Package: DEXSeq

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DEXSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DEXSeq_1.32.0.tar.gz

StartedAt: 2020-04-15 01:48:19 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:53:51 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 332.0 seconds

RetCode: 0

Status:  OK

CheckDir: DEXSeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DEXSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DEXSeq_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/DEXSeq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEXSeq/DESCRIPTION’ ... OK
* this is package ‘DEXSeq’ version ‘1.32.0’
* 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_34629d61ee6b0221ac68c81be6b6781e.RData
  DEXSeq/vignettes/DEXSeq_cache/html/buildExonCountSetDownloadAnno_3ed574a4b24e97d3f74ff7d580fb9304.RData
  DEXSeq/vignettes/DEXSeq_cache/html/buildExonCountSetDownloadAnno_3ed574a4b24e97d3f74ff7d580fb9304.rdb
  DEXSeq/vignettes/DEXSeq_cache/html/buildExonCountSetDownloadAnno_3ed574a4b24e97d3f74ff7d580fb9304.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 or elapsed time > 5s
                          user system elapsed
DEXSeqResults           12.539  0.083  12.734
methods-gr              11.421  0.042  11.831
perGeneQValue           11.352  0.049  11.506
estimateExonFoldChanges 10.625  0.069  10.780
testForDEU               9.510  0.038   9.631
estimateDispersions      7.721  0.034   7.812
* 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-3.10-bioc/meat/DEXSeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DEXSeq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘DEXSeq’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DEXSeq)

name	user	system	elapsed
DEXSeq	0.001	0.001	0.000
DEXSeqDataSet	0.000	0.001	0.001
DEXSeqHTML	0.000	0.000	0.001
DEXSeqResults	12.539	0.083	12.734
accessors	0.280	0.004	0.283
counts	0.019	0.003	0.021
estimateDispersions	7.721	0.034	7.812
estimateExonFoldChanges	10.625	0.069	10.780
methods-gr	11.421	0.042	11.831
perGeneQValue	11.352	0.049	11.506
plotDEXSeq	0	0	0
plotMA	0	0	0
testForDEU	9.510	0.038	9.631