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CHECK report for npGSEA on celaya2

This page was generated on 2019-10-16 12:53:06 -0400 (Wed, 16 Oct 2019).

Package 1113/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
npGSEA 1.20.0
Jessica Larson
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/npGSEA
Branch: RELEASE_3_9
Last Commit: b247f6f
Last Changed Date: 2019-05-02 11:53:47 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: npGSEA
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:npGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings npGSEA_1.20.0.tar.gz
StartedAt: 2019-10-16 05:08:21 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:10:42 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 140.7 seconds
RetCode: 0
Status:  OK 
CheckDir: npGSEA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:npGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings npGSEA_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/npGSEA.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘npGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘npGSEA’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘npGSEA’ 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
* 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
.prepXYZ: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/npGSEA.Rcheck/00check.log’
for details.



Installation output

npGSEA.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL npGSEA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘npGSEA’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘BiocGenerics’ for request: ‘unlist’ when loading ‘npGSEA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘BiocGenerics’ for request: ‘unlist’ when loading ‘npGSEA’
** testing if installed package can be loaded from final location
No methods found in package ‘BiocGenerics’ for request: ‘unlist’ when loading ‘npGSEA’
** testing if installed package keeps a record of temporary installation path
* DONE (npGSEA)

Tests output


Example timings

npGSEA.Rcheck/npGSEA-Ex.timings

nameusersystemelapsed
DF-methods0.0190.0040.024
alphaValue-methods0.0060.0020.009
betaHats-methods0.0050.0010.006
betaStat-methods0.0040.0010.006
betaValue-methods0.0050.0010.006
chiSqStat-methods0.0090.0020.011
geneSetName-methods0.0040.0010.004
getIncidence0.0010.0000.002
npGSEA0.0040.0000.004
npGSEAPlot-methods0.0030.0010.004
npGSEAResultBeta-class0.0020.0010.002
npGSEAResultBetaCollection-class0.0010.0010.002
npGSEAResultChiSq-class0.0010.0010.002
npGSEAResultChiSqCollection-class0.0010.0000.002
npGSEAResultNorm-class0.0010.0000.001
npGSEAResultNormCollection-class0.0010.0010.002
pLeft-methods0.0060.0020.007
pRight-methods0.0050.0020.006
pTwoSided-methods0.0060.0020.007
pValues-methods0.0060.0020.008
show-methods0.0060.0010.007
sigmaSq-methods0.0060.0010.007
stat-methods0.0060.0010.008
xSet-methods0.0080.0030.010
zStat-methods0.0050.0010.007