• using R Under development (unstable) (2025-02-19 r87749)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 20.1.0-rc2     flang version 20.1.0-rc2
• running under: Fedora Linux 40 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘GeoTox/DESCRIPTION’ ... OK
• this is package ‘GeoTox’ version ‘0.2.0’
• 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 ‘GeoTox’ can be installed ... [10s/16s] 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 ... 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 ... [15s/20s] 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 ... [96s/119s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [31s/35s] OK   Running ‘testthat.R’ [30s/35s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [30m/36m] ERROR Error(s) in re-building vignettes: --- re-building ‘introduction.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/GeoTox.Rcheck/vign_test/GeoTox/vignettes/introduction_files/figure-html/unnamed-chunk-3-1.png 672x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 26302 bytes Input file size = 26416 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20429   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 = 20429 Output IDAT size = 20429 bytes (5873 bytes decrease) Output file size = 20507 bytes (5909 bytes = 22.37% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/GeoTox.Rcheck/vign_test/GeoTox/vignettes/introduction_files/figure-html/unnamed-chunk-3-2.png 672x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 30020 bytes Input file size = 30134 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25906   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 = 25906 Output IDAT size = 25906 bytes (4114 bytes decrease) Output file size = 25984 bytes (4150 bytes = 13.77% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/GeoTox.Rcheck/vign_test/GeoTox/vignettes/introduction_files/figure-html/unnamed-chunk-3-3.png 672x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 37871 bytes Input file size = 37997 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31676   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 = 31676 Output IDAT size = 31676 bytes (6195 bytes decrease) Output file size = 31754 bytes (6243 bytes = 16.43% decrease) --- re-building ‘package_data.Rmd’ using rmarkdown --- finished re-building ‘package_data.Rmd’ SUMMARY: processing the following file failed:   ‘introduction.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [8s/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