DEXSeq 1.19.7
Alejandro Reyes
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEXSeq | | Last Changed Rev: 119799 / Revision: 121152 | | Last Changed Date: 2016-08-01 02:48:57 -0700 (Mon, 01 Aug 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf DEXSeq.buildbin-libdir DEXSeq.Rcheck && mkdir DEXSeq.buildbin-libdir DEXSeq.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEXSeq.buildbin-libdir DEXSeq_1.19.7.tar.gz >DEXSeq.Rcheck\00install.out 2>&1 && cp DEXSeq.Rcheck\00install.out DEXSeq-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DEXSeq.buildbin-libdir --install="check:DEXSeq-install.out" --force-multiarch --no-vignettes --timings DEXSeq_1.19.7.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/DEXSeq.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DEXSeq/DESCRIPTION' ... OK
* this is package 'DEXSeq' version '1.19.7'
* 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 ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
estimateExonFoldChanges 8.30 0.00 8.30
DEXSeqResults 7.71 0.03 7.77
methods-gr 6.56 0.02 6.58
perGeneQValue 6.53 0.00 6.54
testForDEU 6.52 0.00 6.52
estimateDispersions 5.39 0.01 5.42
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
estimateExonFoldChanges 8.74 0.00 8.74
methods-gr 7.42 0.02 7.44
DEXSeqResults 7.41 0.00 7.41
perGeneQValue 6.91 0.01 6.93
testForDEU 6.73 0.02 6.74
estimateDispersions 5.88 0.00 5.88
* 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: 1 NOTE
See
'D:/biocbld/bbs-3.4-bioc/meat/DEXSeq.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'DEXSeq' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'DEXSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEXSeq' as DEXSeq_1.19.7.zip
* DONE (DEXSeq)