))
  > to_numeric <- selectMethod(coerce, c("gpc.poly", "numeric"))
  > load("bug1_data.RData")
  > plot(p)  ## loads a polygon, looks fine
  > plot(as(vec, "gpc.poly"))  ## looks fine
  > clip <- to_numeric(p); str(clip)
   num [1:17] 1 7 0 570545 7890092 ...
  > 
  > ## Crashes R 2.14 and 2.15 (32-bit) on Windows
  > vec <- .Call("Rgpc_polygon_clip", vec, clip, 3, PACKAGE="gpclib")
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/gpuR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/gputools.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   5.4Mb
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-33\unhbox\voidb@x \penalty \@M \ {}1.
3/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
Running examples in 'hierformR-Ex.R' failed
The error most likely occurred in:

> ### Name: addstates
> ### Title: Add State ids and classes
> ### Aliases: addstates
> 
> ### ** Examples
> 
> df<-data.frame(winner=c(1,2,3,1,2,3,2,1,2,3,3,1,2,3,4,3,1,3,2,1,1,1,1,2,2),
+ loser=c(2,4,4,4,3,2,1,3,3,4,4,2,3,2,3,4,2,4,3,3,3,2,2,4,3)
+ )
> addstates(df)
Error in `$<-.data.frame`(`*tmp*`, "id", value = c(1L, 3L, 38L, 38L, 38L,  : 
  replacement has 18 rows, data has 25
Calls: addstates -> $<- -> $<-.data.frame
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   1.3Mb
    doc    2.1Mb
    libs   1.1Mb
NB: this package is only installed for sub-architecture 'x64'
File 'iotools/libs/i386/iotools.dll':
  Found non-API call to R: 'getConnection'
File 'iotools/libs/x64/iotools.dll':
  Found non-API call to R: 'getConnection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
StartKappa: no visible global function definition for 'read.csv'
StartKappa: no visible global function definition for 'na.omit'
StartKappa: no visible global function definition for 'write.csv2'
Undefined global functions or variables:
  na.omit read.csv write.csv2
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "read.csv", "write.csv2")
to your NAMESPACE file.
Running examples in 'Knoema-Ex.R' failed
The error most likely occurred in:

> ### Name: Knoema
> ### Title: knoema package! This package works with datasets from knoema.com
> ### Aliases: Knoema
> 
> ### ** Examples
> 
> Knoema("IMFWEO2017Apr", list(country = "512;914", subject = "NGDP_RPCH"),
+            client.id = "bHcV5UkOVyKcBw",
+            client.secret = "/0itYgLqnD0i49kmdBVSZ1qLjPU")
Error: Client error: (403) Forbidden
Execution halted
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 6 SKIPPED: 0 FAILED: 26
  1. Failure: test empty dimension selection error (@test_errors.R#23) 
  2. Failure: test wrong dimension selection error (@test_errors.R#29) 
  3. Failure: test not all dims in filter error (@test_errors.R#45) 
  4. Failure: test incorect frequencies error (@test_errors.R#57) 
  5. Error: get data single series by member id ts (@test_ts.R#3) 
  6. Error: get data multi series by member id ts (@test_ts.R#16) 
  7. Error: get data multi series by member name (@test_ts.R#31) 
  8. Error: get data multi series by member id range (@test_ts.R#45) 
  9. Error: get data single series different frequencies by member id ts (@test_ts.R#59) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Failure: ensure_db (@test-db.R#12) ------------------------------------------
  ensure_db(db) produced warnings.
  
  
  2. Failure: ensure_queue (@test-queue.R#21) ------------------------------------
  q <- ensure_queue("foo", db = db) produced warnings.
  
  
  testthat results ================================================================
  OK: 506 SKIPPED: 0 FAILED: 2
  1. Failure: ensure_db (@test-db.R#12) 
  2. Failure: ensure_queue (@test-queue.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required and available but unsuitable versions:
  'parallel' 'graphics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: (function (...) 
     .subset2(public_bind_env, "finalize")())(<environment>)
  10: .subset2(public_bind_env, "finalize")()
  11: is_open(self$con)
  12: isOpen(con)
  
  Error in signalCondition(e) : 
    no function to return from, jumping to top level
  Calls: <Anonymous> ... isOpen -> .handleSimpleError -> h -> signalCondition
  testthat results ================================================================
  OK: 22 SKIPPED: 0 FAILED: 1
  1. Error: The pipe function (@test_nse.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'macleish-Ex.R' failed
The error most likely occurred in:

> ### Name: etl_extract.etl_macleish
> ### Title: Extract weather data
> ### Aliases: etl_extract.etl_macleish etl_load.etl_macleish
> ###   etl_transform.etl_macleish
> 
> ### ** Examples
> 
> 
> macleish <- etl("macleish")
Not a valid src. Creating a src_sqlite for you at:
D:\temp\Rtmpc51PUR\file434dc78b1dab.sqlite3
Error: The dbplyr package is required to communicate with database backends.
Execution halted
Running examples in 'MANOVA.RM-Ex.R' failed
The error most likely occurred in:

> ### Name: MANOVA.wide
> ### Title: Tests for Multivariate Data in Semi-Parametric Factorial Designs
> ### Aliases: MANOVA.wide
> 
> ### ** Examples
> 
> #Example on producing plastic film from Krzanowski (1998, p. 381), see \code{manova.summary}
> tear <- c(6.5, 6.2, 5.8, 6.5, 6.5, 6.9, 7.2, 6.9, 6.1, 6.3,
+           6.7, 6.6, 7.2, 7.1, 6.8, 7.1, 7.0, 7.2, 7.5, 7.6)
> gloss <- c(9.5, 9.9, 9.6, 9.6, 9.2, 9.1, 10.0, 9.9, 9.5, 9.4,
+            9.1, 9.3, 8.3, 8.4, 8.5, 9.2, 8.8, 9.7, 10.1, 9.2)
> opacity <- c(4.4, 6.4, 3.0, 4.1, 0.8, 5.7, 2.0, 3.9, 1.9, 5.7,
+              2.8, 4.1, 3.8, 1.6, 3.4, 8.4, 5.2, 6.9, 2.7, 1.9)
> rate     <- gl(2,10, labels = c("Low", "High"))
> additive <- gl(2, 5, length = 20, labels = c("Low", "High"))
> example <- data.frame(tear, gloss, opacity, rate, additive)
> fit <- MANOVA.wide(cbind(tear, gloss, opacity) ~ rate * additive, 
+ data = example, iter = 100, CPU = 1)
Error in deparse(...) : unused argument (lex.order = TRUE)
Calls: MANOVA.wide ... split.default -> .NotYetUsed -> gettextf -> sprintf -> deparse
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 162-174 (Introduction_to_MANOVA.RM.Rmd) 
Error: processing vignette 'Introduction_to_MANOVA.RM.Rmd' failed with diagnostics:
unused argument (lex.order = TRUE)
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.2Mb
Loading tidyverse: ggplot2
Loading tidyverse: tibble
Loading tidyverse: tidyr
Loading tidyverse: readr
Loading tidyverse: purrr
Loading tidyverse: dplyr
Conflicts with tidy packages ---------------------------------------------------
filter(): dplyr, stats
lag():    dplyr, stats
Loading required package: lattice
Error in unloadNamespace(package) : 
  namespace 'lattice' is imported by 'nlme', 'Matrix', 'psych', 'mosaic' so cannot be unloaded
Error : .onAttach failed in attachNamespace() for 'mdsr', details:
  call: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, 
  error: Package 'lattice' version 0.20.35 cannot be unloaded
Error: package or namespace load failed for 'mdsr'
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/medSTC.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/memisc.Rcheck/00install.out' for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.6Mb
    misc   1.1Mb
Missing or unexported object: 'tools::CRAN_package_db'
Running 'missing_data.frame.R' [5s]
  Running 'missing_variable.R' [4s]
Running the tests in 'tests/missing_variable.R' failed.
Last 13 lines of output:
  > x <- rep(1:5, each = 2)
  > y <- missing_variable(x, type = "group")
  > 
  > x[1] <- NA
  > y <- missing_variable(x, type = "unordered-categorical")
  > y <- missing_variable(x, type = "ordered-categorical")
  > y <- missing_variable(x, type = "interval")
  > 
  > x <- rbinom(10, size = 1, prob = 0.5)
  > x[1] <- NA
  > y <- missing_variable(x, type = "binary")
  Error in validObject(.Object) : 
    invalid class "binary" object: y : binary variables must have exactly two response categories
  Calls: missing_variable ... .local -> callNextMethod -> .nextMethod -> validObject
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/monoreg.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/mrds.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/mrfDepth.Rcheck/00install.out' for details.
Authors@R field gives persons with no valid roles:
  YouGov [fnd]
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  The following objects are masked from 'package:base':
  
      Filter, Find, Map, Position, Reduce, anyDuplicated, append,
      as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
      get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
      match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
      rbind, rownames, sapply, setdiff, sort, table, tapply, union,
      unique, unsplit, which, which.max, which.min
  
  > test_check('NFP')
  Start tag expected, '<' not found
  Error: 1: Start tag expected, '<' not found
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    CppCode   2.3Mb
    R         3.1Mb
    include   5.5Mb
    libs      1.8Mb
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

LaTeX errors:
! LaTeX Error: File `sfmath.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    help   2.2Mb
    libs   1.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/OpenCL.Rcheck/00install.out' for details.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs     5.8Mb
    models   4.7Mb
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  could not find function "glmnet.cr"
  1: .handleSimpleError(function (e) 
     {
         e$call <- sys.calls()[(frame + 11):(sys.nframe() - 2)]
         register_expectation(e, frame + 11, sys.nframe() - 2)
         signalCondition(e)
     }, "could not find function \"glmnet.cr\"", quote(eval(expr, envir, enclos))) at testthat/test-ordinalNet.R:187
  2: eval(expr, envir, enclos)
  
  testthat results ================================================================
  OK: 44 SKIPPED: 0 FAILED: 1
  1. Error: Elastic net sratio matches glmnetcr::glmnet.cr (@test-ordinalNet.R#187) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'paleofire-Ex.R' failed
The error most likely occurred in:

> ### Name: pfKruskal
> ### Title: Analyse composite records by a Kruskal-Wallis ANOVA
> ### Aliases: pfKruskal
> 
> ### ** Examples
> 
> 
> ## Composite charcoal record for Western Boreal North America:
> ID=pfSiteSel(id_region=="WNA0" & l12==1)
> plot(ID)
> ## Transform data
> res3=pfTransform(ID,method=c("MinMax","Box-Cox","Z-Score"),BasePeriod=c(200,4000))
Loading and preparing data...
Transforming...
Percentage done: 10 20 30 40 50 60 70 80 90 100 
> 
> ## Composite
> comp=pfComposite(res3,bins=seq(from=-500,to=12500,by=1000))
> plot(comp)
> 
> ## Kruskal Wallis Anova
> comparison=pfKruskal(comp)
Error in `$<-.data.frame`(`*tmp*`, "M", value = character(0)) : 
  replacement has 0 rows, data has 13
Calls: pfKruskal -> $<- -> $<-.data.frame
Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  10: src_sqlite(msf_file)
  11: check_dbplyr()
  12: check_pkg("dbplyr", "communicate with database backends", install = FALSE)
  13: glubort(NULL, "The {name} package is required to {reason}.", if (install) "\nPlease install it with `install.packages(\"{name}\")`")
  14: .abort(text)
  
  Error: The dbplyr package is required to communicate with database backends.
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 3
  1. Error: make_area_table creates a data frame with the correct column names (@test_make_area_table.R#16) 
  2. Error: make_pep_table creates a data frame with the correct column names (@test_make_pep_table.R#13) 
  3. Error: map_peptides creates a data frame with the correct column names (@test_map_peptides.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.3/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.3/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  
  testthat results ================================================================
  OK: 187 SKIPPED: 15 FAILED: 1
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   2.1Mb
    libs   2.3Mb
Package required and available but unsuitable version: 'parallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error in re-building vignettes:
  ...
Loading required package: Matrix

Attaching package: 'nlme'

The following object is masked from 'package:lme4':

    lmList

pandoc.exe: Could not determine mime type for `https://raw.githubusercontent.com/jslefche/jslefche.github.io/master/img/shipley_2009.jpg'
CallStack (from HasCallStack):
  error, called at src\Text\Pandoc\SelfContained.hs:156:35 in pandoc-1.19.2.1-3EiBhxep0x773HKxrkonLI:Text.Pandoc.SelfContained
Warning: running command '"D:/compiler/pandoc/pandoc" +RTS -K512m -RTS piecewiseSEM.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output piecewiseSEM.html --smart --email-obfuscation none --self-contained --standalone --section-divs --template "d:\RCompile\CRANpkg\lib\3.3\rmarkdown\rmd\h\default.html" --highlight-style pygments --css "d:\RCompile\CRANpkg\lib\3.3\rmarkdown\rmarkdown\templates\html_vignette\resources\vignette.css" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"' had status 1
Error: processing vignette 'piecewiseSEM.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
Execution halted
Packages which this enhances but not available for checking:
  'org.Ag.eg.db' 'org.Pt.eg.db' 'org.Ss.eg.db' 'org.Bt.eg.db'
  'org.Ce.eg.db' 'org.Cf.eg.db' 'org.Dr.eg.db' 'org.EcK12.eg.db'
  'org.EcSakai.eg.db' 'org.Gg.eg.db' 'org.Mmu.eg.db' 'org.Pf.plasmo.db'
  'org.Xl.eg.db'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.4Mb
Error in re-building vignettes:
  ...
Quitting from lines 122-128 (Maps_and_Timeseries_Plots.Rmd) 
Error: processing vignette 'Maps_and_Timeseries_Plots.Rmd' failed with diagnostics:
cannot open URL 'http://maps.google.com/maps/api/staticmap?center=47,-118&zoom=7&size=640x640&maptype=terain&format=png32&sensor=true'
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/qtbase.Rcheck/00install.out' for details.
Package required but not available: 'qtbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [138s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         seq_len(ncol(x))) else colnames(x))))
  14: initialize(value, ...)
  15: initialize(value, ...)
  16: callNextMethod()
  17: .nextMethod(.Object = .Object, ... = ...)
  18: `as<-`(`*tmp*`, Classi, value = <S4 object of class structure("dtCMatrix", package = "Matrix")>)
  19: asMethod(object, Class, value)
  20: slot(value, what)
  
  testthat results ================================================================
  OK: 1446 SKIPPED: 21 FAILED: 1
  1. Error: dfm_lookup raises error when dictionary has multi-word entries (@test-dfm_lookup.R#82) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [131s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         seq_len(ncol(x))) else colnames(x))))
  14: initialize(value, ...)
  15: initialize(value, ...)
  16: callNextMethod()
  17: .nextMethod(.Object = .Object, ... = ...)
  18: `as<-`(`*tmp*`, Classi, value = <S4 object of class structure("dtCMatrix", package = "Matrix")>)
  19: asMethod(object, Class, value)
  20: slot(value, what)
  
  testthat results ================================================================
  OK: 1446 SKIPPED: 21 FAILED: 1
  1. Error: dfm_lookup raises error when dictionary has multi-word entries (@test-dfm_lookup.R#82) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
    po    2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rcplex.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/RcppOctave.Rcheck/00install.out' for details.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    include   6.3Mb
    libs      2.0Mb
Missing or unexported object: 'tools::package_native_routine_registration_skeleton'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/RDieHarder.Rcheck/00install.out' for details.
Package required but not available: 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rsolr'
Running 'testthat.R' [37s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  6: get_interactions_by_taxa(sourcetaxon = source.taxon.name, interactiontype = interaction.type, 
         targettaxon = target.taxon.names, opts = opts)
  7: read_csv(requesturl)
  8: utils::read.csv(url, stringsAsFactors = FALSE, ...)
  9: read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, 
         comment.char = comment.char, ...)
  10: file(file, "rt")
  
  testthat results ================================================================
  OK: 33 SKIPPED: 0 FAILED: 2
  1. Failure: default prey (@test-globi.R#6) 
  2. Error: interaction matrix can be retrieved (@test-globi.R#108) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    fonts   1.5Mb
    libs    2.0Mb
Error in re-building vignettes:
  ...
mpiler/texmf/fonts/type1/public/amsfonts/cm/cmr8.pfb><D:/Compiler/texmf/fonts/t
ype1/public/amsfonts/cm/cmr9.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts
/cm/cmsltt10.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmss10.pfb><
D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmss8.pfb><D:/Compiler/texmf/f
onts/type1/public/amsfonts/cm/cmss9.pfb><D:/Compiler/texmf/fonts/type1/public/a
msfonts/cm/cmsy10.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmti10.
pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmti12.pfb><D:/Compiler/t
exmf/fonts/type1/public/amsfonts/cm/cmtt10.pfb><D:/Compiler/texmf/fonts/type1/p
ublic/amsfonts/cm/cmtt8.pfb><D:/Compiler/texmf/fonts/type1/public/mathpazo/fplm
ri.pfb><D:/Compiler/texmf/fonts/type1/public/cm-super/sfrm0900.pfb><D:/Compiler
/texmf/fonts/type1/public/cm-super/sfrm1000.pfb><D:/Compiler/texmf/fonts/type1/
urw/palatino/uplr8a.pfb><D:/Compiler/texmf/fonts/type1/urw/palatino/uplri8a.pfb
>
Output written on rgp_introduction.pdf (16 pages, 430970 bytes).
Transcript written on rgp_introduction.log.
"D:/RCompile/recent/R-33~1.3/bin/Rscript" -e "tools::compactPDF('rgp_introduction.pdf', gs_quality='ebook')"
  compacted 'rgp_introduction.pdf' from 421Kb to 203Kb
rm -f Rplots.pdf
rm: cannot remove 'Rplots.pdf': Device or resource busy
make[1]: *** [pdf] Error 1
make[1]: Leaving directory `/cygdrive/d/RCompile/CRANpkg/local/3.3/rgp.Rcheck/vign_test/rgp/vignettes'
Warning: running command 'make' had status 2
Error in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.3/rgp.Rcheck/vign_test/rgp") : 
  running 'make' failed
Execution halted
Found the following significant warnings:
  gdkFuncs.c:1466:31: warning: passing argument 1 of 'gdk_drag_get_protocol' makes pointer from integer without a cast
  gdkFuncs.c:1510:52: warning: passing argument 2 of 'gdk_drag_get_protocol_for_display' makes pointer from integer without a cast
See 'd:/Rcompile/CRANpkg/local/3.3/RGtk2.Rcheck/00install.out' for details.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.6Mb
    libs   4.7Mb
.install_system_dependencies : <anonymous>: no visible global function
  definition for 'unzip'
.install_system_dependencies : install_system_dep: no visible global
  function definition for 'menu'
.install_system_dependencies : install_system_dep: no visible global
  function definition for 'download.file'
as.GParamSpec: no visible global function definition for 'new'
Undefined global functions or variables:
  download.file menu new unzip
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "download.file", "menu", "unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-portable flags in variable 'PKG_CPPFLAGS':
  -g
Found the following significant warnings:
  jri.h:21:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri.c:308:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available


See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rmosek.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'rnaturalearthhires'
Error in re-building vignettes:
  ...
Error : Oops, API did not return json after calling '§dldl  ':
        check your query - or api.oadoi.org may experience problems

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 141-142 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Timeout was reached: Operation timed out after 10015 milliseconds with 0 bytes received
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R   9.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/ROracle.Rcheck/00install.out' for details.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> data(prevsim)
> 
> yearly_incidence(prevsim$entrydate, start_date="2004-01-01", num_years=8)
[1] 107  96  98  88  88 100 107 108
> yearly_incidence(prevsim$entrydate)
 [1]  92 108  98  96  87  87 100 111 104 112
> yearly_incidence(prevsim$entrydate, start_date="2005-05-01", num_years=5)
[1]  98  96  84  89 101
> yearly_incidence(prevsim$entrydate, start_date="2005-05-01")
[1]  98  96  84  89 101 118 107
> yearly_incidence(prevsim$entrydate, num_years=5, end_date="2015-05-01")
[1] 118 107  80   0   0
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  16.11 0.76 17.56 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Found the following significant warnings:
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
See 'd:/Rcompile/CRANpkg/local/3.3/RQuantLib.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/RSAP.Rcheck/00install.out' for details.
median:
  function(x, na.rm)
median.sym.data.table:
  function(x, na.rm, method, ...)

median:
  function(x, na.rm)
median.sym.data.table:
  function(x, na.rm, method, ...)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Running examples in 'RSDA-Ex.R' failed
The error most likely occurred in:

> ### Name: median.sym.data.table
> ### Title: Symbolic Median
> ### Aliases: median.sym.data.table
> ### Keywords: Median Symbolic
> 
> ### ** Examples
> 
> data(example3)
> sym.data<-example3
> median(sym.data[,2])
[1] 1.5
> median(sym.data[,6] ,method='interval')
Error in median(sym.data[, 6], method = "interval") : 
  unused argument (method = "interval")
Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > 
  > test_check("RSDA")
  1. Error: Mediana simbolica (@test.estadisticos.R#56) --------------------------
  unused argument (method = "interval")
  1: expect_equal(median(example3[, 6], method = "interval"), c(F6 = 5, F6.1 = 89), tolerance = 1e-06) at testthat/test.estadisticos.R:56
  2: compare(object, expected, ...)
  3: median(example3[, 6], method = "interval")
  
  testthat results ================================================================
  OK: 31 SKIPPED: 0 FAILED: 1
  1. Error: Mediana simbolica (@test.estadisticos.R#56) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/Rserve.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/rsolr.Rcheck/00install.out' for details.
getSVGToolTipMode: no visible global function definition for 'dev.cur'
setSVGShapeContents: no visible global function definition for
  'dev.cur'
setSVGShapeToolTip: no visible global function definition for 'dev.cur'
setSVGShapeURL: no visible global function definition for 'dev.cur'
Undefined global functions or variables:
  dev.cur
Consider adding
  importFrom("grDevices", "dev.cur")
to your NAMESPACE file.
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R version 3.3.0 beta (2016-04-13 r70476)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6002) Service Pack 2

locale:
[1] LC_COLLATE=C                 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=C                LC_NUMERIC=C                
[5] LC_TIME=C                   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RSVGTipsDevice_1.0-4
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: shapes and points, tooltips are title + 1 line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
Authors@R field gives persons with no valid roles:
  ERC Grant Agreement number 336167 - the CHAI Project [fnd]
  Lucy D'Agostino McGowan [rev] (Lucy D'Agostino McGowan reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/126)
  Kara  Woo [rev] (Kara Woo reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/126)
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   1.7Mb
Found the following significant warnings:
  Warning: S3 methods '[.xml_missing', '[.xml_nodeset', '[[.xml_missing', 'xml_attr<-.xml_missing', 'xml_attr<-.xml_node', 'xml_attr<-.xml_nodeset', 'xml_attrs<-.xml_missing', 'xml_attrs<-.xml_node', 'xml_attrs<-.xml_nodeset', 'xml_name<-.xml_missing', 'xml_name<-.xml_node', 'xml_name<-.xml_nodeset', 'xml_text<-.xml_missing', 'xml_text<-.xml_node', 'xml_text<-.xml_nodeset', 'as.character.xml_document', 'as.character.xml_missing', 'as.character.xml_node', 'as.character.xml_nodeset', 'as_list.xml_missing', 'as_list.xml_node', 'as_list.xml_nodeset', 'as_xml_document.character', 'as_xml_document.connection', 'as_xml_document.list', 'as_xml_document.raw', 'as_xml_document.response', 'as_xml_document.xml_document', 'as_xml_document.xml_node', 'as_xml_document.xml_nodeset', 'format.xml_node', 'is.na.xml_missing', 'is.na.xml_node', 'is.na.xml_nodeset', 'nodeset_apply.xml_document', 'nodeset_apply.xml_missing', 'nodeset_apply.xml_node', 'nodeset_apply.xml_nodeset', 'print.xml_document', 'print.xml_missing [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.3/selectr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/showtext.Rcheck/00install.out' for details.
Missing or unexported object: 'spatstat::overlap.xypolygon'
Running examples in 'SIBER-Ex.R' failed
The error most likely occurred in:

> ### Name: maxLikOverlap
> ### Title: Calculate the overlap between two ellipses based on the maximum
> ###   likelihood fitted ellipses.
> ### Aliases: maxLikOverlap
> 
> ### ** Examples
> 
> # load in the included demonstration dataset data("demo.siber.data")
> siber.example <- createSiberObject(demo.siber.data) 
> 
> # The first ellipse is referenced using a character string representation 
> # where in "x.y", "x" is the community, and "y" is the group within that 
> # community.
> ellipse1 <- "1.2" 
> 
> # Ellipse two is similarly defined: community 1, group3 
> ellipse2 <- "1.3"
> 
> # the overlap betweeen the corresponding 95% prediction ellipses is given by: 
> ellipse95.overlap <- maxLikOverlap(ellipse1, ellipse2, siber.example,
+ p.interval = 0.95, n = 100)
Error: 'overlap.xypolygon' is not an exported object from 'namespace:spatstat'
Execution halted
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.3/SIBER.Rcheck/vign_test/SIBER") :
  Files named as vignettes but with no recognized vignette engine:
   'vignettes/test-nonnumeric-community-labels.Rmd'
   'vignettes/test-nonnumeric-group-labels.Rmd'
(Is a VignetteBuilder field missing?)
Quitting from lines 89-115 (Ellipse-Overlap.Rmd) 
Error: processing vignette 'Ellipse-Overlap.Rmd' failed with diagnostics:
'overlap.xypolygon' is not an exported object from 'namespace:spatstat'
Execution halted
Running 'demo_article-jss-example1.R' [3s]
  Comparing 'demo_article-jss-example1.Rout' to 'demo_article-jss-example1.Rout.save' ... OK
  Running 'demo_article-jss-example2.R' [4s]
  Comparing 'demo_article-jss-example2.Rout' to 'demo_article-jss-example2.Rout.save' ...47a48,52
> 
>  # maps v3.1: updated 'world': all lakes moved to separate new #
>  # 'lakes' database. Type '?world' or 'news(package="maps")'.  #
> 
> 
  Running 'demo_article-jss.R' [8s]
  Comparing 'demo_article-jss.Rout' to 'demo_article-jss.Rout.save' ... OK
  Running 'demo_cholesky.R' [1s]
  Comparing 'demo_cholesky.Rout' to 'demo_cholesky.Rout.save' ... OK
  Running 'demo_jss15-BYM.R' [3s]
  Comparing 'demo_jss15-BYM.Rout' to 'demo_jss15-BYM.Rout.save' ... OK
  Running 'demo_jss15-Leroux.R' [5s]
  Comparing 'demo_jss15-Leroux.Rout' to 'demo_jss15-Leroux.Rout.save' ... OK
  Running 'demo_spam.R' [1s]
  Comparing 'demo_spam.Rout' to 'demo_spam.Rout.save' ... OK
  Running 'demo_timing.R' [2s]
  Comparing 'demo_timing.Rout' to 'demo_timing.Rout.save' ... OK
  Running 'jss_areal_counts.R' [3s]
  Comparing 'jss_areal_counts.Rout' to 'jss_areal_counts.Rout.save' ... OK
  Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Help for individual functions is also obtained by adding the
  suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
  
  Attaching package: 'spam'
  
