• 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 ‘CoSMoS/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘CoSMoS’ version ‘2.1.0’
• 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 ‘CoSMoS’ can be installed ... [29s/78s] 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 code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [6s/11s] OK
• checking whether the package can be loaded with stated dependencies ... [5s/12s] OK
• checking whether the package can be unloaded cleanly ... [6s/13s] OK
• checking whether the namespace can be loaded with stated dependencies ... [5s/16s] OK
• checking whether the namespace can be unloaded cleanly ... [6s/17s] OK
• checking loading without being on the library search path ... [6s/19s] 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 ... [44s/77s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [60s/119s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [17s/25s] OK   Running ‘testthat.R’ [16s/24s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [171s/281s] ERROR Error(s) in re-building vignettes: --- re-building ‘vignette.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/CoSMoS.Rcheck/vign_test/CoSMoS/vignettes/vignette_files/figure-html/unnamed-chunk-1-1.png 672x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 20474 bytes Input file size = 21356 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19438   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 = 19438 Output IDAT size = 19438 bytes (1036 bytes decrease) Output file size = 19516 bytes (1840 bytes = 8.62% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/CoSMoS.Rcheck/vign_test/CoSMoS/vignettes/vignette_files/figure-html/unnamed-chunk-2-1.png 672x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 23339 bytes Input file size = 24221 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22369   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 22278   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 = 1 f = 0 IDAT size = 22278 Output IDAT size = 22278 bytes (1061 bytes decrease) Output file size = 22356 bytes (1865 bytes = 7.70% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/CoSMoS.Rcheck/vign_test/CoSMoS/vignettes/vignette_files/figure-html/unnamed-chunk-3-1.png 672x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 37082 bytes Input file size = 37208 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27056   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 = 27056 Output IDAT size = 27056 bytes (10026 bytes decrease) Output file size = 27134 bytes (10074 bytes = 27.07% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/CoSMoS.Rcheck/vign_test/CoSMoS/vignettes/vignette_files/figure-html/unnamed-chunk-4-1.png 672x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 19757 bytes Input file size = 20639 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18578   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 = 18578 Output IDAT size = 18578 bytes (1179 bytes decrease) Output file size = 18656 bytes (1983 bytes = 9.61% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/CoSMoS.Rcheck/vign_test/CoSMoS/vignettes/vignette_files/figure-html/unnamed-chunk-5-1.png 672x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 18842 bytes Input file size = 19724 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17605   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 = 17605 Output IDAT size = 17605 bytes (1237 bytes decrease) Output file size = 17683 bytes (2041 bytes = 10.35% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/CoSMoS.Rcheck/vign_test/CoSMoS/vignettes/vignette_files/figure-html/unnamed-chunk-6-1.png 672x672 pixels, 8 bits/pixel, 217 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 11997 bytes Input file size = 12750 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9880   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 = 9880 Output IDAT size = 9880 bytes (2117 bytes decrease) Output file size = 9958 bytes (2792 bytes = 21.90% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/CoSMoS.Rcheck/vign_test/CoSMoS/vignettes/vignette_files/figure-html/unnamed-chunk-8-1.png 672x672 pixels, 3x8 bits/pixel, RGB Input IDAT size = 44889 bytes Input file size = 45027 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 34971   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 = 34971 Output IDAT size = 34971 bytes (9918 bytes decrease) Output file size = 35049 bytes (9978 bytes = 22.16% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/CoSMoS.Rcheck/vign_test/CoSMoS/vignettes/vignette_files/figure-html/unnamed-chunk-9-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 22713 bytes Input file size = 23595 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20094   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 19978   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 = 1 f = 0 IDAT size = 19978 Output IDAT size = 19978 bytes (2735 bytes decrease) Output file size = 20056 bytes (3539 bytes = 15.00% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/CoSMoS.Rcheck/vign_test/CoSMoS/vignettes/vignette_files/figure-html/unnamed-chunk-10-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 26845 bytes Input file size = 27739 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24075   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 24072   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 = 1 f = 0 IDAT size = 24072 Output IDAT size = 24072 bytes (2773 bytes decrease) Output file size = 24150 bytes (3589 bytes = 12.94% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/CoSMoS.Rcheck/vign_test/CoSMoS/vignettes/vignette_files/figure-html/unnamed-chunk-12-1.png 672x624 pixels, 3x8 bits/pixel, RGB Input IDAT size = 81409 bytes Input file size = 81595 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 62186   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 = 62186 Output IDAT size = 62186 bytes (19223 bytes decrease) Output file size = 62264 bytes (19331 bytes = 23.69% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/CoSMoS.Rcheck/vign_test/CoSMoS/vignettes/vignette_files/figure-html/unnamed-chunk-12-2.png 672x624 pixels, 3x8 bits/pixel, RGB Input IDAT size = 105471 bytes Input file size = 105693 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 69214   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 = 69214 Output IDAT size = 69214 bytes (36257 bytes decrease) Output file size = 69292 bytes (36401 bytes = 34.44% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/CoSMoS.Rcheck/vign_test/CoSMoS/vignettes/vignette_files/figure-html/unnamed-chunk-13-1.png 384x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 171387 bytes Input file size = 171705 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 116213   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 = 116213 Output IDAT size = 116213 bytes (55174 bytes decrease) Output file size = 116291 bytes (55414 bytes = 32.27% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/CoSMoS.Rcheck/vign_test/CoSMoS/vignettes/vignette_files/figure-html/unnamed-chunk-14-1.png 672x672 pixels, 3x8 bits/pixel, RGB Input IDAT size = 275248 bytes Input file size = 275722 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 150241   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 = 150241 Output IDAT size = 150241 bytes (125007 bytes decrease) Output file size = 150319 bytes (125403 bytes = 45.48% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/CoSMoS.Rcheck/vign_test/CoSMoS/vignettes/vignette_files/figure-html/unnamed-chunk-15-1.png 672x672 pixels, 3x8 bits/pixel, RGB Input IDAT size = 225581 bytes Input file size = 225983 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 116304   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 = 116304 Output IDAT size = 116304 bytes (109277 bytes decrease) Output file size = 116382 bytes (109601 bytes = 48.50% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/CoSMoS.Rcheck/vign_test/CoSMoS/vignettes/vignette_files/figure-html/unnamed-chunk-16-1.png 672x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 16986 bytes Input file size = 17868 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15999   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 = 15999 Output IDAT size = 15999 bytes (987 bytes decrease) Output file size = 16077 bytes (1791 bytes = 10.02% decrease) Quitting from lines 405-412 [unnamed-chunk-17] (vignette.Rmd) Error: processing vignette 'vignette.Rmd' failed with diagnostics: 'to' must be a finite number --- failed re-building ‘vignette.Rmd’ SUMMARY: processing the following file failed:   ‘vignette.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [10s/12s] 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