DEXSeq 1.18.4
Alejandro Reyes
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/DEXSeq | | Last Changed Rev: 117634 / Revision: 122332 | | Last Changed Date: 2016-05-18 07:20:52 -0700 (Wed, 18 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| oaxaca | 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 && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEXSeq.buildbin-libdir DEXSeq_1.18.4.tar.gz >DEXSeq.Rcheck\00install.out 2>&1 && cp DEXSeq.Rcheck\00install.out DEXSeq-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=DEXSeq.buildbin-libdir --install="check:DEXSeq-install.out" --force-multiarch --no-vignettes --timings DEXSeq_1.18.4.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-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 '1.18.4'
* 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 10.26 0.02 10.34
methods-gr 9.50 0.00 9.50
DEXSeqResults 8.67 0.00 8.80
testForDEU 8.11 0.02 8.12
perGeneQValue 7.79 0.01 7.80
estimateDispersions 6.88 0.01 6.90
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
estimateExonFoldChanges 11.90 0.00 12.23
perGeneQValue 10.88 0.01 10.88
testForDEU 10.61 0.00 10.61
methods-gr 10.53 0.02 10.55
DEXSeqResults 8.91 0.01 8.93
estimateDispersions 8.39 0.00 8.39
* 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
'E:/biocbld/bbs-3.3-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_1.18.4.zip
* DONE (DEXSeq)