  The following objects are masked from 'package:base':
  
      backsolve, forwardsolve
  
  > 
  > test_check("spam")
  testthat results ================================================================
  OK: 496 SKIPPED: 0 FAILED: 0
  Error: is.expectation(exp) is not TRUE
  Execution halted
rmvn.sparse: no visible global function definition for 'rnorm'
rmvn.sparse: no visible global function definition for 'as'
Undefined global functions or variables:
  as rnorm
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    data   3.4Mb
    doc    4.6Mb
    help   5.1Mb
    libs   1.2Mb
Error in re-building vignettes:
  ...
Quitting from lines 92-96 (SSDM.Rmd) 
Error: processing vignette 'SSDM.Rmd' failed with diagnostics:
trying to get slot "projection" from an object of a basic class ("NULL") with no slots
Execution halted
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(statisticalModeling)
  Loading required package: ggplot2
  > 
  > test_check("statisticalModeling")
  Error: gwm() has been removed from `mosaic'.  
      It will be replaced by better tools in `mosaicModel'.
  testthat results ================================================================
  OK: 21 SKIPPED: 0 FAILED: 0
  Execution halted
Running 'testthat.R' [45s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Error in curl::curl_fetch_memory(url, handle = handle) : 
    Timeout was reached: Connection timed out after 10016 milliseconds
  4. Failure: normal usage (@test_usage.R#15) ------------------------------------
  all(dim(tmp) > 0) isn't true.
  
  
  testthat results ================================================================
  OK: 57 SKIPPED: 0 FAILED: 4
  1. Failure: normal usage (@test_usage.R#6) 
  2. Failure: normal usage (@test_usage.R#9) 
  3. Failure: normal usage (@test_usage.R#12) 
  4. Failure: normal usage (@test_usage.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "VignetteforSTPGA.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed

LaTeX errors:
! LaTeX Error: File `dirtytalk.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/sybilSBML.Rcheck/00install.out' for details.
Running 'testthat.R' [23s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > test_check("taxa")
  1. Error: Taxmap can be intialized from queried data (@test--taxmap_parsers.R#127) 
  'names' attribute [1] must be the same length as the vector [0]
  1: lookup_tax_data(raw_data, type = "seq_id", datasets = list(counts = abundance, my_names = common_names, 
         foods = foods), mappings = c(species_id = "id", species_id = "{{name}}", `{{index}}` = "{{index}}"), 
         column = "my_seq") at testthat/test--taxmap_parsers.R:127
  2: stats::setNames(data.frame(class_strings, stringsAsFactors = FALSE), internal_class_name)
  
  testthat results ================================================================
  OK: 414 SKIPPED: 0 FAILED: 1
  1. Error: Taxmap can be intialized from queried data (@test--taxmap_parsers.R#127) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/TDA.Rcheck/00install.out' for details.
Running examples in 'tidyjson-Ex.R' failed
The error most likely occurred in:

> ### Name: companies
> ### Title: Startup company information for 1,000 companies
> ### Aliases: companies
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> library(jsonlite)

Attaching package: 'jsonlite'

The following object is masked from 'package:tidyjson':

    read_json

> 
> # Print the first record (do not run automatically)
> # companies[[1]] %>% prettify
> 
> # Get the key employees data
> key_employees <- companies %>%
+   spread_values(
+     name = jstring("name")
+   ) %>%
+   mutate(
+     company.sort_order = rank(name)
+   ) %>%
+   enter_object("relationships") %>%
+   gather_array("relationship.index") %>%
+   spread_values(
+     is.past = jlogical("is_past"),
+     name = jstring("person", "permalink"),
+     title = jstring("title")
+   )
Error in eval(expr, envir, enclos) : 
  argument "json.column" is missing, with no default
Calls: %>% ... tryCatchList -> tryCatchOne -> doTryCatch -> eval -> eval
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/treethresh.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/uaparserjs.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/uroot.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/vegan.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.6Mb
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         wd_id <- gsub(x = item$item$value, pattern = "http://www.wikidata.org/entity/", 
             replacement = "", fixed = TRUE)
         return(data.frame(item = wd_id, name = ifelse(item$name$value == wd_id, NA, item$name$value), 
             latitutde = as.numeric(point[1]), longitude = as.numeric(point[2]), stringsAsFactors = FALSE))
     })
  5: sparql_query(query)
  6: httr::stop_for_status(result)
  
  testthat results ================================================================
  OK: 21 SKIPPED: 0 FAILED: 2
  1. Error: Simple entity-based geo lookups work (@test_geo.R#5) 
  2. Error: Language-variant entity-based geo lookups work (@test_geo.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [50s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2. Failure: setting cache file (@test_caching_gathering.R#39) ------------------
  all(dim(wp_get_cache()) > 0) isn't true.
  
  
  Error in curl::curl_fetch_memory(url, handle = handle) : 
    Timeout was reached: Connection timed out after 10000 milliseconds
  Error in curl::curl_fetch_memory(url, handle = handle) : 
    Timeout was reached: Connection timed out after 10000 milliseconds
  testthat results ================================================================
  OK: 66 SKIPPED: 0 FAILED: 2
  1. Failure: normal usage (@test_caching_gathering.R#27) 
  2. Failure: setting cache file (@test_caching_gathering.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  11: filter(tbl_df(.data), ...)
  12: filter.tbl_df(tbl_df(.data), ...)
  13: filter_impl(.data, quo)
  
  testthat results ================================================================
  OK: 132 SKIPPED: 0 FAILED: 6
  1. Error: visualization in general works (@test-automat.R#137) 
  2. Failure: visualization of empty automat works (@test-automat.R#145) 
  3. Error: visualization without set state works (@test-automat.R#153) 
  4. Error: visualization with implicit state works (@test-automat.R#162) 
  5. Error: visualization works (@test-automat.R#176) 
  6. Error: edge_present_lab helper works (@test-automat.R#209) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    java   9.7Mb
newXMLDoc: no visible binding for global variable 'doc'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
[[,XMLCodeFile: possible error in updateIds(doc, save = x): unused
  argument (save = x)
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/abcdeFBA.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘Rglpk’ ‘corrplot’ ‘lattice’ ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  x[1]: "\"a\"e\"i\"o\"u\"A\"E\"I\"O\"U\"y"
  y[1]: "aeiouAEIOUy"
  
  
  testthat results ================================================================
  OK: 10 SKIPPED: 0 FAILED: 4
  1. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#30) 
  2. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#32) 
  3. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#33) 
  4. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.2Mb
    libs                    2.9Mb
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'acceptance_sampling_manual.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cf>
          K^^[]^^W>o<fc>h^^Zj<93>^(E<94><98><e1>B<a1><85>`^^GfW<b0>q<91><b5><bb>v<e5><da>MW]<b9><95><ae>tӮ<eb><bf><e0><aa>Y<94>B<b2>H^^P^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.19 ...߾<bd>s<e7>N6<9b><c5>O)<a5><94>rmm<cd>0<8c>B<a1> <a5>dX<ee><ed><ed><e1><95>eY<8f>^^^=<da><dd>ݽ}
                                                  <fb><f6><f2><f2><b2>R^^J
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.20 ...ZYYY[[^^C2<9f>?^^?<8e>-<87><9f><d9>l<d6>4<cd>l6<fb><e2><c5><
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because ACSN-vignette.Rmd appears to be an R Markdown v2 document.
Quitting from lines 70-71 (ACSN-vignette.Rmd) 
Error: processing vignette 'ACSN-vignette.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/adiv.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'AER.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 ...<bc>Aι<ee>M<ea>^^X<84>^^PA^^P<e8><ba>.<84>H$^^R<ba><ae>æ^^GA<d0><ed>v<87>t\<a8>
                                                  <ff><f9><f3><e7>l6[<af><d7>e'D<f4><ea>ի<d5><d5>UT^^[<c3>
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.21 ...ޯP<af><d7><d5>`|H@<f8><93>V<bf>^^Q<c8><c9>9<97>S^^[<86><a1><a6>i(<f7>}^^_<fb>/9<cd>x<f6>}
                                                  <9f><88>@`<c6>؟^^?<be><fb><e3><8f>^^?9N<c3>0d<c3>0<9f>g...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.24 ...^^?<d7>2^^L^^F۷<d
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘AFM-Ex.R’ failed
The error most likely occurred in:

> ### Name: evaluateVariogramModels
> ### Title: evaluateVariogramModels method to evaluate the basic variogram
> ###   models
> ### Aliases: evaluateVariogramModels
> ###   evaluateVariogramModels,AFMImageVariogramAnalysis-method
> 
> ### ** Examples
> 
> library(AFM)
> 
> data("AFMImageOfRegularPeaks")
> # take an extract of the image to fasten the calculation      
> AFMImage<-extractAFMImage(AFMImageOfRegularPeaks, 40, 40, 32)
[1] "40 40 31 40 71 40 71"
> # e.g. AFMImage@fullfilename<-"/users/ubuntu/AFMImageOfRegularPeaks-extract.txt"
> AFMImage@fullfilename<-paste(tempdir(), "AFMImageOfRegularPeaks-extract.txt", sep="/")
>  
> AFMImageAnalyser<-AFMImageAnalyser(AFMImage)
Warning in data.table(lib = c("AFM", "gstat", "fractaldim", "fftwtools"),  :
  Item 1 is of size 4 but maximum size is 5 (recycled leaving remainder of 1 items)
>  
>  # Variogram analysis 
> sampleFitPercentage<-3.43/100
> variogramAnalysis<-AFMImageVariogramAnalysis(sampleFitPercentage)
> variogramAnalysis@omnidirectionalVariogram<- 
+               AFM::calculateOmnidirectionalVariogram(AFMImage=AFMImage,
+                                                      AFMImageVariogramAnalysis=variogramAnalysis)
[1] "using automatic width of 1"
[1] "calculating omnidirectional variogram using width of 1 ..."
Error in CRS("+init") : no colon in init= string
Calls: <Anonymous> -> CRS
Execution halted
Package required and available but unsuitable version: ‘miscF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/alphashape3d.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘timetk’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/alphavantager.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  12: read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
  13: read_xml.character(x, encoding = encoding, ..., as_html = TRUE, options = options)
  14: read_xml.connection(con, encoding = encoding, ..., as_html = as_html, base_url = x, 
         options = options)
  15: open(x, "rb")
  16: open.connection(x, "rb")
  
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: Test that current version is still latest version (@tests.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'amei.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...߾<8d><c6>L&<c3>9<ff><ee><bb><ef>^^Xc_~<f9><e5><f5><eb><d7>s<b9>^^\<ba>q<ce><ef>޽<fb><c5>^^W_\<bc>
                                                  xq~~~aa!<9b><cd><ce><ce><ce>b<e4>\.W<af><d7><c7><c7><c7>^^Y...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ...<9b>^^L<c7>0<8f>Z<ad><86><bb><b2><85><88>8<e7>^^@<92><aa><aa><a6>i<a2><b1>X,<fa><be><8f>G<d0><e2><fb>~4|Å\D
                                                  Ƙ<bc><85><b7><d4>j<b5>v<e6><dc>^^Y8;<c5>ի<8d>ȨSp^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 <c3>0<96><97><97><af>\<b9>
             <e2><ba>.F+^^T^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.24
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: network
network: Classes for Relational Data
Version 1.13.0 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.


Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/analogueExtra.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/animalTrack.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

The following object is masked from 'package:qdap':

    %>%

The following object is masked from 'package:qdapTools':

    id

The following objects are masked from 'package:qdapRegex':

    escape, explain

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 56-58 (ANLP_Documentation.Rmd) 
Error: processing vignette 'ANLP_Documentation.Rmd' failed with diagnostics:
java.lang.UnsupportedClassVersionError: weka/core/tokenizers/NGramTokenizer : Unsupported major.minor version 51.0
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/AnnotationBustR.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
Invalid MIT-MAGIC-COOKIE-1 keyannot : annotlist: no visible global function definition for
  ‘read.table’
annot : annotlist: no visible global function definition for
  ‘write.table’
annot: no visible global function definition for ‘flush.console’
annot: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  flush.console read.table write.table
Consider adding
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/antaresViz.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/AnthropMMD.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Warning: Conversion from REAL(8) to default-kind COMPLEX(4) at (1) might loose precision, consider using the KIND argument
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/appell.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keykristen.colors: no visible global function definition for
  ‘colorRampPalette’
kristen.colors: no visible global function definition for ‘grey’
plot3d.points: no visible global function definition for ‘heat.colors’
plot3d.points: no visible global function definition for ‘plot’
ragged.image: no visible global function definition for ‘heat.colors’
ragged.image: no visible global function definition for ‘image’
scatterplot.density: no visible global function definition for ‘grey’
scatterplot.density: no visible global function definition for ‘image’
scatterplot.density: no visible global function definition for ‘abline’
scatterplot.density: no visible global function definition for ‘lm’
scatterplot.density: no visible global function definition for ‘legend’
vertical.image.legend: no visible global function definition for ‘par’
vertical.image.legend: no visible global function definition for
  ‘image’
vertical.image.legend: no visible global function definition for ‘axis’
vertical.image.legend: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box colorRampPalette grey heat.colors image legend lm par
  plot
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘AffymetrixDataTestFiles’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ARTP2.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ASIP.Rcheck/00install.out’ for details.
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  
  Attaching package: 'llama'
  
  The following object is masked from 'package:BBmisc':
  
      normalize
  
  > test_check("aslib")
  Loading required package: aslib
  Error in .jnew("weka/core/Instances", .jcast(reader, "java/io/Reader")) : 
    java.lang.UnsupportedClassVersionError: weka/core/Instances : Unsupported major.minor version 51.0
  Calls: test_check ... eval -> parseASScenario -> read.arff -> .jnew -> .External
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/AtelieR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/auk.Rcheck/00install.out’ for details.
Running examples in ‘autothresholdr-Ex.R’ failed
The error most likely occurred in:

> ### Name: auto_thresh
> ### Title: Automatically threshold an image.
> ### Aliases: auto_thresh auto_thresh_mask auto_thresh_apply_mask
> 
> ### ** Examples
> 
> img <- EBImage::readImage(system.file("extdata", "eg.tif",
+                           package = "autothresholdr"), as.is = TRUE)
> auto_thresh(img, "huang")
Error in rJava::.jnew("Auto_Threshold_R") : 
  java.lang.UnsupportedClassVersionError: Auto_Threshold_R : Unsupported major.minor version 52.0
Calls: auto_thresh -> <Anonymous> -> .External
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  java.lang.UnsupportedClassVersionAuto_Threshold_R : Unsupported major.minor version 52.0
  1: expect_equal(auto_thresh(img, "IJD"), auto_thresh(img, "default")) at testthat/test_thresh.R:6
  2: compare(object, expected, ...)
  3: auto_thresh(img, "IJD")
  4: rJava::.jnew("Auto_Threshold_R")
  
  testthat results ================================================================
  OK: 2 SKIPPED: 0 FAILED: 2
  1. Error: mean_stack_thresh works (@test_stack_thresh.R#5) 
  2. Error: auto_thresh works (@test_thresh.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 40-43 (autothresholdr.Rmd) 
Error: processing vignette 'autothresholdr.Rmd' failed with diagnostics:
java.lang.UnsupportedClassVersionError: Auto_Threshold_R : Unsupported major.minor version 52.0
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   1.6Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
Error in re-building vignettes:
  ...
  input string 487 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bartMachine.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          o^^[<d5>^^V?uh<92>yJ=<b9><b4>/qG8q<86>V<a4>-JSy<c3>C<aa>^^\!<8b>%^^[^^T<84><c4>^^V<f5>^^O`<c3>6<cb>v^^A6^^H...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...T*e<9a><a6>eY<f1>u<92>R<fe><f0><c3>^^O<b6>m^^O^^O^^O<a3><f4><e7><9f>^^?<fe>裏<ae>\<b9>
                                                  <92>L&<e3><f1>x<c0><b8><ab><cf>^^Gݸq<a3>X,nV:55<b5><b3>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...ȣG<8f><c0><86>eY<9f>}<f6>^^Y$MU <a2>^^O?<fc>0<9d>N^^O^^O^^O<ef>r
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/baseballDBR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 8-9 (./child/ex5-2.Rnw) 
Quitting from lines 44-44 (./child/ex5-2.Rnw) 
Error: processing vignette 'article2-vignette.Rnw' failed with diagnostics:
cannot open connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bayesCL.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/BayesCR.Rcheck/00install.out’ for details.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  10.2Mb
Package unavailable to check Rd xrefs: ‘mritc’
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  18.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/BayesTwin.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in ‘BCEs0-Ex.R’ failed
The error most likely occurred in:

> ### Name: bces0
> ### Title: Bayesian Cost-Effectiveness models in the presence of structural
> ###   zeros
> ### Aliases: bces0 bces0.default
> ### Keywords: JAGS Markov Chain Monte Carlo Bayesian models for
> ###   cost-effectiveness analysis
> 
> ### ** Examples
> 
> data(acupuncture)
> m <- bces0(data,dist.c="gamma",dist.e="beta",n.iter=1000,n.burnin=500,n.chains=2)
Installing package into ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/BCEs0.Rcheck’
(as ‘lib’ is unspecified)
Error in contrib.url(repos, "source") : 
  trying to use CRAN without setting a mirror
Calls: bces0 -> bces0.default -> install.packages -> contrib.url
Execution halted
Package suggested but not available for checking: ‘beadarrayExampleData’
Running examples in ‘beadarrayFilter-Ex.R’ failed
The error most likely occurred in:

> ### Name: MLM.beadarray
> ### Title: Multi-level Mixed model
> ### Aliases: MLM.beadarray
> ### Keywords: differential expression
> 
> ### ** Examples
> 
> require(beadarrayExampleData)
Loading required package: beadarrayExampleData
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘beadarrayExampleData’
> data(exampleSummaryData)
Warning in data(exampleSummaryData) :
  data set ‘exampleSummaryData’ not found
> exampleSummaryDatalog2 <- channel(exampleSummaryData, "G")[1:40,]
Error in channel(exampleSummaryData, "G") : 
  object 'exampleSummaryData' not found
Execution halted
Package required but not available: ‘rggobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'beanplot.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^S<dd>^^Z^^?<9a><be><a1>w@frn<ef><d5><da>2<a6>^^\<f0><f6><95>+i<a1><f0>.^^DM<c1><e8>Fp<d7>U<f7><ae><dd>	<ae><dc><f6>/<90>׽<a2><88>.<b2>m^^V
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...<cd>qb-s<fd>H<ee><e2>w<f3>0o?<92><c6>&jj~<8b>rr<be><e6><s~<e7><f9>8<e7>L^^G<ea><f5>:<9d>\D
                                                  ~<f4>^^@<ba><8b><be>x<bd><8c><be>x<bd><8c><be>x<bd><8c><be>x<bd><8c><be>x<bd>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.19 ...<d3>D<ce><ce><ce>N"<91><d0>ZW<ab>U<d3>4<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    libs  46.2Mb
Invalid MIT-MAGIC-COOKIE-1 keybeqi2: no visible global function definition for ‘na.omit’
beqi2: no visible global function definition for ‘browseURL’
readAMBI: no visible global function definition for ‘read.csv’
readBEQI: no visible global function definition for ‘read.csv’
readERF: no visible global function definition for ‘read.csv’
readTWN: no visible global function definition for ‘read.csv’
read_ITI_FIBI: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  browseURL na.omit read.csv
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "browseURL", "read.csv")
to your NAMESPACE file.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 425 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'betareg-ext.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.17 ...x(^^T<f2>}?^^R<89>^^L,<e7><d3><e2><ff>۴<^^Q<f0>Ȝs<d7>uM<d3>ܩZ<cb>[<fc><f4>}
                                                  ?^^T^^J
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.18 ...<9a>f<ad>V<b3>,<eb><db>o<bf>=z<f4><e8><c4>ĄeYB^^HM<d3>^^P3p<ce>QF<83><9d>D^^Q]<8c>^
                                                  6<9b><cd>d2B^^H<c7>q^^P<be><98><a6>iY^^V^^Q#...
! Extra }, or forgotten $.
l.18 ...t<ee>ܹF<a3><c1>^^X[XX0M3<91>H^^P<d1><db>o<bf>m<9a><e6><f0><f0>0^^Q<f9><be><af>$A<d9><f7>}
                                                  <df><f7>5<ad>#<ce
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/BETS.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/biclique.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   4.4Mb
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in is.na(verts[, 2]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 3]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 1]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 3]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 1]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 2]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in normalizePath(f2) :
  path[1]="./webshot155cb71ba05dc.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot155cb71ba05dc.png': No such file or directory
Quitting from lines 233-236 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      5.4Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Running examples in ‘Biocomb-Ex.R’ failed
The error most likely occurred in:

> ### Name: Biocomb-package
> ### Title: Tools for Data Mining
> ### Aliases: Biocomb-package Biocomb
> ### Keywords: package feature selection classification information gain
> ###   Relative cost curves HUM roc auc
> 
> ### ** Examples
> 
> data(data_test)
> # class label must be factor
> data_test[,ncol(data_test)]<-as.factor(data_test[,ncol(data_test)])
> 
> # Perform the feature selection using the fast correlation-based filter algorithm
> disc="MDL"
> threshold=0.2
> attrs.nominal=numeric()
> out=select.fast.filter(data_test,disc.method=disc,threshold=threshold,
+ attrs.nominal=attrs.nominal)
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: select.fast.filter ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
Package required and available but unsuitable version: ‘configr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bios2mds.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/birdring.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘GOSemSim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because profiling.Rmd appears to be an R Markdown v2 document.
Quitting from lines 40-46 (profiling.Rmd) 
Error: processing vignette 'profiling.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/blandr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/blastula.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/blockmodeling.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
This data.table install has not detected OpenMP support. It will work but slower in single threaded mode.
Package suggested but not available for checking: ‘RcppTOML’
Found the following significant warnings:
  Warning: Possible change of value in conversion from INTEGER(8) to INTEGER(4) at (1)
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: Dummy argument 'ch_mymsg' at (1) was declared INTENT(OUT) but was not set
  Warning: Dummy argument 'da_gpvals' at (1) was declared INTENT(OUT) but was not set
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Blossom.Rcheck/00install.out’ for details.
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
installed size is 243.0Mb
  sub-directories of 1Mb or more:
    include    2.7Mb
    lib      240.0Mb
installed size is 46.3Mb
  sub-directories of 1Mb or more:
    libs  46.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bootsPLS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bpca.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 434 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 435 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 443 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BradleyTerry.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...<fa><ed>l^^B<d8>`L^^B<e5>;<a0><e7>7߼y<df><fb><fe><bc><df><f7><bd>G_<b3>٤<b3>K<ca><eb><9e>@o<e9>\<bc>
                                                  <d3>L<e7><e2><9d>f:^^W<ef>4ӹx<a7><99><ce><c5>;<cd>t.^^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ADL׭\<ee>
            <e2><d4><d4>SO^^L|V<ad>^^F"^^Q<c9><d0><fd><ac><8e><d9>8]!<86>^^N<ef>Nx<eb>h<ef>^^^Lg<dc><f7><ce>8(<eb>*<b4>^^@X1<c6><e2><f1><b8>^^Pb~...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ...<ab>U<bf><df>^^?<b0><84>^^R^Y<96>^^U<89>D<d0><e6><9c>۶<9d>H$:^^_gO:<f7><bd><d3>Lg\<bc>
                                                  6<a1>%<93>ɜ<cc><<ba><a1>^^C<b0><eb>^^Y<f7><bd><e3>Ĝ^^G...
The control sequence at the end of the top 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘BrailleR-Ex.R’ failed
The error most likely occurred in:

> ### Name: ScatterPlot
> ### Title: Create a standard scatter plot with a few extra elements added
> ###   to the output object
> ### Aliases: FittedLinePlot ScatterPlot plot.scatterplot
> ###   plot.fittedlineplot print.scatterplot print.fittedlineplot
> 
> ### ** Examples
> 
> attach(airquality)
> op = par(mfcol=c(3,2))
> plot(Wind, Ozone, pch=4)
> test1 = ScatterPlot(Wind, Ozone, pch=4)
> test1 #does the plot method work?
> plot(Wind, Ozone)
> abline(coef(lm(Ozone~Wind)), col=4)
> test2 = FittedLinePlot(Wind, Ozone, line.col=4)
Error in as.list(x[setdiff(names(x), ToRemove)]) : 
  attempt to set an attribute on NULL
Calls: FittedLinePlot -> .GrabExtraArgs -> as.list
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/brainR.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyscene4d: no visible global function definition for ‘rainbow’
write4D.file : <anonymous>: no visible global function definition for
  ‘col2rgb’
writeWebGL_split : split_triangles: no visible global function
  definition for ‘rgb’
Undefined global functions or variables:
  col2rgb rainbow rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rainbow", "rgb")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/breakfast.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/breathtestcore.Rcheck/00install.out’ for details.
Package required but not available: ‘breathtestcore’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Running examples in ‘c3net-Ex.R’ failed
The error most likely occurred in:

> ### Name: c3net
> ### Title: All in one function to infer network with C3NET
> ### Aliases: c3net
> ### Keywords: misc
> 
> ### ** Examples
> 
> data(expdata)
> data(truenet)
> 
> net <- c3net(expdata, network=TRUE)
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "font".
Calls: c3net ... .tkplot.convert.font -> <Anonymous> -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
rgdal: version: 1.2-5, (SVN revision 648)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.2, released 2016/10/24
 Path to GDAL shared files: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rgdal/gdal
 Loaded PROJ.4 runtime: Rel. 4.9.1, 04 March 2015, [PJ_VERSION: 491]
 Path to PROJ.4 shared files: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rgdal/proj
 Linking to sp version: 1.2-4 
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 50-54 (DataExtraction.Rmd) 
Error: processing vignette 'DataExtraction.Rmd' failed with diagnostics:
cannot find ExifTool
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cape.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/capm.Rcheck/00install.out’ for details.
Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:

> ### Name: carpools.hit.overview
> ### Title: Analysis: Analysis of pooled CRISPR screening data using a
> ###   Wilcoxon Test
> ### Aliases: carpools.hit.overview
> ### Keywords: ~Analysis
> 
> ### ** Examples
> 
> data(caRpools)
> 
> data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+   normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
+   control.picks=NULL)
> 
> 
> data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1,
+   fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
+   sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
+   fitType="parametric")
Error in `rownames<-`(`*tmp*`, value = c("CTRL", "CTRL", "TREAT", "TREAT" : 
  duplicate rownames not allowed
Calls: stat.DESeq -> <Anonymous> -> rownames<- -> rownames<-
Execution halted
Error in re-building vignettes:
  ...
Warning in readLines(con) :
  incomplete final line found on 'CaRpools.Rmd'
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because CaRpools.Rmd appears to be an R Markdown v2 document.
Quitting from lines 1875-1881 (CaRpools.Rmd) 
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
duplicate rownames not allowed
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cati.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/catSurv.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error: processing vignette 'causaleffect.ltx' failed with diagnostics:
Running 'texi2dvi' on 'causaleffect.ltx' failed.
LaTeX errors:
! Undefined control sequence.
l.81 \DOI
         {10.18637/jss.v076.i12}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
Execution halted
Running examples in ‘causalMGM-Ex.R’ failed
The error most likely occurred in:

> ### Name: loadSampleData
> ### Title: Load Sample Dataset
> ### Aliases: loadSampleData
> 
> ### ** Examples
> 
> library(rJava)
> mgm_init()
> ds <- loadSampleData()
Error in .jfindClass(as.character(class)) : class not found
Calls: loadSampleData -> J -> jclassName -> .jfindClass
Execution halted
Found the following Makefile(s) without a final LF:
  inst/doc/Makefile
Some ‘make’ programs ignore lines not ending in LF.
The following files look like leftovers/mistakes:
  ‘Causata-vignette.log’
Please remove them from your package.
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cdcsis.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keybw: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cems.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 505 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ChainLadder.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.17 w<ab><b4><b4><90><c1>TQ	\nS
                 ;<e8><d0>7\x<83><df>/<ef><f1><fa>K<df><f5>|<86>p^^H7<c9><f9><90>s^^?<95>&<d0><ef><f7><e1>^^[^^P<fc><ec>^^D&^^Dz<ca>^^Ez<ca>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 w<ab><b4><b4><90><c1>TQ	\nS;<e8><d0>7\x
                       <83><df>/<ef><f1><fa>K<df><f5>|<86>p^^H7<c9><f9><90>s^^?<95>&<d0><ef><f7><e1>^^[^^P<fc><ec>^^D&^^Dz<ca>^^Ez<ca>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.17 ...e3^^X<d8>?<e5>b^^Du[.<97>s<b9><9c>mۙLFUU۶<a7><a
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/childsds.Rcheck/00install.out’ for details.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/clpAPI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/clues.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/clusterSEs.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘moe430a.db’
Error in re-building vignettes:
  ...

