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CHECK report for goProfiles on merida1

This page was generated on 2019-04-16 11:54:51 -0400 (Tue, 16 Apr 2019).

Package 664/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goProfiles 1.44.0
Alex Sanchez
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/goProfiles
Branch: RELEASE_3_8
Last Commit: 9306d2f
Last Changed Date: 2018-10-30 11:41:44 -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: goProfiles
Version: 1.44.0
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_1.44.0.tar.gz
StartedAt: 2019-04-16 00:20:48 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:23:56 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 188.1 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_1.44.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/goProfiles.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 ‘goProfiles/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘goProfiles’ version ‘1.44.0’
* 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     26.778  0.202  27.218
equivalentGOProfiles 22.515  0.272  23.414
fisherGOProfiles      9.024  0.116   9.479
mergeProfilesLists    7.716  0.090   8.101
plotProfiles          6.337  0.070   6.462
printProfiles         6.102  0.075   6.221
basicProfile          4.791  0.215   5.129
* 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/3.5/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
GOTermsList0.0000.0000.001
basicProfile4.7910.2155.129
compSummary0.0000.0010.001
compareGOProfiles4.8100.0684.907
compareGeneLists26.778 0.20227.218
compareProfilesLists000
contractedProfile2.2870.0162.334
conversionFunctions0.0420.0040.046
drosophila0.0030.0020.005
equivClust0.0000.0000.001
equivClust2pdf0.0270.0030.029
equivSummary0.0010.0000.000
equivalentGOProfiles22.515 0.27223.414
expandedLevel1.1900.0341.284
expandedProfile1.4370.0131.458
fisherGOProfiles9.0240.1169.479
fitGOProfile0.0000.0000.001
hugoIds0.0260.0020.028
iterEquivClust000
mergeProfilesLists7.7160.0908.101
ngenes2.8460.0212.905
omimIds0.0060.0020.007
plotProfiles6.3370.0706.462
printProfiles6.1020.0756.221
prostateIds0.0080.0020.011