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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rsubread_2.25.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Rsubread.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* this is package ‘Rsubread’ version ‘2.25.0’
* 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 ‘Rsubread’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... INFO
  installed size is 36.8Mb
  sub-directories of 1Mb or more:
    annot  30.9Mb
    libs    1.1Mb
    qualf   3.4Mb
* 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 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 ... WARNING
Codoc mismatches from Rd file 'cellCounts.Rd':
cellCounts
  Code: function(index, sample, input.mode = "BCL", cell.barcode =
                 NULL, nsubreads = 15, minVotes = 1, maxMismatches =
                 10, minMappedLength = 1, annot.inbuilt = "mm39",
                 annot.ext = NULL, isGTFAnnotationFile = FALSE,
                 GTF.featureType = "exon", GTF.attrType = "gene_id",
                 useMetaFeatures = TRUE, detectJunctions = FALSE,
                 umi.cutoff = NULL, nthreads = 10, nBestLocations = 1,
                 uniqueMapping = FALSE, reportExcludedBarcodes = FALSE,
                 barcoding.mode = "Chromium", cell.level.junctions =
                 NULL, cell.cluster.map = NULL)
  Docs: function(index, sample, input.mode = "BCL", cell.barcode =
                 NULL, nsubreads = 15, minVotes = 1, maxMismatches =
                 10, minMappedLength = 1, annot.inbuilt = "mm39",
                 annot.ext = NULL, isGTFAnnotationFile = FALSE,
                 GTF.featureType = "exon", GTF.attrType = "gene_id",
                 useMetaFeatures = TRUE, detectJunctions = FALSE,
                 umi.cutoff = NULL, nthreads = 10, nBestLocations = 1,
                 uniqueMapping = FALSE, reportExcludedBarcodes = FALSE)
  Argument names in code not in docs:
    barcoding.mode cell.level.junctions cell.cluster.map

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rsubread/libs/Rsubread.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)

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. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
align      54.824 92.869 151.415
propmapped 53.941 93.050 150.941
sublong    15.098  2.275  17.684
buildindex  6.032  1.196   7.471
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/Rsubread.Rcheck/00check.log’
for details.