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML

Attaching package: ‘XML’

The following object is masked from ‘package:tools’:

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘moe430a.db’
Loading required package: RankAggreg
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./clValid-022.pdf): PDF inclusion: required page 
does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                     
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/comato.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyHopkins.index: no visible global function definition for ‘runif’
MBM.em: no visible global function definition for ‘runif’
PAM.cluster: no visible global function definition for ‘dist’
calculate.layout: no visible global function definition for ‘optim’
min.distance: no visible global function definition for ‘dist’
plot.conceptmap: no visible global function definition for ‘par’
plot.conceptmap: no visible global function definition for ‘plot’
plot.conceptmaps: no visible global function definition for ‘plot’
Undefined global functions or variables:
  dist optim par plot runif
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "dist", "optim", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘mogene10sttranscriptcluster.db’
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package required but not available: ‘RcppTOML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/conjoint.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyConjoint: no visible global function definition for ‘dev.new’
Conjoint: no visible global function definition for ‘barplot’
caFactorialDesign: no visible global function definition for ‘cor’
caModel: no visible global function definition for ‘as.formula’
caModel: no visible global function definition for ‘lm’
caModel: no visible global function definition for ‘summary.lm’
caSegmentation: no visible global function definition for ‘kmeans’
caUtilities: no visible global function definition for ‘as.formula’
caUtilities: no visible global function definition for ‘lm’
caUtilities: no visible global function definition for ‘summary.lm’
partutilities: no visible global function definition for ‘as.formula’
partutilities: no visible global function definition for ‘lm’
partutils: no visible global function definition for ‘as.formula’
partutils: no visible global function definition for ‘lm’
profsimcode: no visible global function definition for ‘as.formula’
profsimcode: no visible global function definition for ‘lm’
profsimcode: no visible global function definition for ‘model.matrix’
totalutilities: no visible global function definition for ‘as.formula’
totalutilities: no visible global function definition for ‘lm’
totalutilities: no visible global function definition for
  ‘model.matrix’
utlsplot: no visible global function definition for ‘dev.new’
utlsplot: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  as.formula barplot cor dev.new kmeans lm model.matrix summary.lm
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "barplot")
  importFrom("stats", "as.formula", "cor", "kmeans", "lm",
             "model.matrix", "summary.lm")
to your NAMESPACE file.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   6.5Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/corehunter.Rcheck/00install.out’ for details.
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Invalid MIT-MAGIC-COOKIE-1 keyPackage in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘cpa-Ex.R’ failed
The error most likely occurred in:

> ### Name: cpa-package
> ### Title: Confirmatory Path Analysis through the d-sep tests
> ### Aliases: cpa-package
> ### Keywords: package
> 
> ### ** Examples
> 
> x <- cpa()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: cpa ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    libs  30.8Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cplexAPI.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 238 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 244 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cplm.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<cb>^^L<8e><99><98>y<8b>#<8e><a6><98><d8>^^Fl^^By><b2><ac><f1>̹^^_g~<f7>|<dc>s<8f><db>\<d7>
                                                  <85><97><97><da>_<f4>^^D<9a>K-<f1><8e>3<b5><c4>;<ce><d4>^^R<ef>8<d3>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...}<f6><d9>g<a3><a3><a3>B<88><c5><c5>ť<a5><a5>|>^^?<f9><f2>e|<a4>i^^Zʃ<bd><fd><f0><c3>^^O^^_}
                                                  <f4><91><a6>i׮]<db><c3>tݽS.<97><ab><f2><f4><c1><83>^^G<fb><e8><b3>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ in
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  input string 416 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 422 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'crch.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<cc><db><c0>H<bb>^^^<b7><d8>]<f1>^^\^^Y;-E<f9>)c<c9>O<8a><94><8b>9p<ca>^^A<e5><c2>-g<94>\<f3>
                                                  ^^W<e4><9a>?a9gOsC9^^RiFV^^T<81>4bl...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...^X-&<e2><8d>3&<e2><8d>3&<e2><8d>3&<e2><8d>3&<e2><8d>3&<e2><fd>^^]J)<a5>^^T.N?<d5>Z<f3>}
                                                  <a5><94><d6><fa><ac><96><a7><db><f3><f5><fa><fa><fa><e9>.<b8><93>l?^^L<fe>5|<d3>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.15 .
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/crimCV.Rcheck/00install.out’ for details.
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
D.SN: no visible global function definition for ‘dnorm’
D.SN: no visible global function definition for ‘pnorm’
beta2cp: no visible global function definition for ‘pnorm’
cSFM.est: no visible global function definition for ‘predict’
cSFM.est: no visible global function definition for ‘optim’
cSFM.est: no visible global function definition for ‘qnorm’
cSFM.est: no visible global function definition for ‘cor’
case2.b.initial: no visible global function definition for ‘predict’
case2.b.initial: no visible global function definition for ‘var’
case2.gr: no visible global function definition for ‘pnorm’
case2.gr: no visible global function definition for ‘dnorm’
case2.unmll.optim: no visible global function definition for ‘pnorm’
cp2beta: no visible global function definition for ‘qnorm’
data.generator.y.F: no visible global function definition for ‘cov2cor’
data.generator.y.F: no visible global function definition for ‘rnorm’
data.generator.y.F : <anonymous>: no visible global function definition
  for ‘pnorm’
g: no visible global function definition for ‘dnorm’
g: no visible global function definition for ‘pnorm’
predict.cSFM: no visible global function definition for ‘predict’
predict.cSFM : <anonymous>: no visible global function definition for
  ‘qnorm’
predict.cSFM: no visible global function definition for ‘qnorm’
predict.cSFM: no visible global function definition for ‘pnorm’
predict.kpbb: no visible global function definition for ‘predict’
uni.fpca: no visible global function definition for ‘predict’
Undefined global functions or variables:
  cor cov2cor dnorm optim pnorm predict qnorm rnorm var
Consider adding
  importFrom("stats", "cor", "cov2cor", "dnorm", "optim", "pnorm",
             "predict", "qnorm", "rnorm", "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 510 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 511 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 519 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ctsem.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>[OO^^S<dd>^^W>^^L"^^V<a1><ed><8d><c4>4<98>ڦ<89>yCBZ<92><ae>\<98>
                                           <ba><e8><ce>ĸ1n\<f3>^^UtIܹa/_<a1><bb>&<ee><ba><e8>H\<80><99>8L^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...O^^S<dd>^^W>^^L"^^V<a1><ed><8d><c4>4<98>ڦ<89>yCBZ<92><ae>\<98><ba><e8><ce>ĸ1n\<f3>
                                                  ^^UtIܹa/_<a1><bb>&<ee><ba><e8>H\<80><99>8L^^H<da>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<c4>4<98>ڦ<89>yCBZ<92><ae>\<98><ba><e8><ce>ĸ1n\<f3>^^UtIܹa/_<a1><bb>&<ee><ba><e8>H\<80>
                                                  <99>8L^^H<da>(<93>N^^GR <81>ˌP'<f8><a3><fd>-<9e><f4>...
The control sequence at the end of the top lin
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cudaBayesreg.Rcheck/00install.out’ for details.
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  9: http_error(HEAD(x, ...))
  10: HEAD(x, ...)
  11: request_perform(req, hu$handle$handle)
  12: request_fetch(req$output, req$url, handle)
  13: request_fetch.write_memory(req$output, req$url, handle)
  14: curl::curl_fetch_memory(url, handle = handle)
  
  testthat results ================================================================
  OK: 12 SKIPPED: 5 FAILED: 1
  1. Error: d3_dep-* src href is a valid url (@test_deps.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘d3r’
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 341 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DAKS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<8e><ad>^^_<b6><9c>X<ae><de>A<8c>fgf<e7><cd><fb><cc>{o޼<fd><c4><f7>}<ba><be>^^T<fa><d8>^^S<b8>\^^Z
                                                  <b3>7<ca>4fo<94>i<cc><de>(Ә<bd>Q<a6>1{<a3>L<ff>l<f6>LӔ...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...|~gg端<be><c2><d0><f9>|<de>4<cd>l6<ab>:d^^X<c6>ӧO<f1><ee><cf>><fb>lgg<e7><e1>Ç<b9>\N
                                                  ^^H^^A<96>VVV<a4><94>h<a0><94>^^RB,//<f3>PD<f4>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...?<fe><f9><e7><f9><f9><f9>p8<bc><b2><b2><f2><dd>w<df>^^Y<86><a1><eb>z.<97><db><dc><dc><fc><fe><fb><ef>s<b9>^^\^^F\F
                                                  /DCDB^^W^^J
The control sequence at the end of the top 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/dataCompareR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot16c4d558b2e19.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot16c4d558b2e19.png': No such file or directory
Quitting from lines 57-68 (dataexplorer-intro.Rmd) 
Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/datastructures.Rcheck/00install.out’ for details.
Warning: parse error in file '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/datasus.Rcheck/datasus/doc/Introduction_to_datasus.R':
invalid multibyte character in parser at line 50
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot13df49df9a30.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot13df49df9a30.png': No such file or directory
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/DBKGrad.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/dc3net.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/DCD.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
Invalid MIT-MAGIC-COOKIE-1 keyThere are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘debug.Recall’ ‘debug.eval’ ‘debug.eval.guts’ ‘debug.fun.name’
  ‘evaluator’ ‘find.debug.HQ’ ‘mvb.sys.on.exit’ ‘stepping’
Running examples in ‘DecorateR-Ex.R’ failed
The error most likely occurred in:

> ### Name: DECORATE
> ### Title: Binary classification with DECORATE (Melville and Mooney, 2005)
> ### Aliases: DECORATE
> 
> ### ** Examples
> 
> 
> data(iris)
> y <- as.factor(ifelse(iris$Species[1:100]=="setosa",0,1))
> x <- iris[1:100,-5]
> dec <- DECORATE(x = x, y = y)
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: DECORATE ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
Package required and available but unsuitable version: ‘ftsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
The following objects are masked from 'package:seriation':

    bluered, greenred

The following object is masked from 'package:stats':

    lowess

Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:base':

    isNamespaceLoaded

Loading required package: rngtools
# NOTE - CRAN check detected: limiting maximum number of cores [2/16]
NMF - BioConductor layer [OK] | Shared memory capabilities [OK] | Cores 2/2 | CRAN check
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 925-927 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/dendroExtra.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'desctable'

The following object is masked from 'package:DT':

    datatable

The following objects are masked from 'package:stats':

    IQR, chisq.test, fisher.test

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot5fb33084ba6f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot5fb33084ba6f.png': No such file or directory
Quitting from lines 66-73 (desctable.Rmd) 
Error: processing vignette 'desctable.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   1.3Mb
    libs   1.2Mb
Package suggested but not available for checking: ‘dclone’
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Invalid MIT-MAGIC-COOKIE-1 keyPackage in Depends field not imported from: ‘dplR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.get’ ‘InteractiveDetrending’ ‘RemoveTrend’
Running examples in ‘detrendeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: detrendeR-package
> ### Title: detrendeR - A Graphical User Interface to process and visualize
> ###   tree-ring data using R
> ### Aliases: detrendeR-package detrendeR
> ### Keywords: package
> 
> ### ** Examples
> 
> detrender()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: detrender ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/dfcomb.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/dfmta.Rcheck/00install.out’ for details.
installed size is 41.9Mb
  sub-directories of 1Mb or more:
    libs  41.6Mb
Package required but not available: ‘ALL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required and available but unsuitable version: ‘methods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘dgmb-Ex.R’ failed
The error most likely occurred in:

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Invalid MIT-MAGIC-COOKIE-1 keyWarning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Invalid MIT-MAGIC-COOKIE-1 keyWarning in tclRequire("Tktable") : Tcl package 'Tktable' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: dgmbGui ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/DiceView.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/didrooRFM.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/diffpriv.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/directPA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/DirichletReg.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘glmnet’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘glmnet’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘DivMelt-Ex.R’ failed
The error most likely occurred in:

> ### Name: DivMelt_gui
> ### Title: User Interface for the Diversity Assay Analysis Tool
> ### Aliases: DivMelt_gui
> ### Keywords: interface
> 
> ### ** Examples
> 
> ##
> library (DivMelt)
> DivMelt_gui()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: DivMelt_gui ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
.ccd.1.41: no visible global function definition for ‘rnorm’
.ccd.1.41: no visible global function definition for ‘formula’
.ccd.1.41: no visible global function definition for ‘coef’
.ccd.1.41: no visible global function definition for ‘runif’
.ccd.1.41 : <anonymous>: no visible global function definition for
  ‘as.formula’
.gen.des.old.way: no visible global function definition for ‘runif’
Dopt.augment: no visible global function definition for ‘rnorm’
Dopt.augment: no visible global function definition for ‘as.formula’
Dopt.augment: no visible global function definition for ‘model.matrix’
Dopt.design: no visible global function definition for ‘as.formula’
Dopt.design: no visible global function definition for ‘model.matrix’
Scalc: no visible global function definition for ‘dist’
bbd.design: no visible global function definition for ‘model.matrix’
ccd.augment: no visible global function definition for ‘as.formula’
ccd.augment: no visible global function definition for ‘model.matrix’
ccd.augment: no visible global function definition for ‘model.frame’
ccd.augment: no visible binding for global variable ‘na.pass’
generators.from.design: no visible global function definition for
  ‘formula’
generators.from.design : <anonymous>: no visible global function
  definition for ‘as.formula’
lhs.design: no visible global function definition for ‘cor’
rsm.design: no visible global function definition for ‘as.formula’
rsmformula: no visible global function definition for ‘formula’
Undefined global functions or variables:
  as.formula coef cor dist formula model.frame model.matrix na.pass
  rnorm runif
Consider adding
  importFrom("stats", "as.formula", "coef", "cor", "dist", "formula",
             "model.frame", "model.matrix", "na.pass", "rnorm", "runif")
to your NAMESPACE file.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  2: domino.runCommand(loginCommand, domino.OK, "Login failed", theinput)
  3: domino.runCommandFromDefaultPath(commandAndArgs, successCallback, failureMessage, 
         stdInput)
  4: domino.handleCommandNotFound(failureMessage)
  5: stop(paste("Couldn't find domino client in the PATH or in default locations.\n  Add domino client directory path to PATH environment variable.\n  If you don't have domino client installed follow instructions on 'http://help.dominodatalab.com/client'.\n  If you use R-Studio Domino on GNU/Linux through a desktop launcher, add domino path to the .desktop file.\n\n  If you need more help, email support@dominodatalab.com or visit http://help.dominodatalab.com/troubleshooting\n\n  - ", 
         failureMessage), call. = FALSE)
  
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: The login command works (@test-login.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘dpa-Ex.R’ failed
The error most likely occurred in:

> ### Name: dpa-package
> ### Title: Dynamic Path Approach for Analyzing time-dependent simulation
> ###   data
> ### Aliases: dpa-package dpa
> 
> ### ** Examples
> 
> #Start the GUI with:
> dpa.start()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: dpa.start ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/dprep.Rcheck/00install.out’ for details.
Package required but not available: ‘RODBC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 341 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 352 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DSL.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 ...<ce><fc><fc><bc><e3>8X^^W<c6>X<bb><dd>^^F<fd><9a><a6><e1>E<ac>:^^O8<e7><e3><e9><de>><a1>^^_\^^G
                                                  <8e><ee>^^?<dc>q^^F<c7>1<c8>3^^L^^C<cc><c1>O<a9>3<fb>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 <fa><e8><de>e)<e9><8d><c6>_[<f7><86>^^]<97><e4><9d>^^@0<ad><bd><d7>}7<f2><fe><8c>p<b6>e\<d3>
                                        4<d3><e9><b4>i<9a>H<c0>^^A8<92><f9><f9>y<d3>4www<9f>>}<fa><f9>矟<d1>^^D.-<e7>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
\GenericError  ...                                
                                                    #4  \errhelp \@err@     ...
l.25 ...^^X^^R^^@<c6>&<9b>ͦ<d3><e9>l<d6>L<a7><e3><a6>Yo6<9f><ee><ec><<e7>|<ab>Ri
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because DT.Rmd appears to be an R Markdown v2 document.
Quitting from lines 23-25 (DT.Rmd) 
Error: processing vignette 'DT.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.2Mb
Error in re-building vignettes:
  ...
  input string 371 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 387 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'dtw.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.15 ...4?<fa><e8><a3>w<de>y<87><88>T^^?)<e5><ec><ec>,<98><8f><c7><e3>[[[<bf><fc><f2>˗_~)<84>x>^^C<ed>^
                                                  <e8><c1><83>^^G<fb>Z<ee>޽[<af><d7>{<9a>$<<e4><d9>	{<dd><c9><e1>^...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.15 ...<bf><93>^^?<a1><f6><b1> z><93>^^O<b4><fb><c1><88><cb>KW<9c><bd><93><8a><96><a3>^^P<84><87>^^P²<ac>\.<f7>
                                                  <e8>ѣ^^O><f8> <97>˽<fa>꫻<bb><bb><b3><b3><b3>g<b7><f4><bb>...
! You can't use `\spacefactor' in math mode.
\add@accen
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘ggm’ ‘tcltk’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ggm’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘dynamicGraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: DynamicGraph
> ### Title: DEPRECATED: Simple interface to dynamicGraph
> ### Aliases: DynamicGraph
> ### Keywords: dplot hplot iplot dynamic graphs methods multivariate
> 
> ### ** Examples
> 
> require(tcltk); require(dynamicGraph)
> 
> # Example 1:
> 
> W <- dg(as(new("dg.simple.graph", vertex.names = 1:5), "dg.graph"),
+         control = dg.control(title = "Very simple"))
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: dg ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   9.2Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs     2.4Mb
    models   4.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Eagle.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/easyDes.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/eechidna.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/eegkit.Rcheck/00install.out’ for details.
installed size is 42.5Mb
  sub-directories of 1Mb or more:
    libs  42.2Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 421 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'elrm.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.20 ...V^^AZ^^[<e1>dF^^L{^^C<94>ұ<b1><b1>`0<88><a4>^^[<86>Q<ab>հj<92><c9>d<ae>\<b9>
                                                  ^^B^^@mm<da>^^^<bb>r<a2>f樺ǈ;<cd>4<a7>s...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.25 <c1><8e>N<92>$<d4>:<8c>^^A<d8>^^X<8e><e3>J<a5>R<8b>^^[ ^^G><bd>c,^^Y<9d>B<f5><a9>}
                                             !<d0>^^Y<f8><ec>	<97>𥪪<f5>z<9d><b5><cb>^^Y<d1>X>d<87><8f>u{t!...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.45 x<9c><ed>\<cf>
          k^^[<d7>^^V>Q쪢<89
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘hgu133plus2.db’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/EMCC.Rcheck/00install.out’ for details.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  16.8Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         winslash = "/", mustWork = FALSE), options = "-s")
  23: stop("pandoc document conversion failed with error ", result, call. = FALSE)
  
  testthat results ================================================================
  OK: 62 SKIPPED: 5 FAILED: 2
  1. Error: We return TRUE when validating a valid just created eml object with latin1 encoding (@test-validation.R#75) 
  2. Error: We return TRUE when validating a valid just created eml object (@test-validation.R#89) 
  
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: Person Carl Boettiger <cboettig@gmail.com> was not given any role. 
  2: Person Matthew B. Jones was not given any role. 
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/emma.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘clusterSim’ ‘earth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 46-54 (phylomoji.Rmd) 
Error: processing vignette 'phylomoji.Rmd' failed with diagnostics:
StatTreeHorizontal was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘FactoMineR’ ‘MASS’ ‘Rcmdr’ ‘SensoMineR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespace in Imports field not imported from: ‘BiocParallel’
  All declared Imports should be used.
Missing or unexported object: ‘xcms::profMat’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot26a02d32b059.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot26a02d32b059.png': No such file or directory
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/episensr.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RCytoscape’
Error in re-building vignettes:
  ...
See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...<e5><81>h	ԂXqI<a9><c9><c0>H^^H<b5>N<93>K<c6>C<99><e0>^^D_i<aa>:<d3>&<96><df><e2><d7>9<dc><e7>/}
                                                  <c4>v,Gg!<c6>wν<ba><e7><9e><df>=<f7>|\ydkk<8b>N.<8d>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.15 ...<99><e0>^^D_i<aa>:<d3>&<96><df><
Calls: buildVignettes -> texi2pdf -> texi2dvi
In addition: Warning messages:
1: Argument mod1 is deprecated; please use mods and which instead. 
2: Argument mod2 is deprecated; please use mods and which instead. 
3: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 390 is invalid in this locale
4: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 391 is invalid in this locale
5: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 405 is invalid in this locale
6: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 406 is invalid in this locale
7: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 412 is invalid in this locale
Execution halted
Running examples in ‘erpR-Ex.R’ failed
The error most likely occurred in:

> ### Name: erp.infl
> ### Title: inspect the influence of a subject on the average (single
> ###   electrode).
> ### Aliases: erp.infl
> 
> ### ** Examples
> 
> 
> data(ERPsets)
> 
> erp.infl(base="Exp1_word_subj", numbers=1:20, electrode="OZ", 
+ startmsec=-200, endmsec=1500, erplist=ERPsets)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: erp.infl ... handshake -> fun -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/estprod.Rcheck/00install.out’ for details.
Packages required and available but unsuitable versions:
  ‘SNPRelate’ ‘gdsfmt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/eventstudies.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/EventStudy.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Evomorph.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

The following object is masked from 'package:MASS':

    geyser

Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 437 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 438 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'evtree.tex' failed.
LaTeX errors:
! TeX capacity exceeded, sorry [text input levels=15].
\@filef@und ->evtree.tpt 
                         
l.16 ...BO=<b5><e4><d0><de>r<88><ce>m)<88>B<f1><a1><a5>X^^Em^^E)^^NYX-&<c4>M<bd>x-<8c><9e>\[
                                                  <d3><dd>纛<84>H<ef><f0><a9><e7><ed>S^^\<fd><b0>c'<ca><d3><f7> vg...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'exams.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...^^^{<ec><bd><e7>Rȭ<f4>蛡<85>P^^]bL^^L6^^L<ac>^^W<e1><d6>-^^Y<b4>Y\U
                                                  <e2><8f>ǻU<ed><8d><f3>K<fa>^^O_<f5><fe><ad>^^Sےc'<91><ab>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<a5>RQJY<96>5`'A^^P<ec><ef><ef><97><cb><e5>z<bd>n<9a>&<fa>!<a2><ad><ad><ad><d9><d9>Y4^^[<b0><b7><b8>\q
                                                  <e6>|Ypb<8e>a<ba>D"<81><89>'<a2>z<bd><de><ed>v<cf>1<df>^^W+...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Please use \mathaccent for accents in math mode.
\add@accent ...@sp
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘expands-Ex.R’ failed
The error most likely occurred in:

> ### Name: cellfrequency_pdf
> ### Title: Computes the probability distribution of cellular frequencies
> ###   for a single mutation.
> ### Aliases: cellfrequency_pdf
> 
> ### ** Examples
> 
> freq=seq(0.1,1.0,by=0.01);
> cfd=cellfrequency_pdf(af=0.26,cnv=1.95,pnb=0,freq=freq, max_PM=6)
Error in .jcall("core.utils.Common", "V", "setALLOWED_FREQUENCIES", .jarray(as.double(freq))) : 
  RcallMethod: cannot determine object class
Calls: cellfrequency_pdf -> .jcall -> .External
Execution halted
Errors in running code in vignettes:
when running code in ‘expands.Rnw’
  ...
+     all))

> SPs = clusterCellFrequencies(cfd$densities[toUseIdx, 
+     ], precision)
[1] "Clustering  0 probability distributions..."
[1] "Clustering agglomeration method: average"

  When sourcing ‘expands.R’:
Error: object must be a numeric matrix
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'expands.Rnw' failed with diagnostics:
 chunk 5 
Error in .local(object, ...) : object must be a numeric matrix

Execution halted
Package suggested but not available for checking: ‘golubEsets’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/FAiR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘OpenML’
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  Loading required package: farff
  1. Error: quick test with small arffs (@test_quick.R#6) ------------------------
  java.lang.UnsupportedClassVersionweka/core/Instances : Unsupported major.minor version 51.0
  1: compareRWeka(INST_ARFF_DIR, "iris.arff", data.reader = dreader) at testthat/test_quick.R:6
  2: RWeka::read.arff(path2) at /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/farff.Rcheck/tests/testthat/helper.R:17
  3: .jnew("weka/core/Instances", .jcast(reader, "java/io/Reader"))
  
  testthat results ================================================================
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Error: quick test with small arffs (@test_quick.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  12.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.1Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls in package code:
  ‘akima’ ‘spatial’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in ‘FCMapper-Ex.R’ failed
The error most likely occurred in:

> ### Name: graph.fcm
> ### Title: Fuzzy cognitive map graph
> ### Aliases: graph.fcm
> 
> ### ** Examples
> 
> 
> matrix = matrix(nrow=7,ncol=7)
> matrix[1,] = c(0,-0.5,0,0,1,0,1)
> matrix[2,] = c(1,0,1,0.2,0,0,0.6)
> matrix[3,] = c(0,1,0,0,0,0,0)
> matrix[4,] = c(0.6,0,0,1,0,0,0.1)
> matrix[5,] = c(0,0.5,0,0,1,0,-0.6) 
> matrix[6,] = c(0,0,-1,0,0,0,0)
> matrix[7,] = c(0,0,0,-0.5,0,0,1)
> concept.names = c("A","B","C","D","E","F","G")
> 
> results = nochanges.scenario(matrix,iter=25,concept.names)
> 
> graph.fcm(matrix,concept.sizes=results$Equilibrium_value,concept.names)
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "font".
Calls: graph.fcm ... .tkplot.convert.font -> <Anonymous> -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    libs  38.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fdaPDE.Rcheck/00install.out’ for details.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    libs   6.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fds.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyread.hmd: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/feature.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘parallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tcltk’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
Invalid MIT-MAGIC-COOKIE-1 keyparseHelp: no visible global function definition for ‘help’
parseHelp: no visible global function definition for ‘unzip’
Undefined global functions or variables:
  help unzip
Consider adding
  importFrom("utils", "help", "unzip")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/FieldSim.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyfieldsim: no visible global function definition for ‘rnorm’
midpoint: no visible global function definition for ‘rnorm’
setAtlas_under: no visible global function definition for ‘runif’
setCovf_under : Ibeta: no visible global function definition for
  ‘pbeta’
visualize: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette pbeta rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "pbeta", "rnorm", "runif")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 83-87 (fiftystater.Rmd) 
Error: processing vignette 'fiftystater.Rmd' failed with diagnostics:
ScaleColorPlane was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because Best_Prectices.Rmd appears to be an R Markdown v2 document.
Quitting from lines 2-23 (Best_Prectices.Rmd) 
Error: processing vignette 'Best_Prectices.Rmd' failed with diagnostics:
could not find function "doc_date"
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tkrplot’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘methods’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘fisheyeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: POIcoords<-
> ### Title: Update POI slots
> ### Aliases: POIcoords<-
> 
> ### ** Examples
> 
>    ## IRIS Example
>    data(iris)
>    
>    # distance of each element to each dimension max and min
>    matrizSim = cbind(
+                1 - (max(iris[,1]) - iris[,1]) / (max(max(iris[,1]) - iris[,1])),
+                1 - (max(iris[,2]) - iris[,2]) / (max(max(iris[,2]) - iris[,2])),
+                1 - (max(iris[,3]) - iris[,3]) / (max(max(iris[,3]) - iris[,3])),
+                1 - (max(iris[,4]) - iris[,4]) / (max(max(iris[,4]) - iris[,4])),
+ 
+                1 - (min(iris[,1]) - iris[,1]) / (min(min(iris[,1]) - iris[,1])),
+                1 - (min(iris[,2]) - iris[,2]) / (min(min(iris[,2]) - iris[,2])),
+                1 - (min(iris[,3]) - iris[,3]) / (min(min(iris[,3]) - iris[,3])),
+                1 - (min(iris[,4]) - iris[,4]) / (min(min(iris[,4]) - iris[,4])))
> 
>    # exaggerate diffs
>    matrizSim  = matrizSim^3 
>    
>    # Create POI plot
>    irisPOI = POICreate('POI')
>    irisPOI@matrizSim <- matrizSim
>    irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
+                              'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')
>    POIcoords(irisPOI) <- POICalc(irisPOI ,length(irisPOI@wordsInQuery))
>    irisPOI@docs <- cbind(matrix(seq(1:nrow(irisPOI@objeto))),matrix(seq(1:nrow(irisPOI@objeto))))
>    irisPOI@colores <- c(rep(2,50),rep(3,50),rep(4,50))
>    try(rm('POI.env'), silent = T)
Warning in rm("POI.env") : object 'POI.env' not found
>    plotPOI(irisPOI)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: plotPOI ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fit4NM.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fitur.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
     estimating mean dists
     estimating probs of migration
     estimating median dists
     creating output DONE!
  DONE!
  bird likely did not move, exiting without result
  testthat results ================================================================
  OK: 27 SKIPPED: 0 FAILED: 2
  1. Error: map_flightr_ggmap_works (@test_data_result_summary_and_plotting.R#36) 
  2. Error: plot_util_distr_works (@test_data_result_summary_and_plotting.R#57) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/foodweb.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Error in re-building vignettes:
  ...
  number of items to replace is not a multiple of replacement length
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ClassDiagram.tex' failed.
LaTeX errors:
! Package pgfkeys Error: I do not know the key '/forest/package@options/linguis
tics' and I am going to ignore it. Perhaps you misspelled it.

