Back to Multiple platform build/check report for BioC 3.9
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

CHECK report for GIGSEA on celaya2

This page was generated on 2019-10-16 13:02:41 -0400 (Wed, 16 Oct 2019).

Package 679/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GIGSEA 1.2.0
Shijia Zhu
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GIGSEA
Branch: RELEASE_3_9
Last Commit: 91bc1cd
Last Changed Date: 2019-05-02 11:54:12 -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: GIGSEA
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2019-10-16 03:15:19 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:17:33 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 133.7 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GIGSEA.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 ‘GIGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GIGSEA’ version ‘1.2.0’
* 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                 16.391  2.393  18.961
geneSet2sparseMatrix        15.612  2.402  18.192
permutationMultipleLmMatrix  6.360  0.688   7.127
weightedMultipleLm           6.036  0.232   6.553
* 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/3.6/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
geneSet2Net16.391 2.39318.961
geneSet2sparseMatrix15.612 2.40218.192
gmt2geneSet3.9040.0584.144
matrixPval0.0270.0010.029
orderedIntersect0.0810.0150.096
permutationMultipleLm0.0460.0130.060
permutationMultipleLmMatrix6.3600.6887.127
permutationSimpleLm0.0450.0140.059
permutationSimpleLmMatrix2.1180.5892.772
runGIGSEA0.0010.0010.001
weightedGSEA0.0190.0070.025
weightedMultipleLm6.0360.2326.553
weightedPearsonCorr0.1140.0470.160