* using log directory ‘/srv/hornik/tmp/CRAN_pretest/BPCells.Rcheck’ * using R Under development (unstable) (2025-12-16 r89178) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.6 (2) Debian flang version 21.1.6 (2) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘BPCells/DESCRIPTION’ ... OK * this is package ‘BPCells’ version ‘0.3.2’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/7s] NOTE Maintainer: ‘Benjamin Parks ’ New submission Possibly misspelled words in DESCRIPTION: ATAC (13:51) Suggests or Enhances not in mainstream repositories: chromVARmotifs Availability using Additional_repositories specification: chromVARmotifs yes https://bpcells.github.io/drat ? ? https://bioconductor.org/packages/release/data/annotation Found the following (possibly) invalid URLs: URL: http://www.informatics.jax.org/downloads/reports/MGI_EntrezGene.rpt (moved to https://www.informatics.jax.org:443/downloads/reports/MGI_EntrezGene.rpt) From: man/gene_mapping.Rd Status: 301 Message: Moved Permanently URL: http://www.informatics.jax.org/downloads/reports/MRK_ENSEMBL.rpt (moved to https://www.informatics.jax.org:443/downloads/reports/MRK_ENSEMBL.rpt) From: man/gene_mapping.Rd Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: ‘chromVARmotifs’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... WARNING Found the following executable file: tools/cxx17_filesystem Source packages should not contain undeclared executable files. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .gemini These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. CRAN-pack does not know about .gemini * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘BPCells’ can be installed ... [500s/502s] OK * used C++ compiler: ‘Debian clang version 21.1.6 (3)’ * checking C++ specification ... OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [2s/2s] OK * checking whether startup messages can be suppressed ... [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 ... [23s/23s] 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 line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... [240s/202s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed trackplot_combine 35.277 5.804 31.891 plot_tss_scatter 18.854 3.776 20.897 qc_scATAC 16.808 3.373 17.973 gene_scores 16.759 2.944 15.097 gene_region 16.555 3.106 15.486 plot_tss_profile 15.288 2.533 13.381 gene_score_tiles_archr 13.889 3.132 12.545 trackplot_coverage 13.551 2.640 11.613 trackplot_gene 13.685 2.504 11.618 write_insertion_bedgraph 8.750 0.240 3.495 plot_embedding 5.425 0.053 5.533 Examples with CPU time > 2.5 times elapsed time user system elapsed ratio write_insertion_bedgraph 8.75 0.24 3.495 2.572 * checking PDF version of manual ... [5s/5s] OK * checking HTML version of manual ... [4s/4s] NOTE Found the following HTML validation problems: trackplot_calculate_segment_height.html:19:1 (trackplot_calculate_segment_height.Rd:5): Warning: missing before
    trackplot_calculate_segment_height.html:33:1 (trackplot_calculate_segment_height.Rd:11): Warning: discarding unexpected BPCells.html:8866:1 (trackplot_calculate_segment_height.Rd:5): Warning: missing before
      BPCells.html:8880:1 (trackplot_calculate_segment_height.Rd:11): Warning: discarding unexpected * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 WARNING, 4 NOTEs