See the pgfkeys package documentation for explanation.
Type  H <return>  for immediate help.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘forega-Ex.R’ failed
The error most likely occurred in:

> ### Name: ForecastArima
> ### Title: Floating-Point Genetic Algorithms with Statistical Forecast
> ###   Based Inheritance Operator
> ### Aliases: ForecastArima
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> # Required package forega
> require("forega")
> 
> set.seed(12345)
> 
> # This function has the global minimum at x_1 = pi and x_2 = exp(1)
> f <- function (x){
+ 	return( (x[1]-pi)^2 + (x[2]-2.71828)^2 )
+ }
> 
> # Performing a floating-point genetic algorithm search with forecast probability of 0.10
> res <- forecasting_ga(evalFunc=f, chsize=2, minv=rep(-10.0,2),
+                       maxv=rep(10.0,2), crossprob=0.80, mutationprob=0.01, 
+                       popsize=100, maxiter=1000, MinimumForecastLength=20, 
+                       ForecastFunction=ForecastArima, elitism=2, forecastprob=0.01)
Error: only replacement of elements is allowed
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ForImp.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyForImp: no visible global function definition for ‘head’
ForImp: no visible global function definition for ‘tail’
ForImp: no visible global function definition for ‘dist’
medianimp: no visible global function definition for ‘quantile’
rancatmat: no visible global function definition for ‘runif’
transfmatcat: no visible global function definition for ‘qnorm’
transfmatcat: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dist head qnorm quantile runif sd tail
Consider adding
  importFrom("stats", "dist", "qnorm", "quantile", "runif", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because formattable-data-frame.Rmd appears to be an R Markdown v2 document.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
  input string 346 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Formula.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.22 p<81>'<f6>^^\<f3>`<cc><e9><e7><c0>^^Sa<ee>yB<b0><81><c4>q<9c><fe>7<f2><e7><8a>9/<db><de><fc><b4>\<f1>
                                           <fd>ޫ<9d><c6>E<80><82><f4>^^V<e7>^^\<b8>^^G^^Y0<c6>hG^^W<87><cc>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Missing $ inserted.
<inserted text> 
                $
l.23 ...G<9e>3<97><cb><cd><cc><cc><d4>j5<ac><93>B<a1><b0><b0><b0>P(^^T^^R<89><84>a^^X<aa><aa>nmm)<8a><e2>y^
                                                  <a5>Ra<8c>U*^^U^^\<c3>i<b7><db><c8>|2<c6><f0><ab>^^P<e2>...
! Undefined control sequence.
l.23 ...Ra<8c>U*^^U^^\<c3>i<b7><db><c8>|2<c6><f0><ab>^^P<e2>ѣG<b3><b3><b3>B<88>X,<96><c
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘Rsymphony’

Packages suggested but not available for checking:
  ‘Rsocp’ ‘Rnlminb2’ ‘Rdonlp2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/frequencies.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/frontiles.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyROCscore: no visible global function definition for ‘par’
ROCscore: no visible global function definition for ‘axis’
ROCscore: no visible global function definition for ‘mtext’
ROCscore: no visible global function definition for ‘legend’
alphafrontier.2d: no visible global function definition for ‘par’
alphafrontier.2d: no visible global function definition for ‘polygon’
alphafrontier.2d: no visible global function definition for ‘lines’
alphafrontier.2d: no visible global function definition for ‘points’
alphafrontier.3d: no visible global function definition for ‘layout’
alphafrontier.3d: no visible global function definition for ‘barplot’
alphafrontier.3d: no visible global function definition for ‘axis’
alphafrontier.3d: no visible global function definition for ‘lines’
alphafrontier.3d: no visible global function definition for ‘na.omit’
ordermfrontier.2d: no visible global function definition for ‘par’
ordermfrontier.2d: no visible global function definition for ‘polygon’
ordermfrontier.2d: no visible global function definition for ‘lines’
ordermfrontier.2d: no visible global function definition for ‘points’
ordermscore.boot: no visible global function definition for ‘sd’
Undefined global functions or variables:
  axis barplot layout legend lines mtext na.omit par points polygon sd
Consider adding
  importFrom("graphics", "axis", "barplot", "layout", "legend", "lines",
             "mtext", "par", "points", "polygon")
  importFrom("stats", "na.omit", "sd")
to your NAMESPACE file.
Running examples in ‘FSelector-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.simple.formula
> ### Title: Converting to formulas
> ### Aliases: as.simple.formula
> 
> ### ** Examples
> 
>   data(iris)
>   result <- cfs(Species ~ ., iris)
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: cfs ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.5Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  8: read_data_into_Weka(mf, 1L)
  9: .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List"))
  
  testthat results ================================================================
  OK: 83 SKIPPED: 0 FAILED: 5
  1. Error: Discretization - basic (@test-discretize.R#32) 
  2. Error: Discretization - single NA (independent variable) (@test-discretize.R#47) 
  3. Error: Comparsion with FSelector (@test-information_gain.R#7) 
  4. Error: Test character table (@test-information_gain.R#36) 
  5. Error: Equal bin discretization (@test-information_gain.R#147) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fso.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ftsa.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fullfact.Rcheck/00install.out’ for details.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
Error in re-building vignettes:
  ...
  input string 191 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 192 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 200 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CNY.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.31 ...<f9><f3><a7>\.;q*<e0><88><ed><ed><ed><d0> <ac>~<d0><e6>+W<88><ca><e5>2J<fb>Μ^^@σ<83><83>0<89><f1>x\T
                                                  <c3>^^Q^^Y<e2>~^^H<ed><de>^^U`<8c><f5><f7><f7><e3><93>s<ce>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.34 ΘeY<b9>\N
            <84>x<a2>B^^DX^^@E?T<ed>^^P<91>E<a3>ю<8e><8e>|>/<8a>GD<94><cb>尙<c3><dd>z^^E<f6>^^P+x<^^^I<92>$I<d2>4M<92>$UU^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.36 <8c>C@^^OP^^D\<b2>
                 <c0><fd>\<a6>A<bb>X<ee><a0><cd>7x<8d><a1><f2><d9>ù<87>	<99><9e><9e>~<f4><e8>^^QB<8d><ab>W<af>^^B^^Tt^<f2><a2>]^^Nq<d2>^^@<d4>#O<ab>^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you h
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required and available but unsuitable versions:
  ‘grDevices’ ‘graphics’ ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘gamlss.demo-Ex.R’ failed
The error most likely occurred in:

> ### Name: demoDist
> ### Title: Interface for demonstrating the gamlss.family distributions
> ### Aliases: demoDist
> ### Keywords: distribution regression
> 
> ### ** Examples
> 
> ## do not run 
> demoDist()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: demoDist ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'jss.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.18 <92><a1>><df><ef><af>NJ^^C^^C~<d2><e7>^^[^^Zhl|<fb><f6><ed><e6><a3>ٶ}
                                       <f3><e6>M۶gffZ<b6>ll<86><bd><f6><80>^^V<dc>;^^W<f2><e9>k<f5>X<ea>w<9f><fc><e5><ef>֦...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.18 ...`<8c>QJ3<99>L^^?^^?<ff><e0><e0> ^^@PJ^^S<89>D:<9d>ƨ<ea><ec>ٳ<8b><8b><8b>W<ae>\<99>
                                                  <9e><9e><be>r<e5><ca><de>'<b7><b7>@<e3><87>a<cb>^^^b<96><e6>]fff^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Missing $ inserted.
<inserted text> 
        
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   9.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gastempt.Rcheck/00install.out’ for details.
installed size is 59.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     56.5Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  14.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gdimap.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.4Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    exdata   5.0Mb
Packages suggested but not available for checking: ‘KEGG.db’ ‘reactome.db’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gensphere.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/geoelectrics.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyimage.glm.krige.bayes: no visible global function definition for
  ‘heat.colors’
Undefined global functions or variables:
  heat.colors
Consider adding
  importFrom("grDevices", "heat.colors")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 key.ldots.set: no visible global function definition for ‘getS3method’
grf: no visible global function definition for ‘chull’
image.grf: no visible global function definition for ‘heat.colors’
image.krige.bayes: no visible global function definition for
  ‘heat.colors’
legend.krige: no visible global function definition for ‘heat.colors’
points.geodata: no visible global function definition for
  ‘terrain.colors’
points.geodata: no visible global function definition for ‘gray’
read.geodata: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  chull getS3method gray heat.colors read.table terrain.colors
Consider adding
  importFrom("grDevices", "chull", "gray", "heat.colors",
             "terrain.colors")
  importFrom("utils", "getS3method", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GeoXp.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘stable’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 102-115 (examples-from-paper.Rmd) 
Error: processing vignette 'examples-from-paper.Rmd' failed with diagnostics:
StatEdges was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ggdmc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GGEBiplotGUI.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘GGEBiplotGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: GGEBiplot
> ### Title: GGEBiplotGUI: Interactive GGE Biplots in R
> ### Aliases: GGEBiplot
> 
> ### ** Examples
> 
> data(Ontario)
> GGEBiplot(Data = Ontario)
Invalid MIT-MAGIC-COOKIE-1 keyWarning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: GGEBiplot ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Package required and available but unsuitable version: ‘grid’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotc05e7bb77beb.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotc05e7bb77beb.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot1213b50b8e1fb.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1213b50b8e1fb.png': No such file or directory
Quitting from lines 16-30 (an_introduction.Rmd) 
Error: processing vignette 'an_introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because using_ggmcmc.Rmd appears to be an R Markdown v2 document.
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: tidyr
Loading required package: ggplot2
Registering fonts with R
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Quitting from lines 142-143 (using_ggmcmc.Rmd) 
Error: processing vignette 'using_ggmcmc.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.5Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ghibli.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Packages suggested but not available for checking:
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Error in re-building vignettes:
  ...
  input string 341 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'glmertree.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Oh
           ^^S<dd>^^V?6<af>h<a4>d<de><c5>"!<90><a6>\<f0>I<bf>/<84>@PP(qQ<9e><bb>"HPą^^[<83> .<ba><ea>օ.\(.<ec>f<b6><fe>A^^H<b8><c8><e2>[<d8>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 x<9c><ed>\Oh^^S<dd>^^V?6<af>h<a4>d<de><c5>"!<90><a6>\<f0>
                                I<bf>/<84>@PP(qQ<9e><bb>"HPą^^[<83> .<ba><ea>օ.\(.<ec>f<b6><fe>A^^H<b8><c8><e2>[<d8>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<95>R<9a><a6>y<f7><ee>]<ce><f9><f5><eb><d7>oܸa^^X^^F<be>^^B<df>^^E^^@x<81><d7>8!<e7>\<d3>
                                                  <b4>T^^]<8d><96><be><b6>3LOO^^?<fd><fa>u'O<bd>y<f3>f<87>...
The control sequence at the end of the top line
of your error message was never 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running the tests in ‘tests/bym.R’ failed.
Last 13 lines of output:
  + 
  + kentucky = mergeBugsData(kentucky, kSummary)
  + 
  + if(require('sp', quietly=TRUE)) {
  +   pdf("spplotBym.pdf",height=4,width=8)
  +   print(spplot(kentucky, "FittedRateCounty.mean"))
  +   dev.off()
  + }
  + 
  + }
  Error in R2OpenBUGS::bugs(forBugs$ragged, inits = int2, model.file = "bym.txt",  : 
    Cannot find the OpenBUGS program
  Execution halted
installed size is 49.3Mb
  sub-directories of 1Mb or more:
    libs  48.6Mb
installed size is 54.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  52.8Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gmatrix.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > library('testthat')
  > 
  > test_check('Gmisc')
  Loading required package: Gmisc
  Loading required package: Rcpp
  Loading required package: htmlTable
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  testthat results ================================================================
  OK: 116 SKIPPED: 0 FAILED: 0
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GMSE.Rcheck/00install.out’ for details.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
Error in re-building vignettes:
  ...
  input string 205 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 206 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 214 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'googleVis.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 <ed><c1>E<98>e҃<a7>z<ea>ѣ<82>x^^V<(xt^^?<80><88><ee>\E
                                  <8a>B^^[<88>^^Y<e2><L'a"A:'^^AM<b2><c9>V<fb><98>&Vs<b0><f9>^^\^^^^^\...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...<97><cb>=x<f0>`vv<f6>ڵk<87>^^O^^_<be>x<f1><a2>i<9a><8f>^^_?<f6>}<ff>ʕ+^^W.\<98>
                                                  <9d><9d><d5>4mmmM<92><a4><b9><b9><b9>;w<ee>D^^^<d5>n<b6>[<d3>4...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ^^@^^X<86>^^A^^@<c5>b<b1><eb> {<ba><9f><84><90>r<b9>L<bb>\<b3>
                                  <d9>$<84><8c><8f><8f>˲L^^Hy<f9><f2><a5><e7>y<93><93><93><8d>F^^C^^@<c2>0ܖ<a4>q^^O
The control sequence at the end of the top line
of your error message was nev
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GPC.Rcheck/00install.out’ for details.
Warning: parse error in file '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GPoM.Rcheck/GPoM/doc/II_PreProcessing.R':
invalid multibyte character in parser at line 59
Warning: parse error in file '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GPoM.Rcheck/GPoM/doc/IV_VisualizeOutputs.R':
invalid multibyte character in parser at line 30
installed size is 41.9Mb
  sub-directories of 1Mb or more:
    libs  40.0Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  base log float matrix elements not equivalent
  
  testthat results ================================================================
  OK: 891 SKIPPED: 717 FAILED: 6
  1. Error: gpuMatrix Integer Matrix multiplication (@test_gpuMatrix_algebra.R#318) 
  2. Error: gpuMatrix Single Precision Matrix Cholesky Decomposition (@test_gpuMatrix_chol.R#25) 
  3. Failure: gpuVector Single Precision Element-Wise Logs (@test_gpuVector_math.R#133) 
  4. Error: vclMatrix Integer Matrix multiplication (@test_vclMatrix_algebra.R#307) 
  5. Error: vclMatrix Single Precision Matrix Cholesky Decomposition (@test_vclMatrix_chol.R#25) 
  6. Failure: vclVector Single Precision Matrix Element-Wise Logs (@test_vclVector_math.R#134) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gputools.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   5.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GrammR.Rcheck/00install.out’ for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/groupsubsetselection.Rcheck/00install.out’ for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Errors in running code in vignettes:
when running code in ‘gWidgets.Rnw’
  ...

Loading required package: gWidgetstcltk
Error : .onAttach failed in attachNamespace() for 'gWidgetstcltk', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] invalid command name "option".


  When sourcing ‘gWidgets.R’:
Error: [tcl] invalid command name "toplevel".
Execution halted
Error in re-building vignettes:
  ...
Loading required package: gWidgetstcltk
Loading required package: tcltk
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Loading required package: digest
Error : .onAttach failed in attachNamespace() for 'gWidgetstcltk', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] invalid command name "option".

Loading required package: gWidgetstcltk
Error : .onAttach failed in attachNamespace() for 'gWidgetstcltk', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] invalid command name "option".

Loading required package: gWidgetstcltk
Error : .onAttach failed in attachNamespace() for 'gWidgetstcltk', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] invalid command name "option".


Error: processing vignette 'gWidgets.Rnw' failed with diagnostics:
 chunk 3 
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".

Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gWidgetstcltk.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/h5.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/happybiRthday.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
Invalid MIT-MAGIC-COOKIE-1 keyPackage in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘helixvis-Ex.R’ failed
The error most likely occurred in:

> ### Name: draw_wenxiang
> ### Title: Create wenxiang diagrams to visualize alpha helical sequences.
> ### Aliases: draw_wenxiang
> 
> ### ** Examples
> 
> draw_wenxiang("TestWenxiang", "AREKHLVLLKREGDIWKL")
Error in rJava::.jnew("Sequence") : 
  java.lang.UnsupportedClassVersionError: Sequence : Unsupported major.minor version 52.0
Calls: draw_wenxiang -> <Anonymous> -> .External
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 146-147 (Visualization.Rmd) 
Error: processing vignette 'Visualization.Rmd' failed with diagnostics:
java.lang.UnsupportedClassVersionError: Sequence : Unsupported major.minor version 52.0
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HEMDAG.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hgam.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘grplasso’ ‘lattice’ ‘rgl’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘HIBPwned-Ex.R’ failed
The error most likely occurred in:

> ### Name: account_breaches
> ### Title: Search for data breaches associated with one or more accounts.
> ### Aliases: account_breaches
> 
> ### ** Examples
> 
> account_breaches(c("steff.sullivan@gmail.com","stephanie.g.locke@gmail.com"))
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL certificate problem: Invalid certificate chain
Calls: account_breaches ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  testthat results ================================================================
  OK: 31 SKIPPED: 0 FAILED: 7
  1. Error: account_breaches works for a single account (@test-account_breaches.R#8) 
  2. Error: account_breaches works for multiple accounts (@test-account_breaches.R#54) 
  3. Error: breached_site works (@test-breached_site.R#6) 
  4. Error: breached_sites works (@test-breached_sites.R#6) 
  5. Error: data_classes works (@test-data_classes.R#4) 
  6. Error: pastes works for a single account (@test-pastes.R#8) 
  7. Error: pastes works for multiple accounts (@test-pastes.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 23-24 (HIBP.Rmd) 
Error: processing vignette 'HIBP.Rmd' failed with diagnostics:
SSL certificate problem: Invalid certificate chain
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HiCblock.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HierO.Rcheck/00install.out’ for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        7.8Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hiPOD.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hoardeR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/homals.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HomoPolymer.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HRM.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
    doc    1.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 89-97 (api-packages.Rmd) 
Error: processing vignette 'api-packages.Rmd' failed with diagnostics:
Failed connect to api.github.com:443; Operation now in progress
Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for ‘colMeans’
  Warning: multiple methods tables found for ‘colSums’
  Warning: multiple methods tables found for ‘rowMeans’
  Warning: multiple methods tables found for ‘rowSums’
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/humarray.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HUM.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyCalculate3D: no visible global function definition for ‘persp’
CalculateHUM_Ex: no visible global function definition for ‘combn’
CalculateHUM_Plot: no visible global function definition for ‘plot’
CalculateHUM_Plot: no visible global function definition for ‘polygon’
CalculateHUM_Plot: no visible global function definition for ‘text’
CalculateHUM_Plot: no visible global function definition for ‘points’
CalculateHUM_Plot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  combn lines persp plot points polygon text
Consider adding
  importFrom("graphics", "lines", "persp", "plot", "points", "polygon",
             "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    doc    1.1Mb
    libs   4.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: pdftools
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'unknown' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 163-166 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HURDAT.Rcheck/00install.out’ for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/iBUGS.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   1.3Mb
    doc    2.1Mb
    libs   8.3Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/iClick.Rcheck/00install.out’ for details.
Running examples in ‘iClick-Ex.R’ failed
The error most likely occurred in:

> ### Name: iClick.ARIMA
> ### Title: iClick GUI for ARIMA
> ### Aliases: iClick.ARIMA
> 
> ### ** Examples
> 
> 
> ##External data
> #data("returnsDaily24")
> #y=returnsDaily24[,c(1,5)]
> 
> ## Simulation data
> dat=rnorm(100,5,1)
> y=ts(dat, start = c(1970, 1), frequency = 12)
> 
> iClick.ARIMA(y)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: iClick.ARIMA ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.5Mb
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ICS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cf>
          O^^S<df>^^V?ԇ<bc><89><a4>ÄMCRhnbta<a0>d6Ƙ<94>^^Ekw<fe>]<eb><c2>tk\<c1><bf>Ѕ1q<c9>ưe^^VT^^S^^S<88>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...^S<df>^^V?ԇ<bc><89><a4>ÄMCRhnbta<a0>d6Ƙ<94>^^Ekw<fe>]<eb><c2>tk\<c1>
                                                  <bf>Ѕ1q<c9>ưe^^VT^^S^^S<88>^^S<a7><8d>A...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 <c3>^^PB\<be>
            |<f9>Ǐ^^_<86>a<80>H!D&<93>A7|^^Z<86>a<9a>&c<8c>1<b6><b9><b9>9::jYV&<93>i<e3>z^^O<e0>իWM-+++{{{<bd>X<eb>d^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 cB<88><ef><9e>^^W<c4><e3>Q<c6>^^L<c7><f9>O2^^Yk^^
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  23.9Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/idmTPreg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ifa.Rcheck/00install.out’ for details.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  14.8Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ilc.Rcheck/00install.out’ for details.
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    include   2.8Mb
    libs     18.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/incR.Rcheck/00install.out’ for details.
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
sh: line 1: 75981 Trace/BPT trap: 5       /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/x13binary/bin/x13ashtml /tmp/RtmpucF0C2/x13128ca4f828c6c/iofile -n -s 2> /dev/null
Warning: running command '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/x13binary/bin/x13ashtml /tmp/RtmpucF0C2/x13128ca4f828c6c/iofile -n -s 2>/dev/null' had status 133
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/x13binary/bin/../lib/libgfortran.3.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/x13binary/bin/../lib/libgfortran.3.dylib
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x12f352579
#1  0x12f351945
#2  0x7fff9078d5a9
Error: X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/interactionTest.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/interfr.Rcheck/00install.out’ for details.
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Package required and available but unsuitable version: ‘rcdk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
  input string 443 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 451 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 452 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 460 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'isocir.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<b6>m<cb><f6><81>^^?<c9>?<e5><cc>B^^H<<c4><ef><f0>؞p<b9><cb>~<a6>i~<f3><cd>7<bf><fc><f2><8b>i<9a><86>a\<bf>
                                                  ~]<d7>u<<b7>m<bb>P(<88>^^V<b2>٬a^^X<d8><df><f4><f4><f4>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...<fd><f6><db><fe><9b>xud^^Lݼy<b3>'a<d6>u]Q^^T<f9><a7>a^^X?<fd><f4><93><a2>(<f1>x\^^H
                                                  <f1><e5><97>_^<bb>vm~~~gg<e7><d7>_^^?<9d><9d><9d>5^^L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...<e6>y<fe><fc>y2<99><f4></<99>L<86><a3>^^E^^L,<95>J<9f>^^?<fe><b9><e3>8<99>L<e6>,<c8><eb>^^W\p
                                                  <dd>^^[<90><d7><cf>8<96><e5>4MS<d7>u<c6><d8><c2><c2><c2><d8><d
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
l.19 ...	]<d7>^^AJ^^R<89>D<b3>ٔ<f3><ef><ef><ef>g<b3><d9>J<a5><92><cd>f^^AP8<e7><e5><b2>_(d\^^W
                                                  <97>})<f6>^^@<ca>)D<84>^^_<be><bf><f3><d3>O<8d>7ޘ<e6><fc>2...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten \endgroup.
l.24 <9e>^^P<91>g}}
             ^^]<d8>^^_^^A<8d><88>^^TEY^^<ae><d5>j<e8>^^Z<db><dc><dc>l6<9b>2<b7>B
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or
Calls: buildVignettes -> texi2pdf -> texi2dvi
In addition: Warning messages:
1: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 424 is invalid in this locale
2: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 425 is invalid in this locale
3: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 433 is invalid in this locale
4: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 434 is invalid in this locale
5: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 442 is invalid in this locale
Execution halted
Running the tests in ‘tests/test.R’ failed.
Last 13 lines of output:
  > testMD <- issuesData2md()
  > 
  > # Use default data to generate PDF
  > issuesGenPDF(style = "tint",
  +              RmdLocation =  system.file("rmarkdown/templates/", "tint.Rmd",
  +                                         package = "issueReporter"),
  +              outputFile = tempfile(pattern="ir", fileext=".pdf"),
  +              outputDir = tempdir(),
  +              md = testMD,
  +              setTitle = "Example Notes",
  +              setAuthor = "Author Name")
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Execution halted
Error in re-building vignettes:
  ...
 1: .Call(rmd_b64encode_data, readBin(inFile, "raw", n = fileSize))
 2: paste("data:", mime::guess_type(inFile), ";base64,", .Call(rmd_b64encode_data,     readBin(inFile, "raw", n = fileSize)), sep = "")
 3: .b64EncodeFile(inFile)
 4: sub(src, .b64EncodeFile(inFile), imgSrc, fixed = TRUE)
 5: FUN(X[[i]], ...)
 6: lapply(regmatches(html, m)[[1]], .b64EncodeImgSrc)
 7: unlist(lapply(regmatches(html, m)[[1]], .b64EncodeImgSrc))
 8: .b64EncodeImages(ret)
 9: eval(expr, envir, enclos)
10: eval(quote({    oldwd <- setwd(filedir)    on.exit(setwd(oldwd))    .b64EncodeImages(ret)}), new.env())
11: eval(expr, envir, enclos)
12: eval(expr, p)
13: eval.parent(substitute(eval(quote(expr), envir)))
14: local({    oldwd <- setwd(filedir)    on.exit(setwd(oldwd))    .b64EncodeImages(ret)})
15: markdown::markdownToHTML(out, output, encoding = encoding, ...)
16: knit2html(..., force_v1 = TRUE)
17: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$",     file)) knit2pdf else knit)(file, encoding = encoding, quiet = quiet,     envir = globalenv())
18: vweave(...)
19: engine$weave(file, quiet = quiet, encoding = enc)
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) {    stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)), domain = NA, call. = FALSE)})
24: buildVignettes(dir = "/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Jdmbs.Rcheck/vign_test/Jdmbs")
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.2Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/JumpTest.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/KappaGUI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Kernelheaping.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 238 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 244 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kernlab.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^[G^^[^^?<ec>dc'U<a5>^^N-.u<ba><b2><bb>E<b8><88>e<a3>V^^P<b0>!<dd>^^F<ab><84>^ғo=<e4><a4><d0>C^^O=<e5>VBo<f9>^^C^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.17 ...<f7>}^^Lb<9a>f<9c>5<9f><b8>~<fd>zL<f2><d6><d6><d6>^^XcCCC+++^^_|<f0><c1><fa><fa>z6<9b>}
                                                  <f0><e0><c1><e8><e8><a8><e7>yO<9e><<f1><<8f><88><d2><e9><f4><da><da><da>ŋ^^W...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.17 ...O<9e><<f1><<8f><88><d2><e9><f4><da><da
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/KernSmoothIRT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kmcudaR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kml.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kmlShape.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/komadown.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 100 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kst.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.17 b<84><bd><a5>?^^T<9a>[<c1><bf><a0>^^?Ls^<85><e2>^^_Ћ^^E<a5>$<87>6v<91>\B
                                               <a6><ea><90>[q<d9>M<e8>E^^R<bf><87>^^O>&<ab><8d>k<a2>&<b5><fb>9<88>;...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.22 ^^YIN<ac><a5>^^[\<8a>
                 sY<cc>Q<d7>'<db>a^^P^^Dggg<c9>d^^R<8a>M$^^R<f9>|<9e>u^^N<e3>D<8e><87><8d><9c>ե+_)U,^^Vi<94>^^VB5<98>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.22 ...<88>H<b7>L<a5>^^T<8b>^^A/m<8d><d0><ed>v<85>^^P<be><ef><f3>O^^W<8b>E6㩘<99>',<9a><ca>\<de>
     
