* using log directory ‘/srv/hornik/tmp/CRAN/SRTsim.Rcheck’ * using R Under development (unstable) (2024-08-17 r87027) * 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 ‘SRTsim/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SRTsim’ version ‘0.99.7’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/9s] Note_to_CRAN_maintainers Maintainer: ‘Jiaqiang Zhu ’ * 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 ‘SRTsim’ can be installed ... [11s/11s] 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 ... [3s/3s] OK * checking whether the package can be loaded with stated dependencies ... [3s/3s] OK * checking whether the package can be unloaded cleanly ... [3s/3s] OK * checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK * checking whether the namespace can be unloaded cleanly ... [3s/3s] OK * checking loading without being on the library search path ... [3s/3s] 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 ... [14s/14s] 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 ... [1s/1s] 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 ... [23s/23s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [20s/20s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘SRTsim.Rmd’ using rmarkdown The magick package is required to crop "/srv/hornik/tmp/CRAN/SRTsim.Rcheck/vign_test/SRTsim/vignettes/SRTsim_files/figure-html/tissue simulation metrics comparison-1.png" but not available. ** Processing: /srv/hornik/tmp/CRAN/SRTsim.Rcheck/vign_test/SRTsim/vignettes/SRTsim_files/figure-html/tissue simulation metrics comparison-1.png 1536x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 162172 bytes Input file size = 162478 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 134902 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 = 134902 Output IDAT size = 134902 bytes (27270 bytes decrease) Output file size = 134980 bytes (27498 bytes = 16.92% decrease) The magick package is required to crop "/srv/hornik/tmp/CRAN/SRTsim.Rcheck/vign_test/SRTsim/vignettes/SRTsim_files/figure-html/pattern comparison-1.png" but not available. The magick package is required to crop "/srv/hornik/tmp/CRAN/SRTsim.Rcheck/vign_test/SRTsim/vignettes/SRTsim_files/figure-html/pattern comparison-2.png" but not available. ** Processing: /srv/hornik/tmp/CRAN/SRTsim.Rcheck/vign_test/SRTsim/vignettes/SRTsim_files/figure-html/pattern comparison-1.png 1536x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 356854 bytes Input file size = 357448 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 307734 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 = 307734 Output IDAT size = 307734 bytes (49120 bytes decrease) Output file size = 307812 bytes (49636 bytes = 13.89% decrease) ** Processing: /srv/hornik/tmp/CRAN/SRTsim.Rcheck/vign_test/SRTsim/vignettes/SRTsim_files/figure-html/pattern comparison-2.png 1536x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 239151 bytes Input file size = 239577 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 198156 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 = 198156 Output IDAT size = 198156 bytes (40995 bytes decrease) Output file size = 198234 bytes (41343 bytes = 17.26% decrease) Quitting from lines 148-169 (SRTsim.Rmd) Error: processing vignette 'SRTsim.Rmd' failed with diagnostics: subscript out of bounds --- failed re-building ‘SRTsim.Rmd’ SUMMARY: processing the following file failed: ‘SRTsim.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