############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:vsclust.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings vsclust_1.9.10.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/vsclust.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘vsclust/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘vsclust’ version ‘1.9.10’ * 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 ‘vsclust’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... NOTE enrichSTRING_API: no visible global function definition for ‘new’ runFuncEnrich: no visible global function definition for ‘compareCluster’ runFuncEnrich: no visible global function definition for ‘new’ Undefined global functions or variables: compareCluster new Consider adding importFrom("methods", "new") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE prepare_Rd: vsclust-package.Rd:29-31: Dropping empty section \seealso prepare_Rd: vsclust-package.Rd:32-33: Dropping empty section \examples * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link(s) in Rd file 'enrichSTRING_API.Rd': ‘enrichResult’ ‘clusterProfiler’ Missing link(s) in Rd file 'runFuncEnrich.Rd': ‘compareCluster’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: enrichSTRING_API.Rd: enrichResult, clusterProfiler runFuncEnrich.Rd: compareCluster Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed calcBHI 7.377 0.172 16.726 estimClust.plot 0.170 0.038 13.322 optimalClustNum 0.144 0.023 13.062 estimClustNum 0.094 0.014 11.952 runClustWrapper 0.035 0.004 8.397 ClustComp 0.016 0.005 8.264 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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 ‘Integrate_With_Bioconductor_Objects.Rmd’ using rmarkdown The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/vsclust.Rcheck/vign_test/vsclust/vignettes/Integrate_With_Bioconductor_Objects_files/figure-html/unnamed-chunk-3-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/vsclust.Rcheck/vign_test/vsclust/vignettes/Integrate_With_Bioconductor_Objects_files/figure-html/unnamed-chunk-3-2.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/vsclust.Rcheck/vign_test/vsclust/vignettes/Integrate_With_Bioconductor_Objects_files/figure-html/unnamed-chunk-4-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/vsclust.Rcheck/vign_test/vsclust/vignettes/Integrate_With_Bioconductor_Objects_files/figure-html/unnamed-chunk-5-1.png" but not available. --- finished re-building ‘Integrate_With_Bioconductor_Objects.Rmd’ --- re-building ‘Run_VSClust_Workflow.Rmd’ using rmarkdown The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/vsclust.Rcheck/vign_test/vsclust/vignettes/Run_VSClust_Workflow_files/figure-html/unnamed-chunk-3-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/vsclust.Rcheck/vign_test/vsclust/vignettes/Run_VSClust_Workflow_files/figure-html/unnamed-chunk-4-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/vsclust.Rcheck/vign_test/vsclust/vignettes/Run_VSClust_Workflow_files/figure-html/unnamed-chunk-5-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/vsclust.Rcheck/vign_test/vsclust/vignettes/Run_VSClust_Workflow_files/figure-html/unnamed-chunk-6-1.png" but not available. Quitting from lines 285-298 [unnamed-chunk-7] (Run_VSClust_Workflow.Rmd) Error: processing vignette 'Run_VSClust_Workflow.Rmd' failed with diagnostics: No result. IDs might not be matching or you do not have any significant enrichments --- failed re-building ‘Run_VSClust_Workflow.Rmd’ SUMMARY: processing the following file failed: ‘Run_VSClust_Workflow.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/vsclust.Rcheck/00check.log’ for details.