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/laGP.Rcheck/00install.out’ for details.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs          11.1Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/LCox.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/lctools.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ldhmm.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/lfl.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/libcoin.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/libstableR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/lifecontingencies.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘reactR’
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    libs      18.7Mb
    testdata   1.5Mb
Error in re-building vignettes:
  ...
  input string 785 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'lmer.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Mh
           ^^TK^^P<ae><97>(q$<ee>؈!.L6^^L/($oYX^^Hx^^H<eb>!<a0>'o<de><<eb>ٓ^^A/<a2>O<f0>]ċ^^G<f5>^^]<84><e7>A...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...F<a0><ba>v<ed>Zggg<ad>V{<fd><fa>5^^Q9<8e>388866<a6><94><8a><e3>^^X<fd>^^]<c7><c1><83><ae>^
                                                  <bd><9a>J<a5>l<db>v^^\^^G<9f>J<a9><87>^^O^^_<c6>q|...
! Extra }, or forgotten $.
l.17 Ԓ<da>[}
          <b8>ӄ<f6><a0><9c>0^^L<89>(<9b><cd><e2>^^A<98><ce>0^^L<85>^^BOm<b9>\^^^^^Z^^Z<8a><a2><88><a7>?<9b><cd>"@a<ce>0<8e>eYP{<a1>P<c0>O<<c8><e3>...
I've deleted a group-closing 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/LMERConvenienceFunctions.Rcheck/00install.out’ for details.
Packages required and available but unsuitable versions:
  ‘parallel’ ‘graphics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in readLines(con) :
  incomplete final line found on 'localsolver.Rmd'
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because localsolver.Rmd appears to be an R Markdown v2 document.
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/logcondens.mode.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyNamespace in Imports field not imported from: ‘distr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/logcondens.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 442 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'logcondens.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.16 ...[<f8><f8>㏻~8<9d>NC^^\<cb>d2<ba><ae>^^SB><fd><f4>ӑ<91>^^Q!D&<93><f9>ꫯ<de>}
                                                  <f7><dd>vڙ<9d><9d><b5>,˲,<ce><f9><d7>_^^?=11^^Aa...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.23 ...<aa>mۚ<a6>I<bb>b<8c><fd><fa><eb><af><c8>e<99><aa><aa><c2>-If<c6>X4^^Z-<97>ˊ<a2>p<ce>UU<a5><94>z<bd>^
                                                  7<c9>^^O<91><a3><92><f3><f0><95><c1><be><bb><a7><bf><8c><e8>^^@^<a1>PP^...
! You can't use `\spacefactor' in math mode.
\@ ->\spacefactor 
                  \@m 
l.24 ...<aa><aa>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/longitudinalData.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/loon.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyTOS2D: no visible global function definition for ‘medpolish’
countTextures: no visible global function definition for ‘medpolish’
plot.imageQT: no visible global function definition for ‘segments’
simTexture: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  medpolish rnorm segments
Consider adding
  importFrom("graphics", "segments")
  importFrom("stats", "medpolish", "rnorm")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/lumberjack.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Maeswrap.Rcheck/00install.out’ for details.
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs  15.2Mb
objc[68494]: Class GNotificationCenterDelegate is implemented in both /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/magick.Rcheck/magick/libs/magick.so and /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rsvg/libs/rsvg.so. One of the two will be used. Which one is undefined.
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
Error in re-building vignettes:
  ...
Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Warning in arrange_impl(.data, dots) :
  '.Random.seed' is not an integer vector but of type 'NULL', so ignored
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotcc924daff2c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotcc924daff2c.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot11424aa2620f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot11424aa2620f.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘MANOVA.RM-Ex.R’ failed
The error most likely occurred in:

> ### Name: MANOVA.wide
> ### Title: Tests for Multivariate Data in Semi-Parametric Factorial Designs
> ### Aliases: MANOVA.wide
> 
> ### ** Examples
> 
> #Example on producing plastic film from Krzanowski (1998, p. 381), see \code{manova.summary}
> tear <- c(6.5, 6.2, 5.8, 6.5, 6.5, 6.9, 7.2, 6.9, 6.1, 6.3,
+           6.7, 6.6, 7.2, 7.1, 6.8, 7.1, 7.0, 7.2, 7.5, 7.6)
> gloss <- c(9.5, 9.9, 9.6, 9.6, 9.2, 9.1, 10.0, 9.9, 9.5, 9.4,
+            9.1, 9.3, 8.3, 8.4, 8.5, 9.2, 8.8, 9.7, 10.1, 9.2)
> opacity <- c(4.4, 6.4, 3.0, 4.1, 0.8, 5.7, 2.0, 3.9, 1.9, 5.7,
+              2.8, 4.1, 3.8, 1.6, 3.4, 8.4, 5.2, 6.9, 2.7, 1.9)
> rate     <- gl(2,10, labels = c("Low", "High"))
> additive <- gl(2, 5, length = 20, labels = c("Low", "High"))
> example <- data.frame(tear, gloss, opacity, rate, additive)
> fit <- MANOVA.wide(cbind(tear, gloss, opacity) ~ rate * additive, 
+ data = example, iter = 100, CPU = 1)
Error in deparse(...) : unused argument (lex.order = TRUE)
Calls: MANOVA.wide ... split.default -> .NotYetUsed -> gettextf -> sprintf -> deparse
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 162-174 (Introduction_to_MANOVA.RM.Rmd) 
Error: processing vignette 'Introduction_to_MANOVA.RM.Rmd' failed with diagnostics:
unused argument (lex.order = TRUE)
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘MARSS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘MARSS:::is.diagonal’
  See the note in ?`:::` about the use of this operator.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   5.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mbbefd.Rcheck/00install.out’ for details.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  11.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mdpeer.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.7Mb
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mefa.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 <f0>F<b6>9<dc> <9d>N˗<b9>\N
                  <b6>?<<af><9c><a5>)^^EZ<f4>^^X<d2><e9>t*<95><9a><99><99><91>k<d2>u]<ae><fb><97>_~<f9><f0><c3>^^O
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 Ðmt]<c7><ca>._<be>\<ab>
                 <d5>^^Xc<8c><b1><a9><a9><a9>t:
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 ...^^L^^Yc<ba><ae><e3>^^Fs^^R<b3>w-g'S^^SӒN<a7>Og^^]OBG\^^O
                                                  <ba><ca><d9><c9>t^^Z<b8>^^G<82><a7>w<e9>ҥH$R<a9>T<e2><f1><f8>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.27 ...]<e6>^^D<cf><d9>lvhh<c8>u]<c8><c4>u<dd>۷o<ef><ec><ec><c4>b<b1>L&S<af><d7>^^]<c7><e9><ef><ef><c
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘RODBC’

Package required and available but unsuitable version: ‘mem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/memisc.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mem.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyworkspace_management : tellme: no visible global function definition
  for ‘file.edit’
workspace_management: no visible global function definition for
  ‘object.size’
Undefined global functions or variables:
  file.edit object.size
Consider adding
  importFrom("utils", "file.edit", "object.size")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MergeGUI.Rcheck/00install.out’ for details.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   3.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/metaforest.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘EBImage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘hgu133plus2.db’ ‘hgu133a.db’ ‘hgu95av2.db’
Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘doSMP’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/meteoland.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MetFns.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MetSizeR.Rcheck/00install.out’ for details.
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  11.9Mb
    misc   1.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MFHD.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mhde_article.tex' failed.
Messages:
/usr/local/bin/texi2dvi: biber failed
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MicroStrategyR.Rcheck/00install.out’ for details.
Missing or unexported object: ‘tools::CRAN_package_db’
Running examples in ‘miniGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: makeWidgetCmd
> ### Title: R functions to build a GUI window
> ### Aliases: makeWidgetCmd
> ### Keywords: utilities misc
> 
> ### ** Examples
> 
>   require(tcltk)
>   ##
>   ##  a simple example
>   ## 
>   g <- function(a=1,b=rnorm) {cat("--g--");paste("g(a,b)=",a+b(a))}
>   h <- function(a=1,b=3,c=3) {cat("--h--");paste("h(a,b,c)=",a+b+c)}
>   ## create functions
>   gg <- makeWidgetCmd("Hay it is g !!",g,GRAB=FALSE)
>   hh <- makeWidgetCmd("Hay h here !!",h,GRAB=FALSE)
>   ## calling them
>   gg()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: gg ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Running examples in ‘misc3d-Ex.R’ failed
The error most likely occurred in:

> ### Name: slices3d
> ### Title: Interactive Image Slices of 3D or 4D Volume Data
> ### Aliases: slices3d
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   #Example 1: View of a mixture of three tri-variate normal densities
>   nmix3 <- function(x, y, z, m, s) {
+       0.4 * dnorm(x, m, s) * dnorm(y, m, s) * dnorm(z, m, s) +
+       0.3 * dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) +
+       0.3 * dnorm(x, m, s) * dnorm(y, -1.5 * m, s) * dnorm(z, m, s)
+   }
>   x<-seq(-2, 2, len=40)
>   g<-expand.grid(x = x, y = x, z = x)
>   v<-array(nmix3(g$x,g$y,g$z, .5,.5), c(40,40,40))
>   slices3d(vol1=v, main="View of a mixture of three tri-variate normals", col1=heat.colors(256))
Loading required package: tkrplot
Loading required package: tcltk
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Invalid MIT-MAGIC-COOKIE-1 keyWarning: loading Rplot failed
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: slices3d ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mlDNA.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘mlr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mlrMBO’
Package unavailable to check Rd xrefs: ‘mlrMBO’
Running the tests in ‘tests/run-base.R’ failed.
Last 13 lines of output:
  18: .jnew("weka/core/Attribute", attname[i])
  
  testthat results ================================================================
  OK: 2473 SKIPPED: 2 FAILED: 6
  1. Error: clustering performance (@test_base_clustering.R#16) 
  2. Error: clustering performance with missing clusters (@test_base_clustering.R#28) 
  3. Error: clustering resample (@test_base_clustering.R#42) 
  4. Error: clustering benchmark (@test_base_clustering.R#55) 
  5. Error: clustering tune (@test_base_clustering.R#72) 
  6. Error: check measure calculations (@test_base_measures.R#187) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mlt.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Ok
           ^^[<d7>^^V?^^]?c^^\<8d>.<86><e2><a4>O<91>zy<c1><81>^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 <82> <9b><cd><c2>/<e9>^^R<9d>^^PB^^HQ.<97><e7><e6><e6><98>^^?)e<b9>\N
                                      &<93>D<84><d1>\<d7>%<a2><a5><a5>%L<81><be>Q<e1><f3>\<fd><88><8e>^^F<b2>{W<af>^%"<cf><f3><b0> &<d7>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 <82> <9b><cd><c2>/<e9>^^R<9d>^^PB^^HQ.<97><e7><e6><e6><98>^^?)e<b9>\N&<93>D<84><d1>\<d7>
                                             %<a2><a5><a5>%L<81><be>Q<e1><f3>\<fd><88><8e>^^F<b2>{W<af>^%"<cf><f3><b0> &<d7>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control s
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  input string 341 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'modTempEff.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...2^^F<e2><f5>2^^F<e2><f5>2<9e>m񤔏<bd>TJ<f1><cd>t:<dd>V<ad><c3><e3><96>eI)q<ff><e0>S<b9>\<ce>
                                                  ^^?<93><ab>^^U<8b>E^^?5<a5>^^T^^Z<f1>w<e3><b1>x...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<a5>¯l^^S<d2><ff><e0><c1>^^V<b8>p<f0><92><db><d9><da>ڪxxR<b3><a8>ӹ<e7><dd><c9>	~^^RQ<b9>\<fe>
                                                  <ec><b3><cf><c0>7"<92>R~<f7><dd>w<df>|<f3><cd>G^^_}t<fd><fa>u<d3>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.18 <84>L<a7>Ӧi<82><a5>^^_~<f8><e1><b5>k<d7>r<b9><9c>a^^XB^^H"<ca>f<b3>^^W.\^^X
                                             ^^Y^^Y<d1>4
The control sequence at the end of the top line
of your error message w
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MOEADr.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.7Mb
    libs   2.9Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/monogeneaGM.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/monoreg.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mopa.Rcheck/00install.out’ for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   6.6Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 872 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'moult.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          o<db>F^^V^^?<96>[<cb>,^^RSD<82><ae><e2>]F^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.18 ...<cd><cd>o<be><f9><a6><c7><d4><fd>s<a6><d5><d5><d5>Z<ad>vD<83>^^G^^O^^^<9c><df><e8>c<fe>(<de>^^[\^^Z
                                                  r<f1><c6><ef>ܹs<ac>^^N<b7>o߾|<f9>r.<97>^^[^^_...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten \endgroup.
l.18 ..._<8f>F<a3><cb><cb>ˏ^^^=<92>eY^^P<84><c3><da>3Ʈ_<bf><9e><cd>f<af>_<bf><8e>[۶u]WUu}
                                                  }<bd>\.<a7>R)4VUUQ<94>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Errors in running code in vignettes:
when running code in ‘move.Rnw’
  ...

> load("a.Rdata")

> ggmap(m) + geom_path(data = leroy_df, aes(x = location.long, 
+     y = location.lat))

  When sourcing ‘move.R’:
Error: GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Error in re-building vignettes:
  ...
Loading required package: geosphere
Loading required package: sp
Loading required package: raster
Loading required package: rgdal
rgdal: version: 1.2-8, (SVN revision 663)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.2, released 2016/10/24
 Path to GDAL shared files: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rgdal/gdal
 Loaded PROJ.4 runtime: Rel. 4.9.1, 04 March 2015, [PJ_VERSION: 491]
 Path to PROJ.4 shared files: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rgdal/proj
 Linking to sp version: 1.2-5 
Warning in .local(x, y, time, data, proj, ...) :
  There were NA locations detected and omitted. Currently they are not stored in unusedrecords
Loading required package: ggmap
Loading required package: ggplot2
Loading required package: mapproj
Loading required package: maps

Error: processing vignette 'move.Rnw' failed with diagnostics:
 chunk 15 (label = googleplot) 
Error : GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  30.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/msir.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MSQC.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/msr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mtk.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘MASS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyDesigner.sobol: no visible global function definition for ‘runif’
basicMonteCarlo: no visible global function definition for ‘runif’
lhs003: no visible global function definition for ‘runif’
plmm.mtk : GenereXplmm: no visible binding for global variable ‘poly’
plmm.mtk : calc.plm: no visible global function definition for ‘lm.fit’
plmm.mtk: no visible global function definition for ‘var’
plmm.mtk: no visible global function definition for ‘lm’
plmm.mtk: no visible global function definition for ‘formula’
plmm.mtk: no visible global function definition for ‘update’
plmm.mtk: no visible global function definition for ‘stepAIC’
plot.plmm: no visible global function definition for ‘par’
plot.plmm: no visible global function definition for ‘barplot’
plot.plmm: no visible global function definition for ‘segments’
plot.plmm: no visible global function definition for ‘abline’
plot.plmm: no visible global function definition for ‘title’
plot.plmm: no visible global function definition for ‘legend’
plot.regressionSI: no visible global function definition for ‘par’
plot.regressionSI: no visible global function definition for ‘title’
plot.regressionSI: no visible global function definition for ‘abline’
plot,mtkProcess: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline barplot dev.new formula legend lm lm.fit par poly runif
  segments stepAIC title update var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "par",
             "segments", "title")
  importFrom("stats", "formula", "lm", "lm.fit", "poly", "runif",
             "update", "var")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyNote: found 2 marked UTF-8 strings
Invalid MIT-MAGIC-COOKIE-1 keyNamespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mudfold.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 399 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 400 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 408 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'multgee.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...<9a>J<a5>t]O<a5>R<e9>t<9a><88>8<e7>D<94>J<a5><88>(<93>ɤR)<b0><87>_WVV&&&^^XcW<ae>\<b9>
                                                  u<eb><d6>͛7^^Yc<9c>s<c6>^^X^^Q<c9>U<ee>ܹ<f3><f1>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...^XcW<ae>\<b9>u<eb><d6>͛7^^Yc<9c>s<c6>^^X^^Q<c9>U<ee>ܹ<f3><f1><c7>^^_sί\<b9>
                                                  <92><c9>d<ee>ܹs<ed>ڵt:<fd><cd>7<df>`<e4>n<d4><dc>7<cd><ce><ce>V...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...<c3>@<9a><ae><eb><b8>Q^^@3 ^^G<f0>s<ce>u]<9f><9e><9e><ce>d2<f2><d6>^^A<a8><9d><ec><d9>^^G{ \?
                                                  <ec><e3>퐮뚦<ed><ed>Y<df><ec>u^^W<f5><f4>^7<93>^^O<bd>...
The control sequence a
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is 70.9Mb
  sub-directories of 1Mb or more:
    libs  70.7Mb
Error in re-building vignettes:
  ...
  input string 305 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 306 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 307 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Ch-Errata.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.34 ...<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}
                                                  Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.34 ...<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}
                                                  Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyconceptIndicesSkm: no visible global function definition for
  ‘txtProgressBar’
conceptIndicesSkm: no visible global function definition for
  ‘setTxtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘txtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘setTxtProgressBar’
mvcmb: no visible global function definition for ‘runif’
mvcmb: no visible global function definition for ‘str’
mvcsph: no visible global function definition for ‘pdf’
mvcsph: no visible global function definition for ‘heatmap’
mvcsph: no visible global function definition for ‘dev.off’
mvcsph: no visible global function definition for ‘hclust’
mvcsph: no visible global function definition for ‘dist’
mvcsph: no visible global function definition for ‘str’
Undefined global functions or variables:
  dev.off dist hclust heatmap pdf runif setTxtProgressBar str
  txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "dist", "hclust", "heatmap", "runif")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
                    
! Illegal unit of measure (pt inserted).
<to be read again> 
                   \let 
l.931 \end{tabularx}
                    
! Missing number, treated as zero.
<to be read again> 
                   \let 
l.931 \end{tabularx}
                    
! Illegal unit of measure (pt inserted).
<to be read again> 
                   \let 
l.931 \end{tabularx}
                    
! Missing number, treated as zero.
<to be read again> 
                   \let 
l.931 \end{tabularx}
                    
! Illegal unit of measure (pt inserted).
<to be read 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyplot.matchedwake: no visible global function definition for
  ‘filled.contour’
plot.matchedwake: no visible binding for global variable ‘gray.colors’
plot.matchedwake: no visible global function definition for ‘axis’
plot.matchedwake: no visible global function definition for ‘rect’
slideWakeMatch: no visible binding for global variable ‘lm’
slideWakeMatch: no visible global function definition for ‘as.formula’
slideWakeMatch: no visible global function definition for ‘summary.glm’
Undefined global functions or variables:
  as.formula axis filled.contour gray.colors lm rect summary.glm
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "axis", "filled.contour", "rect")
  importFrom("stats", "as.formula", "lm", "summary.glm")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/My.stepwise.Rcheck/00install.out’ for details.
Running examples in ‘nandb-Ex.R’ failed
The error most likely occurred in:

> ### Name: CorrectForBleaching
> ### Title: Detrend an image series
> ### Aliases: CorrectForBleaching CorrectForBleachingFolder
> 
> ### ** Examples
> 
> library(magrittr)
> img <- ReadImageData(system.file("extdata", "50.tif", package = "nandb"))
> autotau <- CorrectForBleaching(img, "auto")
> setwd(tempdir())
> img <- ReadImageData(system.file('extdata', '50.tif', package = 'nandb'))
> WriteIntImage(img, '50.tif')
Now writing 50.tif.
> WriteIntImage(img, '50again.tif')
Now writing 50again.tif.
> set.seed(33)
> CorrectForBleachingFolder(tau = 1000, mst = "Huang", mcc = 2, na = "s")
Error: 'bplapply' receive data failed:
  error reading from connection
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1. Failure: Brightness works (@test_brightness.R#8) 
  2. Failure: Brightness works (@test_brightness.R#13) 
  3. Failure: BrightnessTimeSeries works (@test_brightness.R#38) 
  4. Failure: BrightnessTimeSeries works (@test_brightness.R#44) 
  5. Failure: BrightnessTimeSeriess works (@test_brightness.R#118) 
  6. Failure: CorrectForBleachingFolder works (@test_detrend.R#30) 
  7. Failure: BestTau works (@test_detrend.R#42) 
  8. Failure: MeanIntensity works (@test_intensity.R#15) 
  9. Failure: MeanIntensity works (@test_intensity.R#35) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nat.nblast.Rcheck/00install.out’ for details.
Running examples in ‘nat.nblast-Ex.R’ failed
The error most likely occurred in:

> ### Name: nblast
> ### Title: Calculate similarity score for neuron morphologies
> ### Aliases: nblast
> 
> ### ** Examples
> 
> # load sample Kenyon cell data from nat package
> data(kcs20, package='nat')
> # search one neuron against all neurons
> scores=nblast(kcs20[['GadMARCM-F000142_seg002']], kcs20)
> # scores from best to worst, top hit is of course same neuron
> sort(scores, decreasing = TRUE)
GadMARCM-F000142_seg002 ChaMARCM-F000586_seg002 GadMARCM-F000423_seg001 
              4043.1766               1914.8224               1772.8506 
GadMARCM-F000442_seg002 FruMARCM-M000115_seg001 FruMARCM-F000085_seg001 
              1007.4565                853.8108                713.2106 
FruMARCM-F001929_seg001 FruMARCM-F001494_seg002 GadMARCM-F000050_seg001 
               604.4071                481.4737                480.4146 
GadMARCM-F000071_seg001 FruMARCM-M001339_seg001 FruMARCM-F000188_seg001 
               448.1516                433.9340                404.0470 
GadMARCM-F000476_seg001 FruMARCM-F000270_seg001 FruMARCM-F000706_seg001 
               313.2021                254.7516                204.2116 
FruMARCM-M000842_seg002 FruMARCM-M001051_seg002 FruMARCM-M001205_seg002 
               196.4543                140.8164               -251.4999 
GadMARCM-F000122_seg001 FruMARCM-F001115_seg002 
              -262.2352               -520.2581 
> hist(scores, breaks=25, col='grey')
> abline(v=1500, col='red')
> 
> # plot query neuron
> open3d()
null 
   1 
> # plot top 3 hits (including self match with thicker lines)
> plot3d(kcs20[which(sort(scores, decreasing = TRUE)>1500)], lwd=c(3,1,1))
Error in xyz.coords(x, y, z, xlab = xlabel, ylab = ylabel, zlab = zlabel,  : 
  'x' is a list, but does not have components 'x', 'y'  and 'z'
Calls: plot3d -> plot3d.default -> xyz.coords
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because NBLAST-Clustering.Rmd appears to be an R Markdown v2 document.
Invalid MIT-MAGIC-COOKIE-1 keyQuitting from lines 56-59 (NBLAST-Clustering.Rmd) 
Error: processing vignette 'NBLAST-Clustering.Rmd' failed with diagnostics:
'x' is a list, but does not have components 'x', 'y'  and 'z'
Execution halted
Package required but not available: ‘standardize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/NB.MClust.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/NeatMap.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keydata.reduction: no visible global function definition for ‘prcomp’
data.reduction: no visible global function definition for ‘hclust’
data.reduction: no visible global function definition for ‘as.dist’
data.reduction: no visible global function definition for ‘cor’
data.reduction: no visible global function definition for ‘dist’
heatmap1: no visible global function definition for ‘sd’
lineplot: no visible global function definition for ‘sd’
normalize: no visible global function definition for ‘sd’
profileplot3d : ColorFunction: no visible global function definition
  for ‘rgb’
profileplot3d : ColorFunction: no visible global function definition
  for ‘colorRamp’
profileplot3d: no visible global function definition for ‘sd’
profileplot3d: no visible global function definition for ‘gray’
Undefined global functions or variables:
  as.dist colorRamp cor dist gray hclust prcomp rgb sd
Consider adding
  importFrom("grDevices", "colorRamp", "gray", "rgb")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "prcomp", "sd")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/neatmaps.Rcheck/00install.out’ for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   4.3Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   5.0Mb
Running examples in ‘network-Ex.R’ failed
The error most likely occurred in:

> ### Name: read.paj
> ### Title: Read a Pajek Project or Network File and Convert to an R
> ###   'Network' Object
> ### Aliases: read.paj read.paj.simplify switchArcDirection
> ###   readAndVectorizeLine
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> require(network)
> 
> par(mfrow=c(2,2))
> 
> test.net.1 <- read.paj("http://vlado.fmf.uni-lj.si/pub/networks/data/GD/gd98/A98.net")
Warning in file(file, "rt") :
  cannot open URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/GD/gd98/A98.net': HTTP status was '0 (null)'
Error in file(file, "rt") : cannot open the connection
Calls: read.paj -> file
Execution halted
Running the tests in ‘tests/read.paj_tests.R’ failed.
Last 13 lines of output:
  > 
  > 
  > 
  > # this file has character encoding issues
  > scotland<-tempfile('scotland',fileext='.zip')
  > download.file('http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip',scotland)
  trying URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip'
  Error in download.file("http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip",  : 
    cannot open URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip'
  In addition: Warning message:
  In download.file("http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip",  :
    cannot open URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip': HTTP status was '0 (null)'
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/neuroim.Rcheck/00install.out’ for details.
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    CppCode       14.1Mb
    R              3.1Mb
    classic-bugs   1.5Mb
    include        5.5Mb
    libs          10.9Mb
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because trees_with_root_edge.Rmd appears to be an R Markdown v2 document.
Error: processing vignette 'vignette_get_nltt_values.Rmd' failed with diagnostics:
(converted from warning) It seems you should call rmarkdown::render() instead of knitr::knit2html() because vignette_get_nltt_values.Rmd appears to be an R Markdown v2 document.
Execution halted
Packages suggested but not available for checking: ‘RcppOctave’ ‘doMPI’
Running examples in ‘NoiseFiltersR-Ex.R’ failed
The error most likely occurred in:

> ### Name: EF
> ### Title: Ensemble Filter
> ### Aliases: EF EF.default EF.formula
> 
> ### ** Examples
> 
> data(iris)
> # We fix a seed since there exists a random partition for the ensemble
> set.seed(1)
> out <- EF(Species~., data = iris, consensus = FALSE)
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: EF ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 190-198 (NoiseFiltersR.Rnw) 
Error: processing vignette 'NoiseFiltersR.Rnw' failed with diagnostics:
java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nonlinearTseries.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/norm2.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nowcasting.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/NPCirc.Rcheck/00install.out’ for details.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/OasisR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/OceanView.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   2.2Mb
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/oec.Rcheck/00install.out’ for details.
installed size is 85.7Mb
  sub-directories of 1Mb or more:
    libs  85.3Mb
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 359 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'OneTwoSamples.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...^^G0X<b9>To<98><e5>R<bd>a<96>K<f5><86>Y.<d5>^^[f<b9>To<98><e5>o<af><9e>^^PB^^H<d1><fd>^
                                                  J)<84><98><9b><9b><8b>~<ed>.|૪<db>]<a5><bb><97>R<a9>$:^^R...
! Undefined control sequence.
l.16 ...A<a0><9e><89>h@^^Z<9e>^^]s<c2>J^^C<b5>U<b7>\:<86>a<96>><cc>Y*<95><ce>f^^\/"<b9>\<ee>
                                                  y<80><bf><e0><e0>^^\<b8><df>SR*<95><a4><94>o<be><f9><e6><f8><f8>x<b3><d9>L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ...a<9a><e6><d6>֖<aa><8e>q^^_Ѝs<ce>^^XS<9b><84> ^^H0^^W<f8><9a><c9>d<80>|h"<a5>\YY
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because ontologySimilarity-GO-example.Rmd appears to be an R Markdown v2 document.
Quitting from lines 46-49 (ontologySimilarity-GO-example.Rmd) 
Error: processing vignette 'ontologySimilarity-GO-example.Rmd' failed with diagnostics:
could not find function "intersection_with_descendants"
Execution halted
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
Missing or unexported object: ‘mlr::makePrediction’
Running examples in ‘OOBCurve-Ex.R’ failed
The error most likely occurred in:

> ### Name: OOBCurve
> ### Title: Out of Bag Learning curve
> ### Aliases: OOBCurve
> 
> ### ** Examples
> 
> library(ranger)
> library(randomForest)
randomForest 4.6-12
Type rfNews() to see new features/changes/bug fixes.

