EGSEA 1.4.1
Monther Alhamdoosh
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/EGSEA | | Branch: RELEASE_3_5 | | Last Commit: cf3c1a9 | | Last Changed Date: 2017-07-19 23:15:42 -0400 (Wed, 19 Jul 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / 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 && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EGSEA.buildbin-libdir EGSEA_1.4.1.tar.gz >EGSEA.Rcheck\00install.out 2>&1 && cp EGSEA.Rcheck\00install.out EGSEA-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=EGSEA.buildbin-libdir --install="check:EGSEA-install.out" --force-multiarch --no-vignettes --timings EGSEA_1.4.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/EGSEA.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.4.1'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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'
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'
plotBars,EGSEAResults: no visible global function definition for
'abline'
Undefined global functions or variables:
GOTERM abline gsSize id kegg.pathways msigdb sig x.data y.data
Consider adding
importFrom("graphics", "abline")
to your NAMESPACE file.
* 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 74.85 1.49 79.25
buildGeneSetDBIdx 26.52 0.19 26.93
egsea 25.23 0.13 25.38
egsea.cnt 21.11 0.01 21.34
buildIdx 9.62 0.13 10.24
buildMSigDBIdx 5.72 0.09 5.81
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
EGSEAResults-methods 84.88 0.99 88.38
buildGeneSetDBIdx 31.14 0.25 31.39
egsea 27.78 0.08 27.86
egsea.cnt 24.31 0.02 24.33
buildIdx 9.21 0.03 9.24
buildMSigDBIdx 7.02 0.03 7.04
* 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
'C:/Users/biocbuild/bbs-3.5-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_1.4.1.zip
* DONE (EGSEA)