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

CHECK report for goProfiles on malbec2

This page was generated on 2019-10-16 11:56:54 -0400 (Wed, 16 Oct 2019).

Package 696/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goProfiles 1.46.0
Alex Sanchez
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/goProfiles
Branch: RELEASE_3_9
Last Commit: 52909bb
Last Changed Date: 2019-05-02 11:53:10 -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: goProfiles
Version: 1.46.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:goProfiles.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings goProfiles_1.46.0.tar.gz
StartedAt: 2019-10-16 02:05:36 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:08:49 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 192.6 seconds
RetCode: 0
Status:  OK 
CheckDir: goProfiles.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:goProfiles.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings goProfiles_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/goProfiles.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘goProfiles/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘goProfiles’ version ‘1.46.0’
* 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 ‘goProfiles’ 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
compareGeneLists     25.462  0.068  26.501
equivalentGOProfiles 18.156  0.075  18.597
fisherGOProfiles      7.651  0.016   7.760
mergeProfilesLists    6.568  0.000   6.765
printProfiles         6.456  0.012   6.583
plotProfiles          6.280  0.012   6.315
* 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

goProfiles.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL goProfiles
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘goProfiles’ ...
** using staged installation
** R
** data
** 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 (goProfiles)

Tests output


Example timings

goProfiles.Rcheck/goProfiles-Ex.timings

nameusersystemelapsed
CD4ids0.0030.0000.003
GOTermsList0.0010.0000.000
basicProfile4.4760.0774.617
compSummary000
compareGOProfiles4.7740.0364.866
compareGeneLists25.462 0.06826.501
compareProfilesLists000
contractedProfile2.2760.0162.320
conversionFunctions0.0380.0000.038
drosophila0.0030.0000.003
equivClust0.0000.0000.001
equivClust2pdf0.0280.0000.028
equivSummary000
equivalentGOProfiles18.156 0.07518.597
expandedLevel1.0620.0161.085
expandedProfile1.2170.0001.219
fisherGOProfiles7.6510.0167.760
fitGOProfile0.0010.0000.000
hugoIds0.0250.0000.025
iterEquivClust0.0010.0000.001
mergeProfilesLists6.5680.0006.765
ngenes2.5630.0002.609
omimIds0.0080.0000.008
plotProfiles6.2800.0126.315
printProfiles6.4560.0126.583
prostateIds0.0070.0000.006