Attaching package: ‘randomForest’

The following object is masked from ‘package:ranger’:

    importance

The following object is masked from ‘package:ggplot2’:

    margin

> 
> # Classification
> data = getTaskData(sonar.task)
> mod = ranger(Class ~., data = data, num.trees = 100, keep.inbag = TRUE)
> 
> # Alternatively use randomForest
> # mod = randomForest(Class ~., data = data, ntree = 100, keep.inbag = TRUE)
> # Alternatively use train of mlr
> # mod = train(makeLearner("classif.ranger", keep.inbag = TRUE), sonar.task)
> 
> # Application of the main function
> results = OOBCurve(mod, measures = list(mmce, auc, brier), task = sonar.task, data = data)
Error: 'makePrediction' is not an exported object from 'namespace:mlr'
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  6: setHyperPars2.Learner(learner, insert(par.vals, args))
  7: stop(msg)
  
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 5
  1. Error: classification ranger (@test_base.R#12) 
  2. Error: regression ranger (@test_base.R#25) 
  3. Error: classification randomForest (@test_base.R#40) 
  4. Error: regression randomForest (@test_base.R#53) 
  5. Error: trained model with mlr (@test_base.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/OpenCL.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘mlr’

Package suggested but not available for checking: ‘farff’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 148.1Mb
  sub-directories of 1Mb or more:
    libs    140.0Mb
    models    4.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/openssl.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot527afa3951b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot527afa3951b.png': No such file or directory
Quitting from lines 22-24 (openwindfarm-vignette.Rmd) 
Error: processing vignette 'openwindfarm-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/optBiomarker.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyavg2Lower: no visible global function definition for ‘optimize’
classificationError.data.frame: no visible binding for global variable
  ‘na.omit’
classificationError.data.frame: no visible global function definition
  for ‘terms’
classificationError.data.frame: no visible binding for global variable
  ‘predict’
classpredict.lda: no visible global function definition for ‘predict’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
simData: no visible global function definition for ‘var’
tnormAvg: no visible global function definition for ‘dnorm’
tnormAvg: no visible global function definition for ‘pnorm’
yapprox: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dnorm na.omit optimize pnorm predict rnorm runif terms var
Consider adding
  importFrom("stats", "approx", "dnorm", "na.omit", "optimize", "pnorm",
             "predict", "rnorm", "runif", "terms", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘org.At.tair.db’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.8Mb
Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘IsoGene’
Invalid MIT-MAGIC-COOKIE-1 keygenRidge: no visible global function definition for ‘plogis’
ordGene: no visible global function definition for ‘anova’
ordGene: no visible global function definition for ‘lm’
ordSelect: no visible binding for global variable ‘sd’
ordSmooth: no visible binding for global variable ‘sd’
plot.ordPen: no visible global function definition for ‘grey’
plot.ordPen: no visible global function definition for ‘devAskNewPage’
plot.ordPen: no visible global function definition for ‘plot’
plot.ordPen: no visible global function definition for ‘lines’
predict.ordPen: no visible global function definition for ‘plogis’
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis plot sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  input string 411 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 412 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 420 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'dicom.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Al
           ^^SG^^W~<b1><89><cc>V<c2><de>^^Q^^T<b6><a1>&<d6>J^^P<a4>D!<c2>B*H<91>s<f0>9<b7><dc>z<e6>^^D<87><f6>^^BG<ae>\9r<ab>P%<84>^^O<95>"...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<de>^^Q^^T<b6><a1>&<d6>J^^P<a4>D!<c2>B*H<91>s<f0>9<b7><dc>z<e6>^^D<87><f6>^^BG<ae>\9
                                                  r<ab>P%<84>^^O<95>".(>`YTj<a4>^^U<b6><eb>?-<b4>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...<83>/<be><f8>b^^O<8b>^^\<f0><d8><eb>61l^^W@y.<97>K<a5>R<d9>l<f6>ȑ#sss<b9>\nzz
                                                  :^^H<d9>B<88>d2^^Y<bc>Q<e5>+<df><f7><a3>Ѩi<9a>B^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 420 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'nifti.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^S[^^[^^?L<95>:P'9Ko1M^^X<90><ca>U<92>\^^FD^^DI^^W<85><ba>r#<fe>]<b9>r<a3>K<b7>ݸ^^U<bb>^^UA^^L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 x<9c><ed>\<cd>k^^S[^^[^^?L<95>:P'9Ko1M^^X<90><ca>U<92>\^^F
                                           D^^DI^^W<85><ba>r#<fe>]<b9>r<a3>K<b7>ݸ^^U<bb>^^UA^^L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...!^^Dc^^L<f7>s<b9><dc><ce><ce>N<a5>Ry<fb><f6>-c^^L<8f>8<e7><9c><f3><e1><e1>aιl"[	!\<d7>
                                                  
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 !<96><96><96><aa><d5><ea><eb>ׯ?|<f8>^^@<af>ptW<b9>\<ae>
   
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘osi-Ex.R’ failed
The error most likely occurred in:

> ### Name: extract_id
> ### Title: Extract components from OSI metadata
> ### Aliases: extract_id extract_keywords extract_name extract_superseded
> ###   extractors
> 
> ### ** Examples
> 
> 
> #Get the names of all licenses
> all_license_metadata <- license_list()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL certificate problem: Invalid certificate chain
Calls: license_list ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 8
  1. Error: All licenses can be retrieved (@test_connectors.R#6) 
  2. Error: Keyword retrieval works (@test_connectors.R#14) 
  3. Error: ID retrieval works (@test_connectors.R#22) 
  4. Error: Content retrieval works (@test_connectors.R#29) 
  5. Error: licenses IDs can be retrieved (@test_extractors.R#4) 
  6. Error: licenses names can be retrieved (@test_extractors.R#11) 
  7. Error: licenses superseded states can be retrieved (@test_extractors.R#18) 
  8. Error: licenses keywords can be retrieved (@test_extractors.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   3.8Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pafdR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/PanJen.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Linking to GEOS 3.4.2, GDAL 2.1.2, proj.4 4.9.1

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Downloading MP data
Downloading constituency data
Warning: Column `party_id` joining character vector and factor, coercing into character vector
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotdc8f5ea6af5c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotdc8f5ea6af5c.png': No such file or directory
Quitting from lines 67-112 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running the tests in ‘tests/regtest-party.R’ failed.
Last 13 lines of output:
  > fit <- rpart(Kyphosis ~ Age + Number + Start, data = kyphosis)
  > pfit <- as.party(fit)
  > all(predict(pfit, newdata = kyphosis, type = "node") == fit$where)
  [1] TRUE
  > 
  > ## J48: iris data
  > library("RWeka")
  > data("iris", package = "datasets")
  > itree <- J48(Species ~ ., data = iris)
  Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
    java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
  Calls: J48 ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
  Execution halted
Errors in running code in vignettes:
when running code in ‘constparty.Rnw’
  ...
       8 0.5408163 0.4591837
       9 0.0729927 0.9270073

> library("RWeka")

> (j48 <- J48(Survived ~ ., data = ttnc))

  When sourcing ‘constparty.R’:
Error: java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Execution halted
Error in re-building vignettes:
  ...
Loading required package: grid

Error: processing vignette 'constparty.Rnw' failed with diagnostics:
 chunk 10 (label = J48) 
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Execution halted
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 419 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'party.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 !8<e7>hV*<95>p]<ad>V?<ff><fc><f3><f9><f9><f9>R<a9><84>^^A<a5>^^X<ed>v<fb><f2><e5><cb>B^^H!D<b9>\<fe>
                                                <f2><cb>/?<f9><e4><93>J<a5>r<e3><c6>
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.19 ...^Uc,^^H^^B<c3>0<a0><<e7><e6><e6>*<95><ca><f8><f8><f8>G^^_}<d4>^^Oϧ|<ef><8d>}<f6><d9>g}
                                                  6<c5><fb>^^SB<f8><be><df>n<b7><a1>֛<cd>f*<95><8a><e3>xcc<a3><db>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rootSolve’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘kinship2’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘rootSolve’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyCall with DUP:
   .C("powerR", as.integer(numOffspring), as.integer(numParents), 
       as.integer(numFamilies), as.integer(additionalOffspringPhenos), 
       as.integer(ascertainment), as.integer(modelGen), as.integer(modelTest), 
       as.double(afreqMarker), as.double(penAA), as.double(penAB), 
       as.double(penBB), as.double(heritability), as.double(contsAscertainmentLower), 
       as.double(contsAscertainmentUpper), as.double(pDiseaseAlleleGivenMarkerAllele), 
       as.double(afreqDSL), as.double(qnorm(1 - alpha/2)), as.double(offset), 
       as.integer(numSim), as.integer(ITERATION_KILLER), result, 
       DUP = FALSE)
DUP is no longer supported and will be ignored.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pbdPROF.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key.win.appendLog: no visible binding for global variable ‘lines’
plotMC : panel: no visible global function definition for ‘points’
plotMC: no visible global function definition for ‘pairs’
plotMC: no visible global function definition for ‘mtext’
plotMC: no visible global function definition for ‘axis’
plotMC: no visible global function definition for ‘par’
readADpaths: no visible global function definition for ‘read.table’
readRep: no visible global function definition for ‘read.table’
saveADpaths: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  axis lines mtext pairs par points read.table write.table
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "pairs", "par",
             "points")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘PBSmodelling-Ex.R’ failed
The error most likely occurred in:

> ### Name: PBSoptions-class
> ### Title: S4: Project Options Class
> ### Aliases: PBSoptions-class print,PBSoptions-method
> ###   show,PBSoptions-method
> ### Keywords: classes methods
> 
> ### ** Examples
> 
> local(envir=.PBSmodEnv,expr={
+   #initialize an option manager with a single logical option
+   .mypkg <- new( "PBSoptions", filename="my_pkg.txt", 
+     initial.options=list( sillyhatday=FALSE ) )
+ 
+   #retrieving an option
+   silly <- getOptions( .mypkg, "sillyhatday" )
+   cat( "today is", ifelse( silly, "silly hat day!", "monday" ), "\n" )
+ 
+   #set an option
+   setOptions( .mypkg, sillyhatday = TRUE, photos = "/shares/silly_hat_photos" )
+ 
+   #create a GUI which works with options
+   createWin( c( 
+     "check name=optionsillyhatday text=\"silly hat day\"",
+     "entry name=optionphotos width=22 mode=character label=\"photos directory\"",
+     "button func=doAction text=save action=saveOptionsGUI(.mypkg)" ), astext = TRUE )
+ 
+   #update GUI values based on values stored in .mypkg's options
+   loadOptionsGUI( .mypkg )
+   print(getOptions( .mypkg ))
+ })
today is monday 
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "tk_setPalette".
Calls: local ... eval -> eval -> createWin -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pcaL1.Rcheck/00install.out’ for details.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   2.1Mb
    libs   6.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pcensmix.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 399 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 400 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 408 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pcse.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...<cb>^^RB^^X<86><c1>^^X#<a2><a5><a5><a5><8f>^^_?r<ce>s<b9>^^\<e7>|ee<e5><fa><f5><eb><8c>1\<cd>
                                                  f<b3><85>BA<8e><8a>1v<ef>޽^^NC?<e8>E<96><97><97><8f>o0?...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...<ba><ae>^^GA^^@<ad><a8><e5>gu<af>^^^O<e0><d4>4<ad>M7EQ<a4>n^^X^^AΣ<a5>\ZXW
                                                  <9a><a6><95><cb>eιi<9a><ae><eb>b<b8><8e><e3>^^DA<c0>9<c7>^^B^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...b<b8><8e><e3>^^DA<c0>9<c7>^^B^^VB^^@<ae><ae><eb>B7<c3>0<e2><f1>8<b6>^^G<d7>uGFF\<d7>
                                                  E?݌<f9><ac><c0><f9><8d>0j^^O<e0>^^D~<a8>5u<98>^^\...
The control sequence at the end of
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘pedometrics-Ex.R’ failed
The error most likely occurred in:

> ### Name: vgmICP
> ### Title: Initial covariance parameters (ICP)
> ### Aliases: vgmICP
> 
> ### ** Examples
> 
> data(meuse, package = "sp")
> icp <- vgmICP(z = log(meuse$copper), coords = meuse[, 1:2])
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Error: Package(s) needed for this function to work but notinstalled: georob
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/permGPU.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/permPATH.Rcheck/00install.out’ for details.
installed size is 47.9Mb
  sub-directories of 1Mb or more:
    libs  47.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pifpaf.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotb385608472c8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotb385608472c8.png': No such file or directory
Quitting from lines 61-64 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pkggraph.Rcheck/00install.out’ for details.
Package required but not available: ‘rggobi’

Depends: includes the non-default packages:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘lattice’ ‘rggobi’ ‘ggplot2’
  ‘proto’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required and available but unsuitable version: ‘SummarizedExperiment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/playwith.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plink.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plot3Drgl.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plsRcox.Rcheck/00install.out’ for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   2.1Mb
Error in re-building vignettes:
  ...
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda

Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pointblank.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/polypoly.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/portes.Rcheck/00install.out’ for details.
File ‘PottsUtils/libs/PottsUtils.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘sw.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  powell.c:700:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  powell.c:724:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/powell.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'd_jss_paper.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...R,<89><ad>qI^J<a6>^^NT^^B<81>^^U6^^P<ac><f8><a5>^^O<c5>}n!<d4>^^O}
                                                  (<ec>e~h<fb>TJMa/3dx<b0>U^^O<83>b<b5>H^^Q...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.15 ...<ec><e8>ڎ<e4>V<8a>~^^Xsu<ee>9<e7><9e><ef>~<df><f9><fe><9d><ef>v^^Y<86>^^A<ed><cb><f7><bd><80><e6><a2>C^
                                                  +<a3>C^+<a3>C^+<a3><cd>ɳ5d^^VJ)<e7><bc>!S^^...
! Extra }, or forgotten $.
l.15 ...<93>MXp<c3>`B<9e>^^?[<eb>1v<ff><f8><e7><a5>^^?W6^^?q<f9>'<d7>T<d7>i<d8><d4>7<bf>]<88><ad>}
                  
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyfnfam: no visible global function definition for ‘qnorm’
fx: no visible global function definition for ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘pnorm’
normplot : <local> : replot: no visible global function definition for
  ‘plot’
normplot : <local> : replot: no visible global function definition for
  ‘dnorm’
normplot : <local> : replot: no visible global function definition for
  ‘points’
normplot : <local> : replot: no visible global function definition for
  ‘lines’
normplot : <local> : regen: no visible global function definition for
  ‘rnorm’
normplot : <local> : regen: no visible global function definition for
  ‘rexp’
nsibs: no visible global function definition for ‘qnorm’
ntdt: no visible global function definition for ‘uniroot’
plotDom: no visible global function definition for ‘plot’
plotNsibs: no visible global function definition for ‘plot’
plotNtdt: no visible global function definition for ‘plot’
plotNtdt: no visible global function definition for ‘lines’
plotNtdt: no visible global function definition for ‘legend’
ptdt: no visible global function definition for ‘optimize’
ptdt: no visible global function definition for ‘uniroot’
ptdt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm legend lines optimize plot pnorm points qnorm rexp rnorm
  uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  ‘KEGG.db’ ‘org.Sc.sgd.db’ ‘org.Ag.eg.db’ ‘org.Pt.eg.db’
  ‘org.Rn.eg.db’ ‘org.Ss.eg.db’ ‘org.At.tair.db’ ‘org.Bt.eg.db’
  ‘org.Ce.eg.db’ ‘org.Cf.eg.db’ ‘org.Dm.eg.db’ ‘org.Dr.eg.db’
  ‘org.EcK12.eg.db’ ‘org.EcSakai.eg.db’ ‘org.Gg.eg.db’ ‘org.Mm.eg.db’
  ‘org.Mmu.eg.db’ ‘org.Pf.plasmo.db’ ‘org.Xl.eg.db’
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/prim.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because PRISMA.Rmd appears to be an R Markdown v2 document.
Quitting from lines 31-43 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    extdata  10.9Mb
    libs      1.2Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/PropClust.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Attaching package: 'Biobase'
  
  The following object is masked from 'package:propr':
  
      abstract
  
  [1] "operating in serial mode"
  Error in aldex.clr(as.data.frame(t(mail)), conds = rep("A", 5), denom = 2) : 
    unused arguments (conds = rep("A", 5), denom = 2)
  Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval -> aldex.clr
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
LastFirstDiscreteSparse: Error while checking: evaluation nested too
  deeply: infinite recursion / options(expressions=)?
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'countreg.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 <c4><eb>g^^Z<88><d7><cf>4^^P<af><9f>i <de>^^Q^^RB^^H!<8e>ޗR<aa><eb>B<a1><80>1RJ\<e0>
                                                o<b5>Z
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.18 \K
       ?<d3><f0><e7><9f>^^?~<fa><d1><d8><e5>R<ca>J<a5><b2><b3><b3><b3><b8><b8><b8><b8><b8><c8>9^^?<f8><f0><a1>m۷n<dd>::<9e>s^<ad>V766^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Missing $ inserted.
<inserted text> 
                $
l.18 ...<f0><e7><9f>^^?~<fa><d1><d8><e5>R<ca>J<a5><b2><b3><b3><b3><b8><b8><b8><b8><b8><c8>9^^?<f8><f0><a1>m۷n<dd>::<9e>s^
         
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pseudo.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 401 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 409 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 410 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 418 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'raschmix.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.19 <82>`ss3<97>˹<ae><9b>L&^^Q<85>^^PQ<b9>\<9e>
                            <99><99><b1>,+<9d>N<c3><ee><a3>?^^H<82><bd><bd>=vhRJ<c4>.<9e><e7><e5>r<b9>C<93><f3><f8>X,<86><c9>^^]ǉ^^N;rN...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 ...<b3><a8>nC!_<d7><ed><e8><be>͹<89><f7>V<e8><8c>`<ee>l<f5><b0><9b><c3>^^Z<a5><94><c2>"<a0>͡&<f6><ab>8g<e5>\<e6>
                                                  <d4>\<9e><9a><ae><fa>ꝑ<ae>y<9d><b3><8d>߃<a2>///<c7><e3>qM<d3>\...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 ...C!_<d7><ed><e8><be>͹<89><f7>V<e8><8c>`<ee>l<f5><b0><9b><c3>^^Z<a5><94><c2>"<a0>͡&<f6><ab>8g<e5>\<e6><d4>\<9e>
                                                  <9a><ae><fa>ꝑ<ae>y<9d><b3><8d>߃<a2>//
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/PsyControl.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qpcR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qtbase.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qtlc.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    contrib   3.7Mb
    doc       2.9Mb
    libs      1.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qualpalr.Rcheck/00install.out’ for details.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  testthat results ================================================================
  OK: 1490 SKIPPED: 6 FAILED: 3
  1. Error: test stm converter: under extreme situations  (@test-convert.R#119) 
  2. Error: dfm_lookup raises error when dictionary has multi-word entries (@test-dfm_lookup.R#82) 
  3. Error: compare the output feature co-occurrence matrix to that of the text2vec package (@test-fcm.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/QuantifQuantile.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 430 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 438 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'quantspec.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.21 ...[L=^^X^^L^^F<83>A<8e>Pض],^^V5M<b3>,<8b>]X0#<a5><c4>Z^^PQ<b9>\<b6>
                                                  ,+^^R<89>X<96><c5>^^A<8e>6<e9>E?{^^\e<e9>N^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 ...A<8e>6<e9>E?{^^\e<e9>N^^Nu^^V<8c><b0>,<8b><88>fff<d2><e9><b4>^^[c<a8>`<db>v<b9>\<8e>
                                                  D"<8c>Ir!VUU<80>
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.25 <a7>ޭ^^@<89>^^H<be>ҹ<b0>^^G<ca><e5>rSSS<b9>\<8e>
                               <88><e0>^^VY<96>utt4<<^^\^^L^^F<a5><94>^<af>^^W^^F4/^^G<e4>!<f7><80>r0<ef>>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.25 ...
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   3.5Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/quickPlot.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/quickregression.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/R2GUESS.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 231 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 232 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 240 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'R2OpenBUGS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\AL
           ^^[W^^S^^^^^L^^FL<8c><97><a7>^^R0N^^V̪nCq<8d><cb>V<88> ^^Q~UT<ad><9a>*<f4><92>S<a2><f6>ƥ<97><f6><94>^^^<a3>ޫ^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten \endgroup.
l.18 ...Tf<92><95><d4>/<aa>^^@e<e1>p^^X9<ee><ec><ec><8c>D"<99>L<a6><b1><b1><f1><e5><97>_<ce>f<b3>O<9e><<d1>u}}
                                                  }<bd><b9><b9><b9><bf><bf>?<9f><cf>744,,,tww<af><ad><ad>577^...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.18 ...f<92><95><d4>/<aa>^^@e<e1>p^^X9<ee><ec><ec><8c>D"<99>L<a6><b1><b1><f1><e5><97>_<ce>f<b3>O<9e><<d1>u}}}
                                                  <bd><b9><b9><b9><bf><bf>?<9f><cf>744,,,tww<af><ad><ad>577^^...
I've deleted a 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/R2STATS.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 231 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 232 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 240 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'R2WinBUGS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.17 ...^L^^L<e8><ba>N^^Hq8^^\8<ad><c7><e3>Y\\,^^V<8b><9d><9d><9d>o<bf><fd><b6>In^^O\<cb>
                                                  <b3>^^H<e3>o<^^^<a7><ba>gf^^H<f6>G,f<fe>]^^S...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<da>ڪiZOO<8f><a6>i<cb><cb><cb>^^V<8b>^^E^^@*<95>Jgg<a7><a2>(<8f>^^^=r:<9d><b9>\<ae>
                                                  V<ab><f5><f5><f5><cd><ce><ce><f6><f7><f7><ff><f6><db>o<ad><ad><ad>^^W/^^^D...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 <9d>?^^?^^^<eb>\N
                <a7>szz^^Z7^^A<ed>jqq<91><e7>yUU<91><b3>|><8f>\<86><c3>a<97>˅@^^\[^^X<86>!<84><9c>9s&<95>J<c5>b1Q^^T^^A<e0>...
The control sequence at the end of the top line
of your error message was neve
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/R330.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘leaps’ ‘rgl’ ‘s20x’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rainbow.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rakeR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/randomForestExplainer.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RAppArmor.Rcheck/00install.out’ for details.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   9.5Mb
Packages suggested but not available for checking: ‘rggobi’ ‘RODBC’
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  26.5Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   4.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rCBA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcdk.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because RClone_qmsevpops.Rmd appears to be an R Markdown v2 document.
Quitting from lines 336-337 (RClone_qmsevpops.Rmd) 
Error: processing vignette 'RClone_qmsevpops.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key.onAttach: no visible global function definition for ‘palette’
.onAttach: no visible global function definition for ‘dev.off’
helpAboutBCA: no visible global function definition for ‘help’
Undefined global functions or variables:
  dev.off help palette
Consider adding
  importFrom("grDevices", "dev.off", "palette")
  importFrom("utils", "help")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyenterTableMHTest : onOK: no visible global function definition for
  ‘na.omit’
startStop: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘depthTools’ ‘tcltk’
  Please remove these calls from your code.
Invalid MIT-MAGIC-COOKIE-1 keycomputeMBD : OnOutput: no visible global function definition for
  ‘tkbutton’
computeMBD: no visible global function definition for ‘tkbutton’
computeMBD : OnPlot: no visible global function definition for
  ‘tkcanvas’
computeMBD : OnPlot: no visible global function definition for
  ‘tkbutton’
computeTmean: no visible global function definition for ‘tkcanvas’
computeTmean: no visible global function definition for ‘tkbutton’
computeTmean : onOK: no visible global function definition for ‘par’
plotCentralCurves: no visible global function definition for ‘tkcanvas’
plotCentralCurves: no visible global function definition for ‘tkbutton’
plotCentralCurves : onOK: no visible global function definition for
  ‘par’
Undefined global functions or variables:
  par tkbutton tkcanvas
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘FrF2.catlg128’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘Rcmdr’ ‘multcomp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘tseries’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘Rcmdr’ ‘TeachingDemos’ ‘abind’ ‘forecast’ ‘tseries’ ‘xts’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls in package code:
  ‘abind’ ‘e1071’ ‘qcc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘ENmisc’ ‘Hmisc’ ‘Rcmdr’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘orloca’ ‘orloca.es’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyRcmdr.new.loca.p: no visible binding for global variable ‘top’
Rcmdr.new.loca.p: no visible binding for global variable ‘buttonsFrame’
Rcmdr.orloca.norm: no visible binding for global variable ‘top’
Rcmdr.orloca.norm : onOK: no visible binding for global variable
  ‘normaVariable’
Rcmdr.orloca.norm: no visible binding for global variable ‘normaFrame’
Rcmdr.orloca.norm: no visible binding for global variable
  ‘buttonsFrame’
Rcmdr.rloca.p: no visible binding for global variable ‘top’
Rcmdr.rloca.p: no visible binding for global variable ‘buttonsFrame’
Rcmdr.zsum: no visible binding for global variable ‘top’
Rcmdr.zsum: no visible binding for global variable ‘buttonsFrame’
Rcmdr.zsummin: no visible binding for global variable ‘top’
Rcmdr.zsummin : onOK: no visible binding for global variable
  ‘algorithmVariable’
Rcmdr.zsummin : onOK: no visible binding for global variable ‘.sol’
Rcmdr.zsummin: no visible binding for global variable ‘algorithmFrame’
Rcmdr.zsummin: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  .sol algorithmFrame algorithmVariable buttonsFrame normaFrame
  normaVariable top
Invalid MIT-MAGIC-COOKIE-1 keyBOXWP: no visible binding for global variable ‘top’
BOXWP: no visible binding for global variable ‘buttonsFrame’
HIST: no visible binding for global variable ‘top’
HIST: no visible binding for global variable ‘buttonsFrame’
QQN: no visible binding for global variable ‘top’
QQN: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  buttonsFrame top
Invalid MIT-MAGIC-COOKIE-1 keyfncLRpROC: no visible global function definition for ‘palette’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘rgb’
fncPairedpROC: no visible global function definition for ‘palette’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncUnpairedpROC: no visible global function definition for ‘palette’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncvpROC: no visible global function definition for ‘palette’
fncvpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncvpROC : onOK : convert: no visible global function definition for
  ‘rgb’
Undefined global functions or variables:
  col2rgb palette rgb
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keySampleSizes: no visible global function definition for ‘xtabs’
SampleSizes: no visible global function definition for ‘weighted.mean’
SampleSizes: no visible global function definition for ‘reshape’
stage1Sample.fn: no visible global function definition for ‘runif’
stage2Sample.fn: no visible global function definition for ‘runif’
strata.options : onOK: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription reshape runif weighted.mean xtabs
Consider adding
  importFrom("stats", "reshape", "runif", "weighted.mean", "xtabs")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘SLC’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘SLC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘car’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘Rcmdr’ ‘car’ ‘colorspace’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyRcmdr.steeptestDij : onOK: no visible binding for global variable
  ‘replications’
Rcmdr.steeptestPij : onOK: no visible binding for global variable
  ‘replications’
Undefined global functions or variables:
  replications
Consider adding
  importFrom("stats", "replications")
to your NAMESPACE file.
Packages suggested but not available for checking: ‘ROpenOffice’ ‘RODBC’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rcplex.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RcppAPT.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    include   4.9Mb
    libs      1.6Mb
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.1Mb
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     24.0Mb
Error in re-building vignettes:
  ...
  input string 420 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 428 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 437 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppEigen-Introduction.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ....<ba><e9>&<8b><aa><9b><92>m+<a1>zg<a9>ـ*<bb><95><fa>^^DbT۲^^H~<84><89><87>)^^Y<e2>6\<8f>
                                                  q<cc>$Ğ<b7><f8><89>+<8b>$<d8>^^F<93>Ɣ<b3><b0>f<ae><ef><9c>{<cf>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...^^B^^[^^_<e1>h_<9e><83><f1>W.ʯ_~<ea><95><f0>N<d3>^^Y<9a><a6>1<c6>dY<c6>vEQ\XX
                                                  <f8>ꫯ<88>HQ^^T<fc>~<fa>駁@<e0><b3><cf>>[YY<d1>4...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten \endgroup.
l.15 ...˲<aa><aa><df>~<fb><ed><ca>ʊ<a2>(+++8Ʒn<dd><da><dc><dc><ec><eb><eb><fb><e2><8b>/:<b6><a1><8b>xg'`}}}
                                                  }}^^]<d7><cb><cb>˧<cc>츄w<98>{o^^[<fc><ed><ed>^W
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      21.4Mb
    libs     11.0Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      7.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RcppOctave.Rcheck/00install.out’ for details.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    include   8.8Mb
    libs      4.7Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    include   6.2Mb
    libs      3.3Mb
Missing or unexported object: ‘tools::package_native_routine_registration_skeleton’
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 379 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rcpp-introduction.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.21 ...^E}۽c<86>HgI^^[]x<bb><f7>ώ<d6>a<8b>Mӄ<87><89><ac><e3><c2><c2>^^Bclnn^^N}
                                                  p<dc><c3>^^X<83><92>@g<ce>9<ec>><bc>-<c3>0|>_<ab><d5>""<c6>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.22 ...<ba><ae><b7>Z-8=<ed>v۲,8^^@^^Hm,<cb>"<a2><95><95>^^U<9f><cf><d7>n<b7><8b><c5>b8^^\^
                                                  XX "EQЧR<a9><e8><ba>.<cb>2F&<a2>b<b1>^^X^^H...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 88.1Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
    lib      52.2Mb
    libs     31.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RcppTOML.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcqp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rcriticor.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcrypt.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcv.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RDieHarder.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rdoxygen.Rcheck/00install.out’ for details.
Running examples in ‘Rdrools-Ex.R’ failed
The error most likely occurred in:

