• using R Under development (unstable) (2025-02-15 r87723)
• 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 ‘paleopop/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘paleopop’ version ‘2.1.7’
• 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 ‘paleopop’ can be installed ... [77s/90s] OK See the install log for details.
• 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 ... [20s/25s] OK
• checking whether the package can be loaded with stated dependencies ... [19s/24s] OK
• checking whether the package can be unloaded cleanly ... [20s/25s] OK
• checking whether the namespace can be loaded with stated dependencies ... [19s/24s] OK
• checking whether the namespace can be unloaded cleanly ... [20s/25s] OK
• checking loading without being on the library search path ... [20s/23s] 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 ... [85s/114s] 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 ... [19s/27s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [24s/30s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [24s/32s] OK   Running ‘testthat.R’ [24s/31s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [31m/22m] ERROR Error(s) in re-building vignettes: --- re-building ‘bison_example.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/paleopop.Rcheck/vign_test/paleopop/vignettes/bison_example_files/figure-html/siberia_raster-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 23308 bytes Input file size = 23410 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19500   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 = 19500 Output IDAT size = 19500 bytes (3808 bytes decrease) Output file size = 19578 bytes (3832 bytes = 16.37% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/paleopop.Rcheck/vign_test/paleopop/vignettes/bison_example_files/figure-html/siberia_raster-2.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 23802 bytes Input file size = 23904 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19715   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 = 19715 Output IDAT size = 19715 bytes (4087 bytes decrease) Output file size = 19793 bytes (4111 bytes = 17.20% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/paleopop.Rcheck/vign_test/paleopop/vignettes/bison_example_files/figure-html/paleoregion-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 22113 bytes Input file size = 22215 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18967   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 = 18967 Output IDAT size = 18967 bytes (3146 bytes decrease) Output file size = 19045 bytes (3170 bytes = 14.27% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/paleopop.Rcheck/vign_test/paleopop/vignettes/bison_example_files/figure-html/hs_raster-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 24616 bytes Input file size = 24730 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20200   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 = 20200 Output IDAT size = 20200 bytes (4416 bytes decrease) Output file size = 20278 bytes (4452 bytes = 18.00% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/paleopop.Rcheck/vign_test/paleopop/vignettes/bison_example_files/figure-html/carrying capacity generator-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 22059 bytes Input file size = 22161 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18391   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 = 18391 Output IDAT size = 18391 bytes (3668 bytes decrease) Output file size = 18469 bytes (3692 bytes = 16.66% decrease)
• checking PDF version of manual ... [9s/11s] 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