Check results for 'MultiPhen'

using R version 4.3.0 alpha (2023-03-31 r84137)
using platform: x86_64-apple-darwin20 (64-bit)
R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0
running under: macOS Ventura 13.3
using session charset: UTF-8
checking for file ‘MultiPhen/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘MultiPhen’ version ‘2.0.3’
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘MultiPhen’ can be installed ... [10s/13s] OK See the install log for details.
checking installed package size ... OK
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking R files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [2s/3s] OK
checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
checking whether the package can be unloaded cleanly ... [2s/3s] OK
checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
checking loading without being on the library search path ... [2s/3s] OK
checking startup messages can be suppressed ... [2s/3s] OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [11s/16s] OK
checking Rd files ... [0s/0s] NOTE checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking contents of ‘data’ directory ... OK
checking data for non-ASCII characters ... [0s/0s] OK
checking data for ASCII and uncompressed saves ... OK
checking sizes of PDF files under ‘inst/doc’ ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [2s/3s] OK
checking for unstated dependencies in vignettes ... OK
checking package vignettes in ‘inst/doc’ ... OK
checking running R code from vignettes ... [4s/4s] OK ‘MultiPhen.Rnw’... [4s/4s] OK
checking re-building of vignette outputs ... [10s/14s] NOTE Error(s) in re-building vignettes: --- re-building ‘MultiPhen.Rnw’ using Sweave Loading required package: MASS Loading required package: abind Loading required package: epitools Loading required package: meta Loading 'meta' package (version 6.2-1). Type 'help(meta)' for a brief overview. Readers of 'Meta-Analysis with R (Use R!)' should install older version of 'meta' package: https://tinyurl.com/dt4y5drs Warning in betasg/normg : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead. Warning in betasg/normg : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead. Warning in betasg/normg : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead. Warning in plot.window(...) : "na.color" is not a graphical parameter Warning in plot.window(...) : "dendrogram" is not a graphical parameter Warning in plot.window(...) : "density.info" is not a graphical parameter Warning in plot.window(...) : "trace" is not a graphical parameter Warning in plot.window(...) : "key" is not a graphical parameter Warning in plot.window(...) : "symbreaks" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "na.color" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "dendrogram" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "density.info" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "trace" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "symbreaks" is not a graphical parameter Warning in title(...) : "na.color" is not a graphical parameter Warning in title(...) : "dendrogram" is not a graphical parameter Warning in title(...) : "density.info" is not a graphical parameter Warning in title(...) : "trace" is not a graphical parameter Warning in title(...) : "key" is not a graphical parameter Warning in title(...) : "symbreaks" is not a graphical parameter Warning in plot.window(...) : "na.color" is not a graphical parameter Warning in plot.window(...) : "dendrogram" is not a graphical parameter Warning in plot.window(...) : "density.info" is not a graphical parameter Warning in plot.window(...) : "trace" is not a graphical parameter Warning in plot.window(...) : "key" is not a graphical parameter Warning in plot.window(...) : "symbreaks" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "na.color" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "dendrogram" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "density.info" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "trace" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "symbreaks" is not a graphical parameter Warning in title(...) : "na.color" is not a graphical parameter Warning in title(...) : "dendrogram" is not a graphical parameter Warning in title(...) : "density.info" is not a graphical parameter Warning in title(...) : "trace" is not a graphical parameter Warning in title(...) : "key" is not a graphical parameter Warning in title(...) : "symbreaks" is not a graphical parameter Warning in .heatm(outC$beta, effPhe, logfun1, opts, TRUE, filek) : unable to make heatmap resultsDir/resultsJoint.heatm.pdf all all beta Warning in max(abs(as.vector(res[, snpinds, , 1]))[pvs < 0.05], na.rm = T) : no non-missing arguments to max; returning -Inf Warning in plot.window(...) : "na.color" is not a graphical parameter Warning in plot.window(...) : "dendrogram" is not a graphical parameter Warning in plot.window(...) : "density.info" is not a graphical parameter Warning in plot.window(...) : "trace" is not a graphical parameter Warning in plot.window(...) : "key" is not a graphical parameter Warning in plot.window(...) : "symbreaks" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "na.color" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "dendrogram" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "density.info" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "trace" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "symbreaks" is not a graphical parameter Warning in title(...) : "na.color" is not a graphical parameter Warning in title(...) : "dendrogram" is not a graphical parameter Warning in title(...) : "density.info" is not a graphical parameter Warning in title(...) : "trace" is not a graphical parameter Warning in title(...) : "key" is not a graphical parameter Warning in title(...) : "symbreaks" is not a graphical parameter Warning in plot.window(...) : "na.color" is not a graphical parameter Warning in plot.window(...) : "dendrogram" is not a graphical parameter Warning in plot.window(...) : "density.info" is not a graphical parameter Warning in plot.window(...) : "trace" is not a graphical parameter Warning in plot.window(...) : "key" is not a graphical