> ### Name: Rdrools-package
> ### Title: A Rules Engine for R based on the popular Java based Drools
> ### Aliases: Rdrools-package Rdrools
> ### Keywords: rulesSession runRules Rdrools
> 
> ### ** Examples
> 
> library(Rdrools)
> data(class)
> data(rules)
> input.columns<-c('name', 'class', 'grade', 'email')
> output.columns<-c('address', 'subject', 'body')
> rules.session<-rulesSession(rules, input.columns, output.columns)
Error in .jnew("org/math/r/drools/DroolsService", rules, input.columns,  : 
  java.lang.UnsupportedClassVersionError: org/math/r/drools/DroolsService : Unsupported major.minor version 51.0
Calls: rulesSession -> .jnew -> .External
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot540327f7e726.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot540327f7e726.png': No such file or directory
Quitting from lines 22-26 (mapDWD.Rmd) 
Error: processing vignette 'mapDWD.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   7.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Packages suggested but not available for checking: ‘RODBC’ ‘RODBCext’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.8Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/redlistr.Rcheck/00install.out’ for details.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs  11.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/redR.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keycook.outliers: no visible global function definition for ‘lm’
cook.outliers: no visible global function definition for
  ‘cooks.distance’
nonparRI: no visible global function definition for ‘quantile’
plot.interval: no visible global function definition for ‘par’
plot.interval: no visible global function definition for ‘plot.new’
plot.interval: no visible global function definition for ‘plot.window’
plot.interval: no visible global function definition for ‘segments’
plot.interval: no visible global function definition for ‘axis’
plot.interval: no visible global function definition for ‘title’
plot.interval: no visible global function definition for ‘legend’
plot.interval: no visible global function definition for ‘box’
plot.interval: no visible global function definition for ‘text’
robust: no visible global function definition for ‘qt’
singleRefLimit: no visible global function definition for ‘qnorm’
singleRefLimit: no visible global function definition for
  ‘shapiro.test’
singleRefLimit: no visible global function definition for ‘ks.test’
Undefined global functions or variables:
  axis box cooks.distance ks.test legend lm par plot.new plot.window
  qnorm qt quantile segments shapiro.test text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "par", "plot.new",
             "plot.window", "segments", "text", "title")
  importFrom("stats", "cooks.distance", "ks.test", "lm", "qnorm", "qt",
             "quantile", "shapiro.test")
to your NAMESPACE file.
Running examples in ‘RefManageR-Ex.R’ failed
The error most likely occurred in:

> ### Name: WriteBib
> ### Title: Create a BibTeX File from a BibEntry Object e Creates a Bibtex
> ###   File from a BibEntry object for use with either BibTeX or BibLaTex.
> ### Aliases: WriteBib
> ### Keywords: IO
> 
> ### ** Examples
> 
> bib <- ReadCrossRef(query = '10.1080/01621459.2012.699793')
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10772 milliseconds
Calls: ReadCrossRef ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Error in re-building vignettes:
  ...
  input string 84 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 85 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 93 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'registry.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>[Ok^^S<dd>^^W>o<fa><ab><b5>Pf<bc> <b1>(i<ea>l*^^H5<a5> <a5>P<c6>EvBw<ee>\<fb>
                                                 1<c4>m<bf><82>[wfe<b1><b8><b0><9b><f8>'Be ^^]<82>]^^H^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<a2>J<a5>2??<af><94><9a><9e><9e><f6>}?<97><cb><d5>j5۶]<d7><c5>x!^^D^^C^^X^^Qv<b9>\<ce>
                                                  <e5>r<f8>Y<ad>V-<cb><c2><e4><fc>^^W7<c3>0<b4>,<ab><95>+0^^@...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<c7>h<b1>2O<8c><ba>u<eb>X[)^^E<ac>Ǌ<b8>ID<bb><bb><bb><90>^^V<88>ª<b0><b1>@,<cb><d0>h4\<d7>
                                                  <85>E
The control sequence at the end of the top line
of your error message was
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/reportROC.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1. Error: can't see environment of caller (@test-env.R#5) 
  2. Error: reprex doesn't write into environment of caller (@test-env.R#11) 
  3. Error: I understand exactly what I'm putting in reprex env (@test-env.R#22) 
  4. Error: reprex: clipboard input works (@test-input.R#12) 
  5. Error: reprex: expression input works (@test-input.R#17) 
  6. Error: reprex: character input works (@test-input.R#23) 
  7. Error: reprex: file input works (@test-input.R#31) 
  8. Error: reprex: file input in a subdirectory works (@test-input.R#40) 
  9. Error: Circular use is detected before render (@test-input.R#47) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/reshapeGUI.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘S4Vectors’

Package suggested but not available for checking: ‘rsolr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/restlos.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyGUI_template : onHelp: no visible global function definition for ‘help’
Undefined global functions or variables:
  help
Consider adding
  importFrom("utils", "help")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Error: processing vignette 'methodbehind_reverseengineeringcensus.ltx' failed with diagnostics:
Running 'texi2dvi' on 'methodbehind_reverseengineeringcensus.ltx' failed.
LaTeX errors:
! Undefined control sequence.
l.54 ...ted to approximate $\lambda$\textsubscript
                                                  {3}, which subsequently pr...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.54 ...ides the necessary $\lambda$\textsubscript
                                                  {1} and $\lambda$\textsubs...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.54 ...xtsubscript{1} and $\lambda$\textsubscript
                                                  {2} parameters. The estima...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
Execution halted
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
installed size is 102.7Mb
  sub-directories of 1Mb or more:
    libs      100.2Mb
    pictures    1.3Mb
Package required and available but unsuitable version: ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.4Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rggobi.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    fonts   1.5Mb
    libs    6.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rgnuplot.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key
(R:76308): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘gWidgetsRGtk2’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘RGtk2’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘RGtk2Extras-Ex.R’ failed
The error most likely occurred in:

> ### Name: gtkDfEdit
> ### Title: gtkDfEdit
> ### Aliases: gtkDfEdit [.gtkDfEdit [<-.gtkDfEdit RGtk2DfEdit
> 
> ### ** Examples
> 
>   win <- gtkWindowNew()

(R:2383): GLib-GObject-WARNING **: invalid (NULL) pointer instance

(R:2383): GLib-GObject-CRITICAL **: g_signal_connect_data: assertion `G_TYPE_CHECK_INSTANCE (instance)' failed

(R:2383): Gtk-WARNING **: Screen for GtkWindow not set; you must always set
a screen for a GtkWindow before using the window

(R:2383): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:2383): Gdk-CRITICAL **: gdk_colormap_get_visual: assertion `GDK_IS_COLORMAP (colormap)' failed

(R:2383): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:2383): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:2383): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:2383): Gdk-CRITICAL **: gdk_window_new: assertion `GDK_IS_WINDOW (parent)' failed

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: .Call(name, ..., PACKAGE = PACKAGE)
 2: .RGtkCall("S_gtk_widget_show_all", object, PACKAGE = "RGtk2")
 3: gtkWidgetShowAll(w)
 4: gtkWindowNew()
An irrecoverable exception occurred. R is aborting now ...
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RGtk2.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because intro_rhandsontable.Rmd appears to be an R Markdown v2 document.
Quitting from lines 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rhpc.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls in package code:
  ‘doMC’ ‘doSNOW’ ‘e1071’ ‘fftw’ ‘foreach’ ‘jpeg’ ‘png’ ‘rggobi’
  ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘parallel’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Codoc mismatches from documentation object 'c,Medline-method':
\S4method{c}{Medline}
  Code: function(x, ..., recursive = FALSE)
  Docs: function(x, ...)
  Argument names in code not in docs:
    recursive
Invalid MIT-MAGIC-COOKIE-1 keyrite : loadHistory: no visible global function definition for
  ‘savehistory’
rite : saveGist: no visible global function definition for ‘browseURL’
rite : uploadToRPubs : processEntry: no visible global function
  definition for ‘browseURL’
rite : runCode: no visible global function definition for ‘savehistory’
rite : runCode: no visible global function definition for ‘loadhistory’
rite : knittxt: no visible global function definition for ‘Sweave’
rite : knittxt: no visible global function definition for ‘browseURL’
rite : addHighlighting : addHighlight: no visible global function
  definition for ‘packageDescription’
rite : addHighlighting : addHighlight: no visible global function
  definition for ‘na.omit’
rite : about : <anonymous>: no visible global function definition for
  ‘browseURL’
rite : <anonymous>: no visible global function definition for
  ‘capture.output’
rite : <anonymous>: no visible global function definition for
  ‘update.packages’
rite : <anonymous>: no visible global function definition for ‘help’
rite : f1: no visible global function definition for ‘help’
rite : f1: no visible global function definition for ‘help.search’
rite : commandCompletion: no visible global function definition for
  ‘apropos’
rite : findreplace : <anonymous>: no visible global function definition
  for ‘browseURL’
Undefined global functions or variables:
  Sweave apropos browseURL capture.output help help.search loadhistory
  na.omit packageDescription savehistory update.packages
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "Sweave", "apropos", "browseURL", "capture.output",
             "help", "help.search", "loadhistory", "packageDescription",
             "savehistory", "update.packages")
to your NAMESPACE file.
Note: information on .o files is not available
File ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RkMetrics.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rLindo.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RLT.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RMark.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rmgarch.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Running the tests in ‘tests/RMongo-Ex.R’ failed.
Last 13 lines of output:
  +   
  +   # print(length(output))
  +   print(as.character(output[1]))
  + 
  +   checkEquals("{ \"_id\" : \"bar\"}", as.character(output[1]))
  +   # checkEquals("bar", as.character(output[1]))
  + }
  > 
  > test.dbInsertDocument()
  Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
    com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
  Calls: test.dbInsertDocument ... dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck -> .Call
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rmosek.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rMouse.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rmpi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from INTEGER(8) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rmumps.Rcheck/00install.out’ for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RnavGraph.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key.isPath: no visible global function definition for ‘tail’
.isPath: no visible global function definition for ‘head’
navGraph : <anonymous>: no visible global function definition for
  ‘tail’
navGraph : <anonymous>: no visible global function definition for ‘sd’
navGraph: no visible global function definition for ‘colors’
ng_image_array_gray : <anonymous>: no visible global function
  definition for ‘grey’
scagGraph: no visible global function definition for ‘quantile’
closeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.off’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.new’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.cur’
plot,NG_graph-ANY: no visible global function definition for ‘box’
plot,NG_graph-ANY: no visible global function definition for ‘axis’
plot,NG_graph-ANY: no visible global function definition for ‘points’
plot,NG_graph-ANY: no visible global function definition for ‘text’
plot,NG_graph-ANY: no visible global function definition for ‘segments’
updateViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.set’
Undefined global functions or variables:
  axis box colors dev.cur dev.new dev.off dev.set grey head points
  quantile sd segments tail text
Consider adding
  importFrom("grDevices", "colors", "dev.cur", "dev.new", "dev.off",
             "dev.set", "grey")
  importFrom("graphics", "axis", "box", "points", "segments", "text")
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Running examples in ‘RnavGraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: ng_get_color
> ### Title: Extract point coloring from an active navGraph session for a
> ###   particular data set.
> ### Aliases: ng_get_color
> 
> ### ** Examples
> 
> ## Define a NG_data object
> ng.iris <- ng_data(name = "IrisData", data = iris[,1:4])
> 
> ## start a navGraph session
> nav <- navGraph(ng.iris)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: navGraph ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Errors in running code in vignettes:
when running code in ‘RnavGraph.Rnw’
  ...
> sel <- sample(x = 1:11000, size = 600)

> p.digits <- digits[, sel]

> ng.i.digits <- ng_image_array_gray("USPS Handwritten Digits", 
+     p.digits, 16, 16, invert = TRUE, img_in_row = FALSE)

  When sourcing ‘RnavGraph.R’:
Error: [tcl] invalid command name "image".
Execution halted
Error in re-building vignettes:
  ...
    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Invalid MIT-MAGIC-COOKIE-1 keyWarning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE

RnavGraph Version 0.1.8
Please read the package vignette. Use vignette("RnavGraph").


Invalid MIT-MAGIC-COOKIE-1 keyWarning in tclRequire("Img") : Tcl package 'Img' not found
Can not load the tk Img extension. Hence you can not use the 'ng_image_files' R function. Read the package vignette on how to set up tcl/tk.
Loading required package: grid

Error: processing vignette 'RnavGraph.Rnw' failed with diagnostics:
 chunk 57 
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "image".

Execution halted
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
installed size is 95.5Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     93.4Mb
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/roadoi.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error : Oops, API did not return json after calling '§dldl  ':
        check your query - or api.oadoi.org may experience problems

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 141-142 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Timeout was reached
Execution halted
Error in re-building vignettes:
  ...
  input string 547 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 548 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 556 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RobPer_vignette.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^[G^^[^^?,<bf><ae><ba>`K^^Y^^B<89>P<ea>j<bb>PhIP<9d><ee>%<84>^^V<e5><a0>R<e8>!<b7><fc>^^C<a5><e4>_p<8f>9<94>B.=<b6>Đ<d2>^^F...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...^z^^ZrՒ^^@N8<c1><ff>r<b2>m{'<88><8e><c0>9Ȕ֥<de>?<c1><8d>~<f3><cd>7s<b9>\^^T
                                                  EP<98><87>=萃<b3><bf><dd>CD<83>B<ab>՚<9e><9e><c6>'^^QE...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 <e3><d6>n<b7><d1>^^E^^?<a5>-^^C^^U^^D<c1><cc>̌<ef><fb><b9>\^^N
                                      <f5><ad>V<cd>,˂<89>c<9e>(<97><cb>e!^^D<8f>hY<96>뺨L<9c>p^^_g<cf><f7>}^^...
The control sequence at the end of the top line
of your error message was never \def'ed. I
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
Running examples in ‘robustX-Ex.R’ failed
The error most likely occurred in:

> ### Name: rbwheel
> ### Title: Multivariate Barrow Wheel Distribution Random Vectors
> ### Aliases: rbwheel
> ### Keywords: distribution robust
> 
> ### ** Examples
> 
> set.seed(17)
> rX8 <- rbwheel(1000,8, fullResult = TRUE, scaleAfter=FALSE)
> with(rX8, stopifnot(all.equal(X, X0 %*% A,    tol = 1e-15),
+                     all.equal(X0, X %*% t(A), tol = 1e-15)))
> ##--> here, don't need to keep X0 (nor A, since that is Qrot(p))
> 
> ## for n = 100,  you  don't see "it", but may guess .. :
> n <- 100
> pairs(r <- rbwheel(n,6))
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> ## for n = 500, you *do* see it :
> n <- 500
> pairs(r <- rbwheel(n,6))
> ## show explicitly
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> ## but increasing sig2 does help:
> pairs(r <- rbwheel(n,6, sig2 = .2))
> 
> ## show explicitly
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> set.seed(12)
> pairs(X <- rbwheel(n, 7, spherize=TRUE))
> colSums(X) # already centered
[1] -3.129441e-15  6.151329e-15 -8.555656e-15  2.352285e-15  2.428613e-16
[6]  3.505876e-15 -3.537101e-15
> 
> if(require("ICS")) {
+   # ICS: Compare M-estimate [Max.Lik. of t_{df = 2}] with high-breakdown :
+   stopifnot(require("MASS"))
+   X.paM <- ics(X, S1 = cov, S2 = function(.) cov.trob(., nu=2)$cov, stdKurt = FALSE)
+   X.paM.<- ics(X, S1 = cov, S2 = function(.) tM(., df=2)$V, stdKurt = FALSE)
+   X.paR <- ics(X, S1 = cov, S2 = function(.) covMcd(.)$cov, stdKurt = FALSE)
+   plot(X.paM) # not at all clear
+   plot(X.paM.)# ditto
+   plot(X.paR)# very clear
+ }
Loading required package: ICS
Loading required package: mvtnorm
Loading required package: MASS
Error in S2(c(0.906882501852091, -2.27769597461744, -1.05320504986729,  : 
  could not find function "covMcd"
Calls: ics -> do.call -> S2
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RockFab.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RODBC.Rcheck/00install.out’ for details.
Package required but not available: ‘RODBC’

Package suggested but not available for checking: ‘RODBC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ROracle.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rotations.Rcheck/00install.out’ for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rothermel.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keybestFM: no visible global function definition for ‘data’
gaRoth: no visible global function definition for ‘data’
ros: no visible global function definition for ‘na.omit’
rosunc: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpanel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rpdb.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keycell.density.default: no visible binding for global variable
  ‘universalConstants’
conect.pdb: no visible binding for global variable ‘elements’
masses.default: no visible binding for global variable ‘elements’
toSymbols.character: no visible binding for global variable ‘elements’
toSymbols.integer: no visible binding for global variable ‘elements’
visualize.coords: no visible binding for global variable ‘elements’
visualize.coords: no visible binding for global variable ‘rgb’
Undefined global functions or variables:
  elements rgb universalConstants
Consider adding
  importFrom("grDevices", "rgb")
to your NAMESPACE file.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpg.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rpoppler.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘graphics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RProtoBuf-paper.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.23 ...<a2>i^^ZVn3*<80><b0>^^X<89>^^H8<e5>ryqq<b1>^^W<d3><d2>_PV<af><d7>MӔۃ\<c9>
                                                  [<bd>^<cf>f<b3><9f>}<f6><99>i<9a><b0><ae><a0>,<93><c9>lmm<c9>w<a4>iZ...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.24 ...<af><d7>q^^T^^Yc<d3><d3><d3>D<e4><fb>>^^Q<c1>^^?<f4><de><e5>^^[<a4>r<b6><a9><d6>Q<9a><f6>"<8b>e}
                                                  X<ce>|><8f><bc><f8><d0>V^^Nc^^L6
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.25 ^^AW&<93>	^^G<96>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RQuantLib.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rsample.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RSAP.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 305-308 (article.Rnw) 
Error: processing vignette 'article.Rnw' failed with diagnostics:
Please run "rscala::scalaInstall()" or install Scala manually.
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RSDA.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rsgcc.Rcheck/00install.out’ for details.
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rsml.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
Package required and available but unsuitable version: ‘S4Vectors’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 47.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  45.6Mb
installed size is 61.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  57.9Mb
installed size is 246.1Mb
  sub-directories of 1Mb or more:
    libs  243.8Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rsurfer.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rsymphony.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rugarch.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RunuranGUI.Rcheck/00install.out’ for details.
installed size is 32.5Mb
  sub-directories of 1Mb or more:
    libs  31.9Mb
Missing or unexported object: ‘xml2::xml_find_first’
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘pixmap’ which was already attached by Depends.
  Please remove these calls from your code.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyrvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
installed size is 45.8Mb
  sub-directories of 1Mb or more:
    libs  45.5Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RVowpalWabbit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RVPedigree.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RWeka.Rcheck/00install.out’ for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs    8.3Mb
    yacas   1.3Mb
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘vcd’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘foreign’ ‘ggplot2’ ‘grid’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘foreign:::adQuote’
  See the note in ?`:::` about the use of this operator.
Invalid MIT-MAGIC-COOKIE-1 keycalc.hist.breaks: no visible global function definition for
  ‘nclass.Sturges’
calc.hist.breaks: no visible global function definition for ‘nclass.FD’
calc.hist.breaks: no visible global function definition for
  ‘nclass.scott’
check.class: no visible global function definition for ‘as.formula’
gtkColorSelectionForPlotGetColor: no visible global function definition
  for ‘rgb’
gtkColorSelectionWidgetNew: no visible global function definition for
  ‘colors’
gtkFileChooserDialogFilteredActivate: no visible binding for global
  variable ‘theme_grey’
localize: no visible global function definition for ‘localeToCharset’
summary.CrossTable : twoDimTable: no visible global function definition
  for ‘addmargins’
summary.CrossTable: no visible global function definition for
  ‘assocstats’
write.spss: no visible global function definition for ‘write.table’
write.stata: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  addmargins as.formula assocstats colors localeToCharset nclass.FD
  nclass.Sturges nclass.scott rgb theme_grey write.table
Consider adding
  importFrom("grDevices", "colors", "nclass.FD", "nclass.Sturges",
             "nclass.scott", "rgb")
  importFrom("stats", "addmargins", "as.formula")
  importFrom("utils", "localeToCharset", "write.table")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Package suggested but not available for checking: ‘org.Sc.sgd.db’
Error in re-building vignettes:
  ...
  input string 432 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sandwich-CL.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Ml
           ^^S<c9>^^R.b o<a4>`<d3>^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 !^^D.>|<f8>p<e8><d0>!<d3>4<85>^^P<a6>i<b6><e9><f9><be>osAd<db>6<94><ff>B<e9><d6><f6>"(<fa>\^^E
                                                <80>S/<b7>m<9b>om}^^\3<b6><b5>A<a0>c<eb>[<b8><b0>T*uD&u...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.17 ...c<eb>[<b8><b0>T*uD&u	N<f4><a9>X,<e2>^^E<d3><d3>Ӹf^^A<e4><84>^^PJ)۶o߾}
                                                  <eb><d6>-^^T^^R^^QP<84>^^V>~<fc>x<ec><d8>1`^...
I
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/scanstatistics.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
    opponent.vote, turnout, winner, winner.bmi, winner.height,
    winner.party, winner.vote

The following objects are masked from stature (pos = 5):

    election, opponent, opponent.height, opponent.party,
    opponent.vote, turnout, winner, winner.bmi, winner.height,
    winner.party, winner.vote

The following objects are masked from stature (pos = 6):

    election, opponent, opponent.height, opponent.party,
    opponent.vote, turnout, winner, winner.bmi, winner.height,
    winner.party, winner.vote

