• using R Under development (unstable) (2024-12-18 r87448)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.5 (1)     Debian flang-new version 19.1.5 (1)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘easybio/DESCRIPTION’ ... OK
• this is package ‘easybio’ version ‘1.1.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘fgsea’
• 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 ‘easybio’ can be installed ... OK See the install log for details.
• 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 ... [2s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the package can be unloaded cleanly ... [1s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
• checking loading without being on the library search path ... [2s/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 ... [10s/13s] OK
• checking Rd files ... [1s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... INFO Package unavailable to check Rd xrefs: ‘fgsea’
• 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 R/sysdata.rda ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [4s/5s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [2s/3s] OK   Running ‘testthat.R’ [2s/2s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [11s/16s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘example-bulk-rna-seq-workflow.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/easybio.Rcheck/vign_test/easybio/vignettes/example-bulk-rna-seq-workflow_files/figure-html/unnamed-chunk-5-1.png 480x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 37293 bytes Input file size = 37419 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26826   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 = 26826 Output IDAT size = 26826 bytes (10467 bytes decrease) Output file size = 26904 bytes (10515 bytes = 28.10% decrease) Quitting from lines 142-145 [unnamed-chunk-8] (example-bulk-rna-seq-workflow.Rmd) Error: processing vignette 'example-bulk-rna-seq-workflow.Rmd' failed with diagnostics: there is no package called 'fgsea' --- failed re-building ‘example-bulk-rna-seq-workflow.Rmd’ --- re-building ‘example-single-cell-annotation.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/easybio.Rcheck/vign_test/easybio/vignettes/example-single-cell-annotation_files/figure-html/unnamed-chunk-4-1.png 720x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 38828 bytes Input file size = 38954 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33406   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 = 33406 Output IDAT size = 33406 bytes (5422 bytes decrease) Output file size = 33484 bytes (5470 bytes = 14.04% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/easybio.Rcheck/vign_test/easybio/vignettes/example-single-cell-annotation_files/figure-html/unnamed-chunk-9-1.png 720x672 pixels, 3x8 bits/pixel, RGB Input IDAT size = 89061 bytes Input file size = 89259 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 73263   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 = 73263 Output IDAT size = 73263 bytes (15798 bytes decrease) Output file size = 73341 bytes (15918 bytes = 17.83% decrease) --- finished re-building ‘example-single-cell-annotation.Rmd’ SUMMARY: processing the following file failed:   ‘example-bulk-rna-seq-workflow.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR