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BioC 3.4: CHECK report for npGSEA on morelia

This page was generated on 2016-09-21 03:53:14 -0700 (Wed, 21 Sep 2016).

Package 826/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
npGSEA 1.9.0
Jessica Larson
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/npGSEA
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: npGSEA
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings npGSEA_1.9.0.tar.gz
StartedAt: 2016-09-20 10:40:03 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:41:16 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 73.3 seconds
RetCode: 0
Status:  OK 
CheckDir: npGSEA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings npGSEA_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/npGSEA.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.9.0’
* 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 installed files from ‘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-3.4-bioc/meat/npGSEA.Rcheck/00check.log’
for details.


npGSEA.Rcheck/00install.out:

* installing *source* package ‘npGSEA’ ...
** R
** inst
** preparing package for lazy loading
No methods found in "BiocGenerics" for requests: unlist
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: unlist
* DONE (npGSEA)

npGSEA.Rcheck/npGSEA-Ex.timings:

nameusersystemelapsed
DF-methods0.0130.0010.013
alphaValue-methods0.0060.0000.006
betaHats-methods0.0040.0000.005
betaStat-methods0.0040.0000.003
betaValue-methods0.0030.0000.004
chiSqStat-methods0.0070.0000.007
geneSetName-methods0.0030.0000.003
getIncidence0.0010.0000.001
npGSEA0.0030.0000.003
npGSEAPlot-methods0.0030.0000.003
npGSEAResultBeta-class0.0010.0010.002
npGSEAResultBetaCollection-class0.0010.0000.002
npGSEAResultChiSq-class0.0020.0000.002
npGSEAResultChiSqCollection-class0.0010.0000.001
npGSEAResultNorm-class0.0010.0000.001
npGSEAResultNormCollection-class0.0010.0000.001
pLeft-methods0.0040.0000.005
pRight-methods0.0050.0000.005
pTwoSided-methods0.0040.0010.004
pValues-methods0.0040.0000.004
show-methods0.0040.0000.004
sigmaSq-methods0.0050.0000.004
stat-methods0.0040.0000.004
xSet-methods0.0050.0010.006
zStat-methods0.0040.0000.005