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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DEXSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DEXSeq_1.42.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/DEXSeq.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEXSeq/DESCRIPTION’ ... OK
* this is package ‘DEXSeq’ version ‘1.42.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocParallel', 'Biobase', 'SummarizedExperiment', 'IRanges',
  'GenomicRanges', 'DESeq2', 'AnnotationDbi', 'RColorBrewer',
  'S4Vectors'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... NOTE
Found the following non-portable file paths:
  DEXSeq/vignettes/DEXSeq_cache/html/buildExonCountSet2FindBAMs2_4b49fbfbdb6be189c81e955b20383f0c.RData
  DEXSeq/vignettes/DEXSeq_cache/html/buildExonCountSetDownloadAnno_b75367c7fe90529cfb51eb7230691ce2.RData
  DEXSeq/vignettes/DEXSeq_cache/html/buildExonCountSetDownloadAnno_b75367c7fe90529cfb51eb7230691ce2.rdb
  DEXSeq/vignettes/DEXSeq_cache/html/buildExonCountSetDownloadAnno_b75367c7fe90529cfb51eb7230691ce2.rdx

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DEXSeq’ can be installed ... OK
* checking installed package size ... OK
* 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 R 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
DEXSeqResults           17.756  0.220  17.998
estimateExonFoldChanges 17.027  0.048  17.104
methods-gr              16.438  0.047  16.851
perGeneQValue           15.878  0.034  15.948
testForDEU              14.110  0.113  14.241
estimateDispersions     12.318  0.026  12.363
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/DEXSeq.Rcheck/00check.log’
for details.