* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
clang version 20.1.0-rc3
flang version 20.1.0-rc3
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘PLNmodels/DESCRIPTION’ ... OK
* this is package ‘PLNmodels’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘PLNmodels’ can be installed ... [302s/258s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/PLNmodels-00install.html' for details.
* used C++ compiler: ‘clang version 20.1.0-rc3’
* checking installed package size ... INFO
installed size is 6.0Mb
sub-directories of 1Mb or more:
data 1.4Mb
doc 2.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘ZIPLN.R’
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [7s/10s] OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... [7s/11s] OK
* checking loading without being on the library search path ... [7s/10s] OK
* checking whether startup messages can be suppressed ... [7s/11s] OK
* checking use of S3 registration ... 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 ... [43s/58s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [35s/43s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [10s/19s] ERROR
Running ‘testthat.R’ [9s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(PLNmodels)
This is packages 'PLNmodels' version 1.2.0
Use future::plan(multicore/multisession) to speed up PLNPCA/PLNmixture/stability_selection.
>
> test_check("PLNmodels")
*** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
1: cpp_test_nlopt()
2: eval_bare(expr, quo_get_env(quo))
3: quasi_label(enquo(object), label, arg = "object")
4: expect_true(cpp_test_nlopt())
5: eval(code, test_env)
6: eval(code, test_env)
7: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
15: test_code(desc, code, env = parent.frame(), reporter = reporter)
16: test_that("PLN: cpp internals are sane", { expect_true(cpp_test_nlopt()) expect_true(cpp_test_packing())})
17: eval(code, test_env)
18: eval(code, test_env)
19: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
23: doTryCatch(return(expr), name, parentenv, handler)
24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
25: tryCatchList(expr, classes, parentenv, handlers)
26: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
27: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
28: source_file(path, env = env(env), desc = desc, error_call = error_call)
29: FUN(X[[i]], ...)
30: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
33: tryCatchList(expr, classes, parentenv, handlers)
34: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
35: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
36: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
37: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
38: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
39: test_check("PLNmodels")
An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [150s/203s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘Import_data.Rmd’ using rmarkdown
--- finished re-building ‘Import_data.Rmd’
--- re-building ‘PLN.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLN_files/figure-html/geometricalInsight-1.png
672x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 73644 bytes
Input file size = 73818 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 55474
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 55474
Output IDAT size = 55474 bytes (18170 bytes decrease)
Output file size = 55552 bytes (18266 bytes = 24.74% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLN_files/figure-html/fitted-1.png
672x480 pixels, 8 bits/pixel, 253 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7493 bytes
Input file size = 8342 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5921
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5921
Output IDAT size = 5921 bytes (1572 bytes decrease)
Output file size = 5999 bytes (2343 bytes = 28.09% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLN_files/figure-html/plot covariance-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 95567 bytes
Input file size = 95777 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 79023
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 79023
Output IDAT size = 79023 bytes (16544 bytes decrease)
Output file size = 79101 bytes (16676 bytes = 17.41% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLN_files/figure-html/weighted-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 10818 bytes
Input file size = 11688 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9157
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9157
Output IDAT size = 9157 bytes (1661 bytes decrease)
Output file size = 9235 bytes (2453 bytes = 20.99% decrease)
--- finished re-building ‘PLN.Rmd’
--- re-building ‘PLNLDA.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNLDA_files/figure-html/vcov-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 69845 bytes
Input file size = 70019 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56181
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56181
Output IDAT size = 56181 bytes (13664 bytes decrease)
Output file size = 56259 bytes (13760 bytes = 19.65% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNLDA_files/figure-html/plot_model-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 100473 bytes
Input file size = 100695 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 77122
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 77122
Output IDAT size = 77122 bytes (23351 bytes decrease)
Output file size = 77200 bytes (23495 bytes = 23.33% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNLDA_files/figure-html/predicted_scores-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 40834 bytes
Input file size = 40960 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33856
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33856
Output IDAT size = 33856 bytes (6978 bytes decrease)
Output file size = 33934 bytes (7026 bytes = 17.15% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNLDA_files/figure-html/plot_model_cov-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 99957 bytes
Input file size = 100179 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 77728
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 77728
Output IDAT size = 77728 bytes (22229 bytes decrease)
Output file size = 77806 bytes (22373 bytes = 22.33% decrease)
--- finished re-building ‘PLNLDA.Rmd’
--- re-building ‘PLNPCA.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNPCA_files/figure-html/plot nocov-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25197 bytes
Input file size = 25311 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20461
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20461