The following object is masked from package:SciencesPo:

    turnout

.data was converted to a dataframe
Warning: New theme missing the following elements: axis.line.x, axis.line.y, panel.grid.major, panel.grid.minor
Quitting from lines 1090-1091 (SciencesPo.Rmd) 
Error: processing vignette 'SciencesPo.Rmd' failed with diagnostics:
invalid 'times' argument
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SDD.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Error in re-building vignettes:
  ...
  input string 439 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 447 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 448 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 456 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'semPLS-intro.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...<f4><af>i<9a>^^X<a2><94>m<db>['<8c>^^N<e9><85><de><eb><fd>ư<b0><b0><c0>^^X<b3>,<eb><e4>ɓW<ae>\1
                                                  M<f3><fe><fd><fb>W<af>^^^UB<98><a6><f9><f8><f1><e3><c9><c9>I<a5>T<bd>^<bf>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ^^E^^\^^R<c2>^^[<fe>.,,<80>^^Y<a5><d4><e5>˗<a5><94>+++<b6>m^^S\<95>
                                           RB<88><f9><f9><f9>~<ad><a7><cf>ҋK<c4><d2>><cd><ff><8e><d9><db>o^^ZڽA<a6>=<a9>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 <82>?s<b9><94>m<bb><8d><c6><fb><9c>^^_<e5><fc>^^?^^WS<c3>0<94>R<8e><e3><cc><ce>΢^^Ec<b1>\<f2>
                                             E<a4><94><89>Db}}}bb<a2><d9>l&^^R<89>f<b3>)<84><a8>T
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs   8.8Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sergeant.Rcheck/00install.out’ for details.
installed size is 131.8Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    libs    123.3Mb
    sqlite    1.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/shinyRGL.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SIBER.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sidier.Rcheck/00install.out’ for details.
randomDAG: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbinom
Consider adding
  importFrom("stats", "rbinom")
to your NAMESPACE file.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
Package required but not available: ‘snakecase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Packages required and available but unsuitable versions: ‘stats’ ‘parallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 438 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'smacof.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.15 ...<a5>^^_<a0><af><fd>^^D}+<81><d0>B<a1>)^^T^^D<85><fa><cd>T^^T^^Y<e3>Bڻ )F<89>^
                                                  <86>]-Eر3޵<e2><ec>ub<f9>><fc>аqbKJ<ac>$<d2><d5>...
! Undefined control sequence.
l.19 ^^Y{<fd>҈#g<f2><9b>o<be>^^Y<d0><d0>w<ee><dc>^^QB<ec><ee><ee><ea><ba><fe><e3><8f>?^<bf>~<bd>P(\<bb>
                                               vM<fd>>{<f6>lcc<e3><87>^^_~<f0><OJ<d9>;<cc><f6>N#<ae><9c>o<8a>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 ...<9a><a6>9<d0>8^^]4<96><de>K^^D{<e5><fb>~:<9d><a6>X<d6>^^H<b1>^^Y^^Q<f9><be>OD<b9>\NJ
                         
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/smoothtail.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/snakecase.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/soundgen.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sourceR.Rcheck/00install.out’ for details.
Running examples in ‘SPACECAP-Ex.R’ failed
The error most likely occurred in:

> ### Name: SPACECAP
> ### Title: Fits spatially-explicit capture recapture models
> ### Aliases: SPACECAP
> 
> ### ** Examples
> 
> SPACECAP()
Invalid MIT-MAGIC-COOKIE-1 keyError in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: SPACECAP ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Package required but not available: ‘SpaDES.core’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘quickPlot’

Package suggested but not available for checking: ‘SpaDES.tools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘quickPlot’ ‘SpaDES.addins’ ‘SpaDES.core’ ‘SpaDES.tools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘quickPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.2Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  Attaching package: 'spam'
  
  The following objects are masked from 'package:base':
  
      backsolve, forwardsolve
  
  > 
  > test_check("spam")
  testthat results ================================================================
  OK: 496 SKIPPED: 0 FAILED: 0
  Error: is.expectation(exp) is not TRUE
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotc2412bdcf402.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotc2412bdcf402.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sparseMVN.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/spatgraphs.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SpatialAcc.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SpatialFloor.Rcheck/00install.out’ for details.
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    data   3.4Mb
    doc    4.6Mb
    help   5.2Mb
    libs   1.6Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  14.8Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: 'lgamma' declared at (1) is also the name of an intrinsic.  It can only be called via an explicit interface or if declared EXTERNAL.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SPECIES.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sphereplot.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPackage in Depends field not imported from: ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error in re-building vignettes:
  ...
  input string 415 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'UsingSpikeSlabGAM.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<c1>
          k^^[W^^S<9f>H5<89><88>><ad>^^_	qm<b3><de><f5><83>^^^<fa><d5><c8>^^B^^]J^^N<a9>|0^^T<f7><90>[(<f4>\^^D<fd>z<ed><b5><87><9e>K}O...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<ad>^^_	qm<b3><de><f5><83>^^^<fa><d5><c8>^^B^^]J^^N<a9>|0^^T<f7><90>[(<f4>\^^D
                                                  <fd>z<ed><b5><87><9e>K}O/<ba><f9><d0>@<bd>^^D;<82><86><84>,]<ab>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...^D^^V<ad>^^WU<95><a9><fd><bc>k<c5>]<b7>X<fa>^^N?4<ec><e7>ږ<94>ڎ<e5>j^^Nb<f5><f6
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sprint.Rcheck/00install.out’ for details.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  11.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/spup.Rcheck/00install.out’ for details.
Running examples in ‘SRRS-Ex.R’ failed
The error most likely occurred in:

> ### Name: SRRS-package
> ### Title: The Stepwise Response Refinement Screener (SRRS)
> ### Aliases: SRRS-package
> 
> ### ** Examples
> 
> SRRS()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: SRRS ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ss3sim.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SSN.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SSRMST.Rcheck/00install.out’ for details.
Packages required but not available: ‘stacomirtools’ ‘RODBC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/standardize.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    include   8.6Mb
    lib       1.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/StatDA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/stddiff.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

The following object is masked from 'package:dplyr':

    combine

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=georgia&zoom=5&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=georgia&sensor=false
Quitting from lines 220-233 (Details.Rmd) 
Error: processing vignette 'Details.Rmd' failed with diagnostics:
GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyDetailOpLines: no visible global function definition for
  ‘tkProgressBar’
DetailOpLines: no visible global function definition for
  ‘setTkProgressBar’
MultiTrainWithInventory: no visible global function definition for
  ‘tkProgressBar’
MultiTrainWithInventory: no visible global function definition for
  ‘setTkProgressBar’
SimHistory: no visible global function definition for ‘tkProgressBar’
SimHistory: no visible global function definition for
  ‘setTkProgressBar’
Undefined global functions or variables:
  setTkProgressBar tkProgressBar
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Number of test functions: 18 
  Number of errors: 1 
  Number of failures: 0 
  
   
  1 Test Suite : 
  stremr unit testing - 18 test functions, 1 error, 0 failures
  ERROR in test.speedglm.allestimators10Kdata: Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 1)
  
  Execution halted
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    libs  30.6Mb
Running examples in ‘subspaceMOA-Ex.R’ failed
The error most likely occurred in:

> ### Name: DSC_HDDStream
> ### Title: Density-based Projected Clustering over High-Dimensional Data
> ### Aliases: DSC_HDDStream
> 
> ### ** Examples
> 
> dsc <- DSC_HDDStream()
Error in rJava::.jcall("moa/r_interface/OneStageClusterer", returnSig = "Lmoa/r_interface/RCompatibleDataStreamClusterer;",  : 
  RcallMethod: cannot determine object class
Calls: DSC_HDDStream -> <Anonymous> -> .External
Execution halted
Package required but not available: ‘d3r’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/surveydata.Rcheck/00install.out’ for details.
installed size is 64.7Mb
  sub-directories of 1Mb or more:
    libs  64.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
Invalid MIT-MAGIC-COOKIE-1 keydlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyprocessSocket: no visible global function definition for ‘URLdecode’
Undefined global functions or variables:
  URLdecode
Consider adding
  importFrom("utils", "URLdecode")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
  Warning: 'erfc' declared at (1) is also the name of an intrinsic.  It can only be called via an explicit interface or if declared EXTERNAL.
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1)
  apply.f:86:0: warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  burnop.f:29:0: warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  harvestop.f:166:0: warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  harvestop.f:195:0: warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  harvgrainop.f:168:0: warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  harvkillop.f:175:0: warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  plantop.f:87:0: warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  rewind_init.f:171:0: warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1)
  sweep.f:56:0: warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
  rewind_init.f:172:0: warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SWATmodel.Rcheck/00install.out’ for details.
Package required but not available: ‘timetk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘cplexAPI’ ‘clpAPI’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sybilSBML.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/symbolicDA.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 426 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'symmoments.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Ol
           ^^S<cb>^^Y<ff>b;^^?^^\<c0><bb>+^^^<90><86>8<b1><b6><e5>E<b4><c1><a1><b2>z^^H^^R5<95>,UBꡕ,<bd>'<ae>O^^QG<de>^^A<e5>^^]...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 <e9>j^^Op<b9>\<82>
               <94><ac><aa><a2><de><d7>^^?<fc>à<89>f<b3><db><d0>y<88><eb><d2>-f=<99><d1>M]<dd>9<bd><b3><a7><fb><f0><f6><f7><f1>o<be><f2>5A<e0><86><a1><8a>zg<b7><95>.=<f7><e7><bf><fe><fb>?<e9><cd>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...<9e><be>x<f1><a2>,<cb>^^V<8b><85><e7><
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/taxa.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘GISTools’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  34.7Mb
Invalid MIT-MAGIC-COOKIE-1 keyaniplotevents: no visible global function definition for ‘plot’
aniplotevents: no visible global function definition for ‘lines’
cbfs: no visible global function definition for ‘rnorm’
cbfs: no visible global function definition for ‘runif’
cbfs_red: no visible global function definition for ‘arima.sim’
cbfs_red: no visible global function definition for ‘runif’
eventCluster: no visible global function definition for ‘princomp’
eventCluster: no visible global function definition for ‘kmeans’
measures: no visible global function definition for ‘sd’
measures: no visible global function definition for ‘var’
measures: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘Box.test’
noiseTests: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘ar’
plotevents: no visible global function definition for ‘plot’
plotevents: no visible global function definition for ‘lines’
ur.za.fast : roll: no visible global function definition for ‘coef’
ur.za.fast : roll: no visible global function definition for ‘lm’
Undefined global functions or variables:
  Box.test PP.test ar arima.sim coef kmeans lines lm plot princomp
  rnorm runif sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "Box.test", "PP.test", "ar", "arima.sim", "coef",
             "kmeans", "lm", "princomp", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Running examples in ‘TELP-Ex.R’ failed
The error most likely occurred in:

> ### Name: telp
> ### Title: The Base Function of This Package The Free Evocation of Words
> ###   Technique
> ### Aliases: telp
> ### Keywords: function
> 
> ### ** Examples
> 
> telp()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: telp ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tensorr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/termstrc.Rcheck/00install.out’ for details.
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs       6.9Mb
    tessdata  31.0Mb
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tetraclasse.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 398 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'texreg.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^[<d7>^^V?<95><f2><d1>!A<d2>}-AQQ,.^^D<c3>Kp^^D^^C<85>^^Z<8a>C0Y4P^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.18 RJ<a5><94>^^P^^BS<e7><f3>y)<a5><e3>8B^^H<c3>0<94>R/^
                                 <bc>8s<e6><cc>ݻw<85><82>^^P<c2>4M)<e5><ec>쬮<eb><85>B<81><88><a4><94>RJ<d3>4<85>^^PJ<a9><d5><d5><d5>...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.21 ...<8b>MMM^^]dÃa<ce>a<db>VG<86><c3>1<a7><94>ҶmP	<e4><c2>/3-^^X<8c>y<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.5Mb
    libs   4.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/textTinyR.Rcheck/00install.out’ for details.
Running examples in ‘timetk-Ex.R’ failed
The error most likely occurred in:

> ### Name: tk_augment_timeseries
> ### Title: Augment the time series signature to the data
> ### Aliases: tk_augment_timeseries tk_augment_timeseries_signature
> 
> ### ** Examples
> 
> library(tidyquant)
Loading required package: lubridate

Attaching package: ‘lubridate’

The following object is masked from ‘package:base’:

    date

Loading required package: quantmod
Loading required package: xts
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

Loading required package: TTR
Version 0.4-0 included new data defaults. See ?getSymbols.
Loading required package: tidyverse
Loading tidyverse: ggplot2
Loading tidyverse: tibble
Loading tidyverse: tidyr
Loading tidyverse: readr
Loading tidyverse: purrr
Loading tidyverse: dplyr
Conflicts with tidy packages ---------------------------------------------------
as.difftime(): lubridate, base
date():        lubridate, base
filter():      dplyr, stats
first():       dplyr, xts
intersect():   lubridate, base
lag():         dplyr, stats
last():        dplyr, xts
setdiff():     lubridate, base
union():       lubridate, base

Attaching package: ‘tidyquant’

The following object is masked from ‘package:dplyr’:

    as_tibble

The following object is masked from ‘package:tibble’:

    as_tibble

> library(timetk)
> 
> FANG %>%
+     filter(symbol == "FB") %>%
+     tk_augment_timeseries_signature()
Error in eval(expr, envir, enclos) : object 'FANG' not found
Calls: %>% -> eval -> eval
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  The following object is masked from 'package:dplyr':
  
      as_tibble
  
  The following object is masked from 'package:tibble':
  
      as_tibble
  
  Error in eval(expr, envir, enclos) : object 'FANG' not found
  Calls: test_check ... force -> source_file -> eval -> eval -> %>% -> eval -> eval
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Error in re-building vignettes:
  ...
Conflicts with tidy packages ----------------------------------------------
as.difftime(): lubridate, base
date():        lubridate, base
filter():      dplyr, stats
first():       dplyr, xts
intersect():   lubridate, base
lag():         dplyr, stats
last():        dplyr, xts
setdiff():     lubridate, base
union():       lubridate, base

Attaching package: 'tidyquant'

The following object is masked from 'package:dplyr':

    as_tibble

The following object is masked from 'package:tibble':

    as_tibble

Quitting from lines 69-72 (TK00_Time_Series_Coercion.Rmd) 
Error: processing vignette 'TK00_Time_Series_Coercion.Rmd' failed with diagnostics:
could not find function "tq_transmute"
Execution halted
drawGraph: no visible global function definition for ‘eqmcc’
drawGraph: no visible global function definition for ‘pdf’
drawGraph: no visible global function definition for ‘par’
drawGraph: no visible global function definition for ‘plot’
drawGraph: no visible global function definition for ‘segments’
drawGraph: no visible global function definition for ‘lines’
drawGraph: no visible global function definition for ‘text’
drawGraph: no visible global function definition for ‘dev.off’
drugRank: no visible global function definition for ‘aggregate’
floating2: no visible global function definition for ‘cor’
timma: no visible global function definition for ‘median’
timma: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  aggregate cor dev.off eqmcc lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Running the tests in ‘tests/simple.R’ failed.
Last 13 lines of output:
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > 
  > ## run in the R session temp.dir. which gets cleaned
  > setwd(tempdir())                        
  > 
  > ## process html -- should work everywhere
  > file.copy(system.file("examples", "simpleHtml.Rmd", package="tint"), "simpleHtml.Rmd")
  [1] TRUE
  > rmarkdown::render("simpleHtml.Rmd")
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘boot’ ‘lattice’ ‘splines’ ‘tcltk’
  Please remove these calls from your code.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tkrgl.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘rgl’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key.my.tkdev: no visible global function definition for ‘X11’
tkpersp : draw: no visible global function definition for ‘par’
tkpersp : draw: no visible global function definition for ‘persp’
Undefined global functions or variables:
  X11 par persp
Consider adding
  importFrom("grDevices", "X11")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
Running examples in ‘tm.plugin.dc-Ex.R’ failed
The error most likely occurred in:

> ### Name: tm_map.DCorpus
> ### Title: Transformations on Distributed Corpora
> ### Aliases: tm_map.DCorpus
> 
> ### ** Examples
> 
> data("crude")
> tm_map(as.DCorpus(crude), content_transformer(tolower))
Warning in file(con, "w") :
  cannot open file '/var/folders/8q/c881c7rn7_x34vj58f4ywhvm0000h3/T//Rtmpb0djBE/DSL-20160505-034420-gjoxfxyrqb/chunk-15dc814df4a7b': No such file or directory
Error in file(con, "w") : cannot open the connection
Calls: tm_map ... DS_write_lines -> <Anonymous> -> <Anonymous> -> file
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/TNC.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘TeachingDemos’ ‘ash’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: ggplot2

Attaching package: 'trackeR'

The following object is masked from 'package:base':

    append

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Quitting from lines 90-91 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Package suggested but not available for checking: ‘OpenStreetMap’
Error in re-building vignettes:
  ...
 [>] max. distance: 139.84
 [>] neighborhood radius: 13.98
 [>] 1 representative(s) selected, coverage=46% (threshold=35%)
 [>] 88 distinct sequence(s)
 [>] number of objects (sum of weights): 196.82
 [>] max. distance: 139.84
 [>] neighborhood radius: 13.98
 [>] 4 representative(s) selected, coverage=39% (threshold=35%)
 [>] 148 distinct sequence(s)
 [>] number of objects (sum of weights): 99.22
 [>] max. distance: 139.84
 [>] neighborhood radius: 13.98
 [>] 5 representative(s) selected, coverage=38% (threshold=35%)
 [>] 89 distinct sequence(s)
Warning in readLines(log, warn = FALSE) :
  invalid input found on input connection 'TraMineR-state-sequence.log'
Warning in readLines(con, warn = FALSE) :
  invalid input found on input connection 'TraMineR-state-sequence.log'
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TraMineR-state-sequence.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
Packages required and available but unsuitable versions:
  ‘grid’ ‘phyloseq’ ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggfittext’

Package required and available but unsuitable version: ‘grid’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/treethresh.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tRophicPosition.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/TSclust.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘grDevices’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘TSodbc’ ‘RODBC’
Packages unavailable to check Rd xrefs: ‘TSodbc’, ‘RODBC’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
Sep 13, 2017 12:24:49 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData
INFO: The sdmx call returned messages in the footer:
 Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]]
Sep 13, 2017 12:24:49 PM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData
INFO: The sdmx call returned messages in the footer:
 Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]]

  When sourcing ‘Guide.R’:
Error: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxXmlContentException: The query: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT did not match any time series on the provider.
Execution halted
when running code in ‘GuideAppendix.Stex’
  ...

> options(continue = "  ")

> user <- Sys.getenv("MYSQL_USER")

> setup <- RMySQL::dbConnect(RMySQL::MySQL(), dbname = "test")

  When sourcing ‘GuideAppendix.R’:
Error: Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
Execution halted
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    doc         2.2Mb
    dummydata   1.4Mb
    libs       19.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/uniqueAtomMat.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.4Mb
Running examples in ‘uplift-Ex.R’ failed
The error most likely occurred in:

> ### Name: checkBalance
> ### Title: Standardized Differences for Stratified Comparisons
> ### Aliases: checkBalance
> ### Keywords: uplift xBalance
> 
> ### ** Examples
> 
> library(uplift)
> 
> set.seed(12345)
> dd <- sim_pte(n = 1000, p = 20, rho = 0, sigma =  sqrt(2), beta.den = 4)
> dd$treat <- ifelse(dd$treat == 1, 1, 0) 
> 
> checkBalance(treat ~ X1 + X2 + X3 + X4 + X5 + X6 , data = dd)
     strata  unstrat                                                              
     stat    treat=0  treat=1 adj.diff adj.diff.null.sd std.diff     z            
vars                                                                              
X1          0.01152  -0.00596 -0.01748         0.06006  -0.01840 -0.29103         
X2          0.03160  -0.02812 -0.05972         0.06236  -0.06057 -0.95778         
X3          0.01145  -0.02242 -0.03387         0.06355  -0.03370 -0.53303         
X4          0.01533  -0.03551 -0.05083         0.06370  -0.05046 -0.79801         
X5          -0.06440 0.02370  0.08810          0.06153  0.09060  1.43175          
X6          0.02237  -0.02177 -0.04414         0.06308  -0.04425 -0.69980         
---Overall Test---
        chisquare df p.value
unstrat      4.54  6   0.604
---
Signif. codes:  0 ‘***’ 0.001 ‘** ’ 0.01 ‘*  ’ 0.05 ‘.  ’ 0.1 ‘   ’ 1 
Error in ncol(DT) : object 'DT' not found
Calls: <Anonymous> ... withOptions -> tryCatch -> do.call -> <Anonymous> -> ncol
Execution halted
installed size is 68.8Mb
  sub-directories of 1Mb or more:
    libs  67.9Mb
Package which this enhances but not available for checking: ‘lumberjack’
Unknown package ‘lumberjack’ in Rd xrefs
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/vanddraabe.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/VarfromPDB.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 428 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 437 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vars.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ?<f1><8b><96><eb><96>;<d9>l6^^V<8b>uM<<c3>0n޼<99>N<a7>1\Y
                                 <96><f1><a6><96><fb><9a><a6><a5>R)<88>^^Z<8f><c7><f9>D^^D<83><c1>D"<a1><eb><ba>,˲,뺎6<f8><9a>J<a5>^^N...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 <bd>MMM<e1><9a>c^^?^^?<ff><ee>ݻ^^O^^_><9c><9b><9b><8b><c7>㌱<d9><d9>Y<bc><e8>$^^L\<cc>
                                                <84>H<d7><f5><d3><c7><dd>!<ba>,<9e><ae><eb>D<f4><e1><87>^^_z<9e>G<c7><fa><a1>cB...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 0<c6>X<b5>ZE\<e6>
             <a7>.<98>L<c7>[H~n<c7><e3>q<90><b6><a5>^^_<f4><cf>?<fd>!<de>)<8c><b8><88><a6><a5><8b>^^\n<e3>^^X^^Xc<b0>^^G|<c7>^^X^^[<94><f3><f3><f3>t<ec>	^...
The control sequence at the end o
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   2.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   3.5Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/vcov.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/VDA.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keycv.vda.le.default: no visible global function definition for ‘predict’
cv.vda.r.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/VecStatGraphs3D.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyDrawDensity3D: no visible global function definition for ‘colorRamp’
DrawDensity3D: no visible global function definition for ‘rgb’
ReadFromFile3D: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in ‘VecStatGraphs3D-Ex.R’ failed
The error most likely occurred in:

> ### Name: DrawModuleAndAngleDistribution3D
> ### Title: Graphic representation of Module and Angle Distribution.
> ### Aliases: DrawModuleAndAngleDistribution3D
> ### Keywords: graphics
> 
> ### ** Examples
> 
>    FileName<-system.file("data/XYZcoor.txt", package="VecStatGraphs3D")
>    dat<-LoadData3D(FileName, Type=1)
>    DrawModuleAndAngleDistribution3D(dat, plane="XY");
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: DrawModuleAndAngleDistribution3D ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
Running examples in ‘VeryLargeIntegers-Ex.R’ failed
The error most likely occurred in:

> ### Name: 01. Basics
> ### Title: Very Large Integers Basics
> ### Aliases: '01. Basics' as.vli as.vli.default as.vli.character
> ###   as.vli.numeric asnumeric asnumeric.default asnumeric.vli
> ###   as.integer.vli as.character.vli vli print.vli is.vli
> 
> ### ** Examples
> 
> ## Creating a new vli object
> x <- as.vli("-89027148538375418689123052")
> 
> ## Printing a vli object
> print(x)
Very Large Integer: 
[1] -89027148538375418689123052
> 
> ## Testing the class
> is.vli(x)
[1] TRUE
> 
> ## Coercing into a character object
> as.character(x)
[1] "-89027148538375418689123052"
> 
> ## Accessing to the attributes of the vli object
> x$sign
[1] -1
> x$value
[1]   89  271 4853 8375 4186 8912 3052
> x$length
[1] 26
> 
> ## Punctuation signs are ignored
> as.vli("2345.25")
Very Large Integer: 
[1] 234525
> 
> 
> 
> ### * <FOOTER>
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  19.653 0.142 19.798 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
Error: segfault from C stack overflow
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/VGAM.Rcheck/00install.out’ for details.
Running examples in ‘VisuClust-Ex.R’ failed
The error most likely occurred in:

> ### Name: FuzzyPlot
> ### Title: Displays a Fuzzy Plot
> ### Aliases: FuzzyPlot
> 
> ### ** Examples
> 
> 
> library(cluster)
> library(MASS)
> 
> # The example data
> data("MilchSmall")
> 
> M <- scale(MilchSmall[3:6])
> D <- dist(M)
> S <- sammon(D)
Initial stress        : 0.00738
stress after  10 iters: 0.00227, magic = 0.500
stress after  20 iters: 0.00204, magic = 0.500
stress after  30 iters: 0.00203, magic = 0.500
> F <- fanny(D, 6)
> 
> FuzzyPlot(S$points, F$membership, labels=MilchSmall[,2], 
+ 	clusterColors=c("red", "green", "magenta", "yellow", "blue", "black"))
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: FuzzyPlot ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 49.1Mb
  sub-directories of 1Mb or more:
    libs  48.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/wand.Rcheck/00install.out’ for details.
Running examples in ‘wbsts-Ex.R’ failed
The error most likely occurred in:

> ### Name: tau.fun
> ### Title: Universal thresholds
> ### Aliases: tau.fun
> ### Keywords: threshold
> 
> ### ** Examples
>  
> 
> cps=c(400,470)
> set.seed(101)
> y=sim.pw.ar(N =2000,sd_u = 1,b.slope=c(0.4,-0.6,0.5),br.loc=cps)[[2]]
> #tau.fun(y) is the default value for C_i
> #Binary segmentation
> wbs.lsw(y,M=1)$cp.aft
NULL
> #Wild binary segmentation
> wbs.lsw(y,M=3500)$cp.aft
Error in while (ind.max < 0 | ind.max > e) { : 
  missing value where TRUE/FALSE needed
Calls: wbs.lsw -> uh.wbs
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/webglobe.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/weightr.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘org.Mm.eg.db’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/wktmo.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/WMCapacity.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/wnominate.Rcheck/00install.out’ for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/wooldridge.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because wordcloud.Rmd appears to be an R Markdown v2 document.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
  input string 432 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'WRS2.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.19 ...VB<e0>+W^^L<ce>O?<fd>^^T^^X[^^&"<ec>^^G"<82>p<e5>rYJ	<81><98>x&<b9>\<ce>
                                                  <f3><bc>d2	A<85>^^PA^^P<94>J%<f4><80>^^[<ef>g<a5>T...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 <95>l<f1><81><93>T*<85>ꥮ<eb>^^T<b9>^^]<88>sv<df><f7><85>^^P<cb><cb>˨^^Qan<9c><d7>an\2
                                                <8b><a6>s<b6>m+<a5><82>  "]<d7><f9><e4><bd><d1>h^^Pѩ<ca><ea>)<fa><b0>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.29 èV<ab><8b><8b><8b>tb<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/WufooR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/x12GUI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/xbreed.Rcheck/00install.out’ for details.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
newXMLDoc: no visible binding for global variable ‘doc’
xmlFlatListTree : f: no visible binding for global variable ‘nodeNames’
xmlFlatListTree : f: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘parentCount’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘parentCount’
xmlFlatListTree : <anonymous>: no visible binding for global variable
  ‘e’
xmlFlatTree : <anonymous>: no visible binding for global variable ‘e’
[[,XMLCodeFile: possible error in updateIds(doc, save = x): unused
  argument (save = x)
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Xplortext.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/xtensor.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/YplantQMC.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/YuGene.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/zstdr.Rcheck/00install.out’ for details.