* using log directory 'd:/RCompile/CRANincoming/R-devel/BPCells.Rcheck' * using R Under development (unstable) (2025-12-15 r89175 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * 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 ... 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 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 whether package 'BPCells' can be installed ... OK * used C++ compiler: 'g++.exe (GCC) 14.3.0' * checking C++ specification ... OK * checking installed package size ... 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 ... 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 whether startup messages can be suppressed ... 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 ... [27s] OK * checking Rd files ... 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 ... 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 ... WARNING File 'BPCells/libs/x64/BPCells.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Object: '../tools/highway/lib/libhwy.a' Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking examples ... [217s] NOTE Examples with CPU (user + system) or elapsed time > 10s user system elapsed trackplot_combine 34.14 5.34 32.23 gene_region 16.79 2.80 18.17 plot_tss_scatter 15.98 3.28 20.75 gene_scores 15.45 3.28 14.75 qc_scATAC 15.03 2.92 18.11 gene_score_tiles_archr 14.11 3.18 13.68 plot_tss_profile 14.86 2.18 13.48 trackplot_gene 12.77 2.61 11.41 trackplot_coverage 11.96 2.83 11.45 write_insertion_bedgraph 12.76 0.59 5.26 plot_embedding 13.11 0.09 13.11 * checking PDF version of manual ... [15s] OK * checking HTML version of manual ... [22s] 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:8870:1 (trackplot_calculate_segment_height.Rd:5): Warning: missing before
      BPCells.html:8884:1 (trackplot_calculate_segment_height.Rd:11): Warning: discarding unexpected * DONE Status: 1 WARNING, 4 NOTEs