parameter Warning in plot.window(...) : "symbreaks" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "na.color" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "dendrogram" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "density.info" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "trace" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "symbreaks" is not a graphical parameter Warning in title(...) : "na.color" is not a graphical parameter Warning in title(...) : "dendrogram" is not a graphical parameter Warning in title(...) : "density.info" is not a graphical parameter Warning in title(...) : "trace" is not a graphical parameter Warning in title(...) : "key" is not a graphical parameter Warning in title(...) : "symbreaks" is not a graphical parameter Warning in .heatm(outC$beta, effPhe, logfun1, opts, TRUE, filek) : unable to make heatmap resultsDir/resultsBackwardSelection.heatm.pdf all all beta Warning in plot.window(...) : "na.color" is not a graphical parameter Warning in plot.window(...) : "dendrogram" is not a graphical parameter Warning in plot.window(...) : "density.info" is not a graphical parameter Warning in plot.window(...) : "trace" is not a graphical parameter Warning in plot.window(...) : "key" is not a graphical parameter Warning in plot.window(...) : "symbreaks" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "na.color" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "dendrogram" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "density.info" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "trace" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "symbreaks" is not a graphical parameter Warning in title(...) : "na.color" is not a graphical parameter Warning in title(...) : "dendrogram" is not a graphical parameter Warning in title(...) : "density.info" is not a graphical parameter Warning in title(...) : "trace" is not a graphical parameter Warning in title(...) : "key" is not a graphical parameter Warning in title(...) : "symbreaks" is not a graphical parameter Warning in plot.window(...) : "na.color" is not a graphical parameter Warning in plot.window(...) : "dendrogram" is not a graphical parameter Warning in plot.window(...) : "density.info" is not a graphical parameter Warning in plot.window(...) : "trace" is not a graphical parameter Warning in plot.window(...) : "key" is not a graphical parameter Warning in plot.window(...) : "symbreaks" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "na.color" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "dendrogram" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "density.info" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "trace" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "symbreaks" is not a graphical parameter Warning in title(...) : "na.color" is not a graphical parameter Warning in title(...) : "dendrogram" is not a graphical parameter Warning in title(...) : "density.info" is not a graphical parameter Warning in title(...) : "trace" is not a graphical parameter Warning in title(...) : "key" is not a graphical parameter Warning in title(...) : "symbreaks" is not a graphical parameter Warning in .manhattan(topl, logfun, beta1 = NULL, paste(opts$mPhen.title, : NAs introduced by coercion Warning in plot.window(...) : "na.color" is not a graphical parameter Warning in plot.window(...) : "dendrogram" is not a graphical parameter Warning in plot.window(...) : "density.info" is not a graphical parameter Warning in plot.window(...) : "trace" is not a graphical parameter Warning in plot.window(...) : "key" is not a graphical parameter Warning in plot.window(...) : "symbreaks" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "na.color" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "dendrogram" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "density.info" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "trace" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "symbreaks" is not a graphical parameter Warning in title(...) : "na.color" is not a graphical parameter Warning in title(...) : "dendrogram" is not a graphical parameter Warning in title(...) : "density.info" is not a graphical parameter Warning in title(...) : "trace" is not a graphical parameter Warning in title(...) : "key" is not a graphical parameter Warning in title(...) : "symbreaks" is not a graphical parameter Warning in plot.window(...) : "na.color" is not a graphical parameter Warning in plot.window(...) : "dendrogram" is not a graphical parameter Warning in plot.window(...) : "density.info" is not a graphical parameter Warning in plot.window(...) : "trace" is not a graphical parameter Warning in plot.window(...) : "key" is not a graphical parameter Warning in plot.window(...) : "symbreaks" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "na.color" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "dendrogram" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "density.info" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "trace" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter Warning in plot.xy(xy, type, ...) : "symbreaks" is not a graphical parameter Warning in title(...) : "na.color" is not a graphical parameter Warning in title(...) : "dendrogram" is not a graphical parameter Warning in title(...) : "density.info" is not a graphical parameter Warning in title(...) : "trace" is not a graphical parameter Warning in title(...) : "key" is not a graphical parameter Warning in title(...) : "symbreaks" is not a graphical parameter Warning in betag/(betag %*% betag) : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead. Error: processing vignette 'MultiPhen.Rnw' failed with diagnostics: Running 'texi2dvi' on 'MultiPhen.tex' failed. LaTeX errors: ! LaTeX Error: File `underscore.sty' not found. Type X to quit or <RETURN> to proceed, or enter new name. (Default extension: sty) ! Emergency stop. <read *> l.12 \usepackage {Sweave}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘MultiPhen.Rnw’ SUMMARY: processing the following file failed: ‘MultiPhen.Rnw’ Error: Vignette re-building failed. Execution halted
checking PDF version of manual ... [4s/5s] OK
DONE Status: 2 NOTEs
using check arguments '--no-clean-on-error '