Xi Wang
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/SeqGSEA |
| Branch: RELEASE_3_7 |
| Last Commit: 910d86d |
| Last Changed Date: 2018-04-30 10:35:29 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:37:08 -0400 (Wed, 17 Oct 2018).
| Package 1348/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SeqGSEA 1.20.0 Xi Wang
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: SeqGSEA |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SeqGSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SeqGSEA_1.20.0.tar.gz |
| StartedAt: 2018-10-17 04:46:40 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 04:54:50 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 490.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SeqGSEA.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SeqGSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SeqGSEA_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/SeqGSEA.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SeqGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeqGSEA' version '1.20.0'
* 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 'SeqGSEA' 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'estiExonProbVar'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DENBStatPermut4GSEA: no visible global function definition for
'%dopar%'
DENBStatPermut4GSEA: no visible global function definition for
'foreach'
DENBStatPermut4GSEA: no visible binding for global variable 'i'
DENBTest: no visible global function definition for 'p.adjust'
DEpermutePval: no visible global function definition for 'p.adjust'
DSpermute4GSEA: no visible global function definition for '%dopar%'
DSpermute4GSEA: no visible global function definition for 'foreach'
DSpermute4GSEA : <anonymous>: no visible binding for global variable
'i'
DSpermutePval: no visible global function definition for 'p.adjust'
calES.perm: no visible global function definition for '%dopar%'
calES.perm: no visible global function definition for 'foreach'
calES.perm: no visible binding for global variable 'i'
calES.perm: no visible global function definition for '%do%'
calES.perm: no visible binding for global variable 'j'
loadExonCountData : <anonymous>: no visible global function definition
for 'read.table'
plotES : <anonymous>: no visible global function definition for
'density'
plotES: no visible global function definition for 'density'
plotES: no visible global function definition for 'plot'
plotES : <anonymous>: no visible global function definition for
'points'
plotES: no visible global function definition for 'points'
plotES: no visible global function definition for 'colors'
plotES: no visible global function definition for 'lines'
plotES: no visible global function definition for 'legend'
plotES: no visible global function definition for 'dev.off'
plotGeneScore: no visible global function definition for 'plot'
plotGeneScore: no visible global function definition for 'lines'
plotGeneScore: no visible global function definition for 'colors'
plotGeneScore: no visible global function definition for 'points'
plotGeneScore: no visible global function definition for 'matlines'
plotGeneScore: no visible global function definition for 'legend'
plotGeneScore: no visible global function definition for 'dev.off'
plotSig: no visible global function definition for 'plot'
plotSig: no visible global function definition for 'points'
plotSig: no visible global function definition for 'colors'
plotSig: no visible global function definition for 'legend'
plotSig: no visible global function definition for 'dev.off'
plotSigGeneSet: no visible global function definition for 'par'
plotSigGeneSet: no visible global function definition for 'layout'
plotSigGeneSet: no visible global function definition for 'plot'
plotSigGeneSet: no visible global function definition for 'lines'
plotSigGeneSet : <anonymous>: no visible global function definition for
'lines'
plotSigGeneSet: no visible global function definition for 'colors'
plotSigGeneSet: no visible global function definition for 'text'
plotSigGeneSet: no visible global function definition for 'density'
plotSigGeneSet: no visible global function definition for 'legend'
plotSigGeneSet: no visible global function definition for 'dev.off'
runSeqGSEA: no visible global function definition for 'makeCluster'
runSeqGSEA: no visible global function definition for 'write.table'
signifES : <anonymous>: no visible global function definition for
'median'
writeScores: no visible global function definition for 'write.table'
writeSigGeneSet: no visible global function definition for
'write.table'
Undefined global functions or variables:
%do% %dopar% colors density dev.off foreach i j layout legend lines
makeCluster matlines median p.adjust par plot points read.table text
write.table
Consider adding
importFrom("grDevices", "colors", "dev.off")
importFrom("graphics", "layout", "legend", "lines", "matlines", "par",
"plot", "points", "text")
importFrom("stats", "density", "median", "p.adjust")
importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'SeqGeneSet,numeric,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runSeqGSEA 18.41 0.11 31.59
topDSExons 10.83 0.02 10.84
normFactor 10.74 0.03 10.77
topDSGenes 10.56 0.00 10.57
DSresultGeneTable 9.83 0.00 9.83
scoreNormalization 9.08 0.03 9.11
genpermuteMat 8.43 0.01 8.46
DSresultExonTable 7.90 0.00 7.92
DSpermute4GSEA 7.70 0.03 7.73
DSpermutePval 7.55 0.00 7.55
loadGenesets 1.26 0.02 8.67
convertSymbol2Ensembl 0.25 0.00 6.54
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runSeqGSEA 15.92 0.07 33.70
DSresultGeneTable 11.84 0.00 11.84
normFactor 9.63 0.00 9.63
topDSGenes 9.57 0.00 9.58
DSpermutePval 9.53 0.00 9.53
genpermuteMat 9.25 0.00 9.25
topDSExons 9.13 0.00 9.13
DSresultExonTable 8.94 0.00 8.94
scoreNormalization 8.80 0.00 8.80
DSpermute4GSEA 8.18 0.00 8.17
convertSymbol2Ensembl 0.28 0.01 7.09
* 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 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/SeqGSEA.Rcheck/00check.log'
for details.
SeqGSEA.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/SeqGSEA_1.20.0.tar.gz && rm -rf SeqGSEA.buildbin-libdir && mkdir SeqGSEA.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SeqGSEA.buildbin-libdir SeqGSEA_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL SeqGSEA_1.20.0.zip && rm SeqGSEA_1.20.0.tar.gz SeqGSEA_1.20.0.zip
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install for i386
* installing *source* package 'SeqGSEA' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SeqGSEA'
finding HTML links ... done
DENBStat4GSEA html
DENBStatPermut4GSEA html
DENBTest html
DEpermutePval html
DEscore html
DSpermute4GSEA html
DSpermutePval html
DSresultExonTable html
DSresultGeneTable html
GSEAresultTable html
GSEnrichAnalyze html
GS_example html
RCS_example html
ReadCountSet-class html
finding level-2 HTML links ... done
SeqGSEA-package html
SeqGeneSet-class html
calES html
calES.perm html
convertEnsembl2Symbol html
convertSymbol2Ensembl html
counts-methods html
estiExonNBstat html
estiGeneNBstat html
exonID html
exonTestability html
geneID html
geneList html
genePermuteScore html
geneScore html
geneSetDescs html
geneSetNames html
geneSetSize html
geneTestability html
genpermuteMat html
getGeneCount html
label html
loadExonCountData html
loadGenesets html
newGeneSets html
newReadCountSet html
normES html
normFactor html
plotES html
plotGeneScore html
plotSig html
plotSigGeneSet html
rankCombine html
runDESeq html
runSeqGSEA html
scoreNormalization html
signifES html
size html
subsetByGenes html
topDEGenes html
topDSExons html
topDSGenes html
topGeneSets html
writeScores html
writeSigGeneSet html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'SeqGSEA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SeqGSEA' as SeqGSEA_1.20.0.zip
* DONE (SeqGSEA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'SeqGSEA' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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SeqGSEA.Rcheck/examples_i386/SeqGSEA-Ex.timings
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SeqGSEA.Rcheck/examples_x64/SeqGSEA-Ex.timings
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