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CHECK report for goProfiles on merida2

This page was generated on 2019-04-09 13:24:16 -0400 (Tue, 09 Apr 2019).

Package 686/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goProfiles 1.45.0
Alex Sanchez
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/goProfiles
Branch: master
Last Commit: 81570a4
Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018)
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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: goProfiles
Version: 1.45.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:goProfiles.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings goProfiles_1.45.0.tar.gz
StartedAt: 2019-04-09 01:17:00 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:20:09 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 188.3 seconds
RetCode: 0
Status:  OK 
CheckDir: goProfiles.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:goProfiles.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings goProfiles_1.45.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/goProfiles.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.45.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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     28.913  0.251  29.311
equivalentGOProfiles 22.588  0.287  22.959
fisherGOProfiles      7.361  0.101   7.566
printProfiles         6.619  0.082   6.719
mergeProfilesLists    6.512  0.075   6.665
plotProfiles          6.063  0.078   6.183
compareGOProfiles     5.337  0.082   5.475
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL goProfiles
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘goProfiles’ ...
** 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
* DONE (goProfiles)

Tests output


Example timings

goProfiles.Rcheck/goProfiles-Ex.timings

nameusersystemelapsed
CD4ids0.0030.0010.004
GOTermsList0.0010.0000.000
basicProfile4.0200.1924.249
compSummary0.0010.0000.001
compareGOProfiles5.3370.0825.475
compareGeneLists28.913 0.25129.311
compareProfilesLists000
contractedProfile2.8380.0222.866
conversionFunctions0.0470.0040.051
drosophila0.0030.0020.005
equivClust0.0000.0000.001
equivClust2pdf0.0310.0030.034
equivSummary0.0010.0000.000
equivalentGOProfiles22.588 0.28722.959
expandedLevel1.1610.0341.199
expandedProfile1.1530.0141.184
fisherGOProfiles7.3610.1017.566
fitGOProfile0.0000.0000.001
hugoIds0.0160.0020.017
iterEquivClust000
mergeProfilesLists6.5120.0756.665
ngenes2.4890.0202.524
omimIds0.0090.0010.010
plotProfiles6.0630.0786.183
printProfiles6.6190.0826.719
prostateIds0.0070.0010.009