• 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 the install log 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