Package: goProfiles

Version: 1.46.0

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_1.46.0.tar.gz

StartedAt: 2019-10-16 03:20:37 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:24:53 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 256.5 seconds

RetCode: 0

Status:  OK

CheckDir: goProfiles.Rcheck

Warnings: 0

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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_1.46.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/goProfiles.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 ‘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 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     31.399  0.486  32.243
equivalentGOProfiles 24.593  0.579  26.508
fisherGOProfiles      9.537  0.186  10.214
mergeProfilesLists    8.160  0.141   8.892
plotProfiles          8.024  0.185   8.410
printProfiles         7.956  0.147   8.171
compareGOProfiles     6.174  0.222   6.618
basicProfile          6.025  0.328   6.765
* 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

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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’ ...
** 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)

name	user	system	elapsed
CD4ids	0.006	0.003	0.009
GOTermsList	0	0	0
basicProfile	6.025	0.328	6.765
compSummary	0.001	0.000	0.000
compareGOProfiles	6.174	0.222	6.618
compareGeneLists	31.399	0.486	32.243
compareProfilesLists	0.000	0.000	0.001
contractedProfile	3.062	0.034	3.181
conversionFunctions	0.057	0.007	0.065
drosophila	0.004	0.003	0.007
equivClust	0.001	0.000	0.001
equivClust2pdf	0.039	0.005	0.045
equivSummary	0.001	0.000	0.001
equivalentGOProfiles	24.593	0.579	26.508
expandedLevel	1.337	0.064	1.484
expandedProfile	1.577	0.021	1.782
fisherGOProfiles	9.537	0.186	10.214
fitGOProfile	0	0	0
hugoIds	0.028	0.004	0.032
iterEquivClust	0	0	0
mergeProfilesLists	8.160	0.141	8.892
ngenes	3.443	0.064	3.642
omimIds	0.011	0.004	0.015
plotProfiles	8.024	0.185	8.410
printProfiles	7.956	0.147	8.171
prostateIds	0.008	0.003	0.011