- using R Under development (unstable) (2024-06-17 r86769)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-14 (GCC) 14.1.0
GNU Fortran (GCC) 14.1.0
- running under: Fedora Linux 36 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘cubar/DESCRIPTION’ ... OK
- this is package ‘cubar’ version ‘0.5.0’
- 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 ‘cubar’ can be installed ... 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 ... 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 ... 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 ... [20s/20s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... OK
Running ‘testthat.R’
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [120s/124s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘cubar.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/cubar.Rcheck/vign_test/cubar/vignettes/cubar_files/figure-html/unnamed-chunk-5-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 36508 bytes
Input file size = 36634 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27458
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 = 27458
Output IDAT size = 27458 bytes (9050 bytes decrease)
Output file size = 27536 bytes (9098 bytes = 24.83% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/cubar.Rcheck/vign_test/cubar/vignettes/cubar_files/figure-html/unnamed-chunk-6-1.png
288x288 pixels, 8 bits/pixel, 241 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3431 bytes
Input file size = 4244 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3079
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 = 3079
Output IDAT size = 3079 bytes (352 bytes decrease)
Output file size = 3157 bytes (1087 bytes = 25.61% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/cubar.Rcheck/vign_test/cubar/vignettes/cubar_files/figure-html/unnamed-chunk-7-1.png
288x288 pixels, 8 bits/pixel, 241 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3340 bytes
Input file size = 4153 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2981
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 = 2981
Output IDAT size = 2981 bytes (359 bytes decrease)
Output file size = 3059 bytes (1094 bytes = 26.34% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/cubar.Rcheck/vign_test/cubar/vignettes/cubar_files/figure-html/unnamed-chunk-9-1.png
288x288 pixels, 8 bits/pixel, 243 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3321 bytes
Input file size = 4140 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2869
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 = 2869
Output IDAT size = 2869 bytes (452 bytes decrease)
Output file size = 2947 bytes (1193 bytes = 28.82% decrease)
trying URL 'http://gtrnadb.ucsc.edu/genomes/eukaryota/Scere3/sacCer3-mature-tRNAs.fa'
Quitting from lines 114-126 [unnamed-chunk-10] (cubar.Rmd)
Error: processing vignette 'cubar.Rmd' failed with diagnostics:
cannot open URL 'http://gtrnadb.ucsc.edu/genomes/eukaryota/Scere3/sacCer3-mature-tRNAs.fa'
--- failed re-building ‘cubar.Rmd’
--- re-building ‘non_standard_genetic_code.Rmd’ using rmarkdown
--- finished re-building ‘non_standard_genetic_code.Rmd’
SUMMARY: processing the following file failed:
‘cubar.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