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CHECK report for GIGSEA on merida1

This page was generated on 2019-04-16 12:10:15 -0400 (Tue, 16 Apr 2019).

Package 648/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GIGSEA 1.0.0
Shijia Zhu
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/GIGSEA
Branch: RELEASE_3_8
Last Commit: 945edad
Last Changed Date: 2018-10-30 11:42:09 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GIGSEA
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GIGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GIGSEA_1.0.0.tar.gz
StartedAt: 2019-04-16 00:17:24 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:19:04 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 100.6 seconds
RetCode: 0
Status:  OK 
CheckDir: GIGSEA.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GIGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GIGSEA_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/GIGSEA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GIGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GIGSEA’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘GIGSEA’ 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
geneSet2Net                 13.820  1.570  15.771
geneSet2sparseMatrix        12.359  1.485  14.276
permutationMultipleLmMatrix  5.927  0.394   6.482
weightedMultipleLm           5.447  0.093   5.615
* 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: OK


Installation output

GIGSEA.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GIGSEA
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘GIGSEA’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GIGSEA)

Tests output


Example timings

GIGSEA.Rcheck/GIGSEA-Ex.timings

nameusersystemelapsed
geneSet2Net13.820 1.57015.771
geneSet2sparseMatrix12.359 1.48514.276
gmt2geneSet3.1630.0333.508
matrixPval0.0270.0010.027
orderedIntersect0.0770.0090.086
permutationMultipleLm0.0420.0060.047
permutationMultipleLmMatrix5.9270.3946.482
permutationSimpleLm0.0280.0040.031
permutationSimpleLmMatrix1.4780.3181.814
runGIGSEA0.0010.0000.000
weightedGSEA0.0180.0030.021
weightedMultipleLm5.4470.0935.615
weightedPearsonCorr0.0970.0280.126