EGSEA 1.1.10
Monther Alhamdoosh
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/EGSEA | | Last Changed Rev: 120926 / Revision: 121152 | | Last Changed Date: 2016-09-13 21:56:21 -0700 (Tue, 13 Sep 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf EGSEA.buildbin-libdir EGSEA.Rcheck && mkdir EGSEA.buildbin-libdir EGSEA.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EGSEA.buildbin-libdir EGSEA_1.1.10.tar.gz >EGSEA.Rcheck\00install.out 2>&1 && cp EGSEA.Rcheck\00install.out EGSEA-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=EGSEA.buildbin-libdir --install="check:EGSEA-install.out" --force-multiarch --no-vignettes --timings EGSEA_1.1.10.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/EGSEA.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 'EGSEA/DESCRIPTION' ... OK
* this is package 'EGSEA' version '1.1.10'
* 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 whether package 'EGSEA' 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 ... NOTE
buildGeneSetDBIdx: no visible binding for global variable 'GOTERM'
buildMSigDBIdx: no visible binding for global variable 'msigdb'
buildMSigDBIdx: no visible binding for global variable 'GOTERM'
generateSummaryPlots: no visible binding for global variable 'x.data'
generateSummaryPlots: no visible binding for global variable 'y.data'
generateSummaryPlots: no visible binding for global variable 'gsSize'
generateSummaryPlots: no visible binding for global variable 'id'
generateSummaryPlots: no visible binding for global variable 'sig'
loadKeggData: no visible binding for global variable 'kegg.pathways'
Undefined global functions or variables:
GOTERM gsSize id kegg.pathways msigdb sig x.data y.data
* 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
EGSEAResults-methods 76.71 0.89 80.65
buildGeneSetDBIdx 29.18 0.14 29.85
egsea 21.37 0.07 21.44
egsea.cnt 20.62 0.01 20.72
buildIdx 7.39 0.05 7.72
buildMSigDBIdx 6.32 0.09 6.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
EGSEAResults-methods 88.67 1.06 91.05
buildGeneSetDBIdx 35.93 0.16 36.08
egsea.cnt 25.60 0.00 25.60
egsea 25.23 0.00 25.24
buildIdx 7.08 0.02 7.10
buildMSigDBIdx 6.68 0.03 6.74
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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: 1 NOTE
See
'D:/biocbld/bbs-3.4-bioc/meat/EGSEA.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'EGSEA' ...
** R
** inst
** preparing package for lazy loading
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
install for x64
* installing *source* package 'EGSEA' ...
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'EGSEA' as EGSEA_1.1.10.zip
* DONE (EGSEA)