* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/liger.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (Debian 13.2.0-25) 13.2.0 GNU Fortran (Debian 13.2.0-25) 13.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘liger/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘liger’ version ‘2.0.1’ * 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 ‘liger’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/liger-00install.html' for details. * used C++ compiler: ‘g++-13 (Debian 13.2.0-25) 13.2.0’ * 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/1s] OK * checking whether the package can be unloaded cleanly ... [0s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/1s] 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 ... [5s/8s] OK * checking Rd files ... [0s/1s] 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 ... [4s/4s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [6s/7s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [14s/17s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘gsea.Rmd’ using rmarkdown Error: processing vignette 'gsea.Rmd' failed with diagnostics: The closing fence on line 87 ("````") in gsea.Rmd does not match the opening fence "```" on line 85. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘gsea.Rmd’ --- re-building ‘interpreting.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-2-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8741 bytes Input file size = 9611 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7175 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 = 7175 Output IDAT size = 7175 bytes (1566 bytes decrease) Output file size = 7253 bytes (2358 bytes = 24.53% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-5-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 65957 bytes Input file size = 66131 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53106 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 = 53106 Output IDAT size = 53106 bytes (12851 bytes decrease) Output file size = 53184 bytes (12947 bytes = 19.58% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-6-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 64262 bytes Input file size = 64424 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52688 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 = 52688 Output IDAT size = 52688 bytes (11574 bytes decrease) Output file size = 52766 bytes (11658 bytes = 18.10% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-7-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 73543 bytes Input file size = 73717 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 61626 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 = 61626 Output IDAT size = 61626 bytes (11917 bytes decrease) Output file size = 61704 bytes (12013 bytes = 16.30% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/liger.Rcheck/vign_test/liger/vignettes/interpreting_files/figure-html/unnamed-chunk-8-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 74745 bytes Input file size = 74931 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63424 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 = 63424 Output IDAT size = 63424 bytes (11321 bytes decrease) Output file size = 63502 bytes (11429 bytes = 15.25% decrease) --- finished re-building ‘interpreting.Rmd’ --- re-building ‘permpvals.Rmd’ using rmarkdown Error: processing vignette 'permpvals.Rmd' failed with diagnostics: The closing fence on line 69 ("````") in permpvals.Rmd does not match the opening fence "```" on line 67. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘permpvals.Rmd’ --- re-building ‘simulation.Rmd’ using rmarkdown Error: processing vignette 'simulation.Rmd' failed with diagnostics: The closing fence on line 93 ("````") in simulation.Rmd does not match the opening fence "```" on line 91. You are recommended to fix either the opening or closing fence of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info. --- failed re-building ‘simulation.Rmd’ SUMMARY: processing the following files failed: ‘gsea.Rmd’ ‘permpvals.Rmd’ ‘simulation.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [5s/7s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 ERROR