Output IDAT size = 20461 bytes (4736 bytes decrease)
Output file size = 20539 bytes (4772 bytes = 18.85% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNPCA_files/figure-html/plot nocov-reverse-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 24189 bytes
Input file size = 24291 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20090
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20090
Output IDAT size = 20090 bytes (4099 bytes decrease)
Output file size = 20168 bytes (4123 bytes = 16.97% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNPCA_files/figure-html/map-1.png
768x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 43552 bytes
Input file size = 43690 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38708
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38708
Output IDAT size = 38708 bytes (4844 bytes decrease)
Output file size = 38786 bytes (4904 bytes = 11.22% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNPCA_files/figure-html/sigma-1.png
672x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 76868 bytes
Input file size = 77054 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63973
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63973
Output IDAT size = 63973 bytes (12895 bytes decrease)
Output file size = 64051 bytes (13003 bytes = 16.88% decrease)
Quitting from lines 224-225 [fviz_biplot] (PLNPCA.Rmd)
Error: processing vignette 'PLNPCA.Rmd' failed with diagnostics:
The value of the argument axes is incorrect. The number of axes in the data is: 1. Please try again with axes between 1 - 1
--- failed re-building ‘PLNPCA.Rmd’
--- re-building ‘PLNmixture.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/objective-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8242 bytes
Input file size = 9112 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7391
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7391
Output IDAT size = 7391 bytes (851 bytes decrease)
Output file size = 7469 bytes (1643 bytes = 18.03% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/plot nocov-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 34363 bytes
Input file size = 34489 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26881
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26881
Output IDAT size = 26881 bytes (7482 bytes decrease)
Output file size = 26959 bytes (7530 bytes = 21.83% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/plot nocov-reverse-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 36273 bytes
Input file size = 36399 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27668
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27668
Output IDAT size = 27668 bytes (8605 bytes decrease)
Output file size = 27746 bytes (8653 bytes = 23.77% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/plot clustering-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 17251 bytes
Input file size = 17353 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12977
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12977
Output IDAT size = 12977 bytes (4274 bytes decrease)
Output file size = 13055 bytes (4298 bytes = 24.77% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/plot reordered data-1.png
288x288 pixels, 8 bits/pixel, 252 colors in palette
Input IDAT size = 2497 bytes
Input file size = 3343 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2131
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2131
Output IDAT size = 2131 bytes (366 bytes decrease)
Output file size = 2977 bytes (366 bytes = 10.95% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNmixture_files/figure-html/predicted_position-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 20662 bytes
Input file size = 20764 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17283
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17283
Output IDAT size = 17283 bytes (3379 bytes decrease)
Output file size = 17361 bytes (3403 bytes = 16.39% decrease)
--- finished re-building ‘PLNmixture.Rmd’
--- re-building ‘PLNnetwork.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNnetwork_files/figure-html/diagnostic-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 23412 bytes
Input file size = 24294 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21544
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21544
Output IDAT size = 21544 bytes (1868 bytes decrease)
Output file size = 21622 bytes (2672 bytes = 11.00% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNnetwork_files/figure-html/plot-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 47309 bytes
Input file size = 47447 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35910
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35910
Output IDAT size = 35910 bytes (11399 bytes decrease)
Output file size = 35988 bytes (11459 bytes = 24.15% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNnetwork_files/figure-html/plot-reverse-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 44173 bytes
Input file size = 44311 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36049
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36049
Output IDAT size = 36049 bytes (8124 bytes decrease)
Output file size = 36127 bytes (8184 bytes = 18.47% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/PLNnetwork_files/figure-html/path_coeff-1.png
672x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 204010 bytes
Input file size = 204376 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 193985
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 193985
Output IDAT size = 193985 bytes (10025 bytes decrease)
Output file size = 194063 bytes (10313 bytes = 5.05% decrease)
Quitting from lines 175-176 [extract models stars] (PLNnetwork.Rmd)
Error: processing vignette 'PLNnetwork.Rmd' failed with diagnostics:
attempt to apply non-function
--- failed re-building ‘PLNnetwork.Rmd’
--- re-building ‘Trichoptera.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/PLNmodels.Rcheck/vign_test/PLNmodels/vignettes/Trichoptera_files/figure-html/count diplay-1.png
672x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 57047 bytes
Input file size = 57197 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44290
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 44290
Output IDAT size = 44290 bytes (12757 bytes decrease)
Output file size = 44368 bytes (12829 bytes = 22.43% decrease)
--- finished re-building ‘Trichoptera.Rmd’
SUMMARY: processing the following files failed:
‘PLNPCA.Rmd’ ‘PLNnetwork.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... [15s/19s] OK
* checking HTML version of manual ... [9s/14s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 1 NOTE