Back to Multiple platform build/check report for BioC 3.11
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

CHECK report for GIGSEA on celaya2

This page was generated on 2020-01-16 13:51:30 -0500 (Thu, 16 Jan 2020).

Package 703/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GIGSEA 1.5.0
Shijia Zhu
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/GIGSEA
Branch: master
Last Commit: 965a3ca
Last Changed Date: 2019-10-29 13:43:15 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 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: GIGSEA
Version: 1.5.0
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_1.5.0.tar.gz
StartedAt: 2020-01-16 04:58:44 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 05:01:08 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 144.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GIGSEA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/GIGSEA.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.5.0’
* 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 (user + system) or elapsed time > 5s
                              user system elapsed
geneSet2Net                 18.245  2.810  22.452
geneSet2sparseMatrix        16.866  2.587  20.132
permutationMultipleLmMatrix  6.492  0.789   7.493
weightedMultipleLm           5.983  0.295   6.290
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GIGSEA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘GIGSEA’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GIGSEA)

Tests output


Example timings

GIGSEA.Rcheck/GIGSEA-Ex.timings

nameusersystemelapsed
geneSet2Net18.245 2.81022.452
geneSet2sparseMatrix16.866 2.58720.132
gmt2geneSet4.3350.0954.838
matrixPval0.0380.0030.044
orderedIntersect0.0990.0170.126
permutationMultipleLm0.0420.0090.052
permutationMultipleLmMatrix6.4920.7897.493
permutationSimpleLm0.0450.0110.057
permutationSimpleLmMatrix2.3980.7323.133
runGIGSEA0.0000.0000.001
weightedGSEA0.0220.0070.029
weightedMultipleLm5.9830.2956.290
weightedPearsonCorr0.1220.0430.166