* using log directory ‘/srv/hornik/tmp/CRAN/ToolsForCoDa.Rcheck’ * using R Under development (unstable) (2024-08-20 r87029) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘ToolsForCoDa/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ToolsForCoDa’ version ‘1.0.7’ * checking CRAN incoming feasibility ... [4s/5s] NOTE Maintainer: ‘Jan Graffelman ’ Found the following (possibly) invalid URLs: URL: From: inst/doc/ToolsForCoDa.html Message: Empty URL * 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 serialization versions ... OK * checking whether package ‘ToolsForCoDa’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [4s/4s] OK * checking Rd files ... [0s/0s] 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 ... [0s/0s] OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [1s/1s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [4s/4s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘ToolsForCoDa.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN/ToolsForCoDa.Rcheck/vign_test/ToolsForCoDa/vignettes/ToolsForCoDa_files/figure-html/unnamed-chunk-3-1.png 576x576 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 9308 bytes Input file size = 10178 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8038 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 = 8038 Output IDAT size = 8038 bytes (1270 bytes decrease) Output file size = 8116 bytes (2062 bytes = 20.26% decrease) ** Processing: /srv/hornik/tmp/CRAN/ToolsForCoDa.Rcheck/vign_test/ToolsForCoDa/vignettes/ToolsForCoDa_files/figure-html/unnamed-chunk-4-1.png 576x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 28239 bytes Input file size = 28353 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22809 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 = 22809 Output IDAT size = 22809 bytes (5430 bytes decrease) Output file size = 22887 bytes (5466 bytes = 19.28% decrease) ** Processing: /srv/hornik/tmp/CRAN/ToolsForCoDa.Rcheck/vign_test/ToolsForCoDa/vignettes/ToolsForCoDa_files/figure-html/ternaries-1.png 576x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15243 bytes Input file size = 16113 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14619 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 14505 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 = 14505 Output IDAT size = 14505 bytes (738 bytes decrease) Output file size = 14583 bytes (1530 bytes = 9.50% decrease) ** Processing: /srv/hornik/tmp/CRAN/ToolsForCoDa.Rcheck/vign_test/ToolsForCoDa/vignettes/ToolsForCoDa_files/figure-html/unnamed-chunk-14-1.png 576x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 92115 bytes Input file size = 92325 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 69512 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 = 69512 Output IDAT size = 69512 bytes (22603 bytes decrease) Output file size = 69590 bytes (22735 bytes = 24.62% decrease) ** Processing: /srv/hornik/tmp/CRAN/ToolsForCoDa.Rcheck/vign_test/ToolsForCoDa/vignettes/ToolsForCoDa_files/figure-html/unnamed-chunk-18-1.png 576x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27393 bytes Input file size = 27507 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22087 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 = 22087 Output IDAT size = 22087 bytes (5306 bytes decrease) Output file size = 22165 bytes (5342 bytes = 19.42% decrease) ** Processing: /srv/hornik/tmp/CRAN/ToolsForCoDa.Rcheck/vign_test/ToolsForCoDa/vignettes/ToolsForCoDa_files/figure-html/unnamed-chunk-27-1.png 576x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 19325 bytes Input file size = 19427 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16344 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 = 16344 Output IDAT size = 16344 bytes (2981 bytes decrease) Output file size = 16422 bytes (3005 bytes = 15.47% decrease) ** Processing: /srv/hornik/tmp/CRAN/ToolsForCoDa.Rcheck/vign_test/ToolsForCoDa/vignettes/ToolsForCoDa_files/figure-html/unnamed-chunk-28-1.png 576x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 12141 bytes Input file size = 12231 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9818 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 = 9818 Output IDAT size = 9818 bytes (2323 bytes decrease) Output file size = 9896 bytes (2335 bytes = 19.09% decrease) File ToolsForCoDA.bib not found in resource path Error: processing vignette 'ToolsForCoDa.Rmd' failed with diagnostics: pandoc document conversion failed with error 99 --- failed re-building ‘ToolsForCoDa.Rmd’ SUMMARY: processing the following file failed: ‘ToolsForCoDa.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE