* using log directory ‘/srv/hornik/tmp/CRAN_pretest/BPCells.Rcheck’
* using R Under development (unstable) (2026-01-07 r89288)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (1)
    Debian flang version 21.1.8 (1)
* 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/6s] NOTE
Maintainer: ‘Benjamin Parks <bparks@alumni.stanford.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  ATAC (13:51)

Suggests or Enhances not in mainstream repositories:
  TFMPvalue, chromVARmotifs
Availability using Additional_repositories specification:
  TFMPvalue        yes   https://bpcells.github.io/drat                           
  chromVARmotifs   yes   https://bpcells.github.io/drat                           
  ?                  ?   https://bioconductor.org/packages/release/data/annotation
* checking package namespace information ... OK
* checking package dependencies ... INFO
Packages suggested but not available for checking:
  'TFMPvalue', 'motifmatchr', 'chromVARmotifs'
* 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 whether package ‘BPCells’ can be installed ... [502s/505s] OK
* used C++ compiler: ‘Debian clang version 21.1.8 (1+b1)’
* checking C++ specification ... INFO
  specified C++17
* 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 ... [247s/206s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
trackplot_combine        36.198  5.969  32.814
plot_tss_scatter         18.855  4.294  21.246
qc_scATAC                17.337  4.090  18.942
gene_region              16.512  3.618  15.793
gene_scores              16.509  3.418  15.308
plot_tss_profile         15.639  3.021  14.022
gene_score_tiles_archr   14.538  3.087  12.992
trackplot_coverage       13.966  2.763  12.093
trackplot_gene           13.986  2.702  12.071
write_insertion_bedgraph  9.287  0.285   3.552
plot_embedding            5.417  0.086   5.482
Examples with CPU time > 2.5 times elapsed time
                          user system elapsed ratio
write_insertion_bedgraph 9.287  0.285   3.552 2.695
* checking PDF version of manual ... [5s/5s] OK
* checking HTML version of manual ... [4s/4s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 NOTEs