* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SCIntRuler.Rcheck’ * using R Under development (unstable) (2025-07-14 r88410) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (Debian 14.2.0-19) 14.2.0 GNU Fortran (Debian 14.2.0-19) 14.2.0 * running under: Debian GNU/Linux 13 (trixie) * using session charset: UTF-8 * checking for file ‘SCIntRuler/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SCIntRuler’ version ‘0.99.6’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [1s/1s] OK * 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 ‘SCIntRuler’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/SCIntRuler-00install.html' for details. * used C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ * 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 ... [11s/14s] OK * checking whether the package can be loaded with stated dependencies ... [9s/11s] OK * checking whether the package can be unloaded cleanly ... [9s/11s] OK * checking whether the namespace can be loaded with stated dependencies ... [9s/11s] OK * checking whether the namespace can be unloaded cleanly ... [10s/13s] OK * checking loading without being on the library search path ... [10s/11s] 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 ... [41s/52s] 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 ... [8s/10s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [17s/23s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed NormData 4.157 0.271 5.097 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [28s/37s] OK Running ‘testthat.R’ [27s/37s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [55s/72s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘SCIntRuler.Rmd’ using rmarkdown Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| The magick package is required to crop "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SCIntRuler.Rcheck/vign_test/SCIntRuler/vignettes/SCIntRuler_files/figure-html/UMAP -1.png" but not available. The magick package is required to crop "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SCIntRuler.Rcheck/vign_test/SCIntRuler/vignettes/SCIntRuler_files/figure-html/UMAP2 -1.png" but not available. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Quitting from SCIntRuler.Rmd:166-200 [integration] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'SCIntRuler.Rmd' failed with diagnostics: `grobs` must be a single grob or a list of grobs, not a list. --- failed re-building ‘SCIntRuler.Rmd’ SUMMARY: processing the following file failed: ‘SCIntRuler.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [5s/6s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 ERROR