* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/clustTMB.Rcheck’ * using R Under development (unstable) (2025-02-14 r87716) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) * running under: Fedora Linux 40 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘clustTMB/DESCRIPTION’ ... OK * this is package ‘clustTMB’ version ‘0.1.0’ * 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 ‘clustTMB’ can be installed ... [7m/14m] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/clustTMB-00install.html' for details. * used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’ * 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... 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 ... OK * checking loading without being on the library search path ... 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 ... [27s/42s] 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 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 ... [7s/10s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [8m/10m] OK Running ‘testthat.R’ [8m/10m] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [32m/23m] ERROR Error(s) in re-building vignettes: --- re-building ‘CovarianceStructure.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/clustTMB.Rcheck/vign_test/clustTMB/vignettes/CovarianceStructure_files/figure-html/fig1-1.png 480x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 76121 bytes Input file size = 76307 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48934 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 = 48934 Output IDAT size = 48934 bytes (27187 bytes decrease) Output file size = 49012 bytes (27295 bytes = 35.77% decrease) --- finished re-building ‘CovarianceStructure.Rmd’ --- re-building ‘SpatialExMeuseData.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/clustTMB.Rcheck/vign_test/clustTMB/vignettes/SpatialExMeuseData_files/figure-html/sample-1.png 576x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 43472 bytes Input file size = 43610 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30466 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 = 30466 Output IDAT size = 30466 bytes (13006 bytes decrease) Output file size = 30544 bytes (13066 bytes = 29.96% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/clustTMB.Rcheck/vign_test/clustTMB/vignettes/SpatialExMeuseData_files/figure-html/pairs-expl-1.png 576x384 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 24151 bytes Input file size = 25033 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22370 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 = 22370 Output IDAT size = 22370 bytes (1781 bytes decrease) Output file size = 22448 bytes (2585 bytes = 10.33% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/clustTMB.Rcheck/vign_test/clustTMB/vignettes/SpatialExMeuseData_files/figure-html/fig1-1.png 384x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 68130 bytes Input file size = 68304 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 42335 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 = 42335 Output IDAT size = 42335 bytes (25795 bytes decrease) Output file size = 42413 bytes (25891 bytes = 37.91% decrease) SUMMARY: processing the following file failed: ‘SpatialExMeuseData.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR