############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ChIPpeakAnno_3.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ChIPpeakAnno.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChIPpeakAnno’ version ‘3.39.0’ * package encoding: UTF-8 * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ChIPpeakAnno’ can be installed ... OK * checking installed package size ... NOTE installed size is 21.1Mb sub-directories of 1Mb or more: R 1.0Mb data 12.6Mb extdata 7.2Mb * checking package directory ... 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... OK * checking Rd files ... OK * checking Rd metadata ... 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 ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed findEnhancers 20.930 0.276 21.206 findMotifsInPromoterSeqs 12.539 0.157 12.712 annotatePeakInBatch 11.317 0.496 11.814 summarizeOverlapsByBins 5.416 0.439 5.590 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘ChIPpeakAnno.Rmd’ using rmarkdown The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/ChIPpeakAnno.Rcheck/vign_test/ChIPpeakAnno/vignettes/ChIPpeakAnno_files/figure-html/unnamed-chunk-9-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/ChIPpeakAnno.Rcheck/vign_test/ChIPpeakAnno/vignettes/ChIPpeakAnno_files/figure-html/unnamed-chunk-9-2.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/ChIPpeakAnno.Rcheck/vign_test/ChIPpeakAnno/vignettes/ChIPpeakAnno_files/figure-html/unnamed-chunk-9-3.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/ChIPpeakAnno.Rcheck/vign_test/ChIPpeakAnno/vignettes/ChIPpeakAnno_files/figure-html/unnamed-chunk-11-1.png" but not available. Quitting from lines 324-339 [unnamed-chunk-14] (ChIPpeakAnno.Rmd) Error: processing vignette 'ChIPpeakAnno.Rmd' failed with diagnostics: failed to load resource name: AH53222 title: Ensembl 87 EnsDb for Mus Musculus reason: file is not a database --- failed re-building ‘ChIPpeakAnno.Rmd’ SUMMARY: processing the following file failed: ‘ChIPpeakAnno.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’ for details.