Package: goProfiles

Version: 1.48.0

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_1.48.0.tar.gz

StartedAt: 2020-04-15 02:46:59 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:50:32 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 213.4 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_1.48.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/goProfiles.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.48.0’
* 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     27.339  0.252  28.140
equivalentGOProfiles 19.319  0.257  19.880
fisherGOProfiles      8.283  0.112   8.582
mergeProfilesLists    6.902  0.092   7.180
plotProfiles          6.300  0.078   6.415
printProfiles         6.060  0.087   6.190
compareGOProfiles     4.928  0.079   5.030
* 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	0.004	0.002	0.006
GOTermsList	0	0	0
basicProfile	4.489	0.229	4.765
compSummary	0.001	0.001	0.001
compareGOProfiles	4.928	0.079	5.030
compareGeneLists	27.339	0.252	28.140
compareProfilesLists	0.000	0.000	0.001
contractedProfile	2.712	0.020	2.856
conversionFunctions	0.045	0.005	0.052
drosophila	0.003	0.002	0.005
equivClust	0.000	0.000	0.001
equivClust2pdf	0.028	0.003	0.032
equivSummary	0.000	0.000	0.001
equivalentGOProfiles	19.319	0.257	19.880
expandedLevel	1.089	0.032	1.143
expandedProfile	1.218	0.016	1.262
fisherGOProfiles	8.283	0.112	8.582
fitGOProfile	0.000	0.001	0.001
hugoIds	0.025	0.002	0.037
iterEquivClust	0.000	0.000	0.001
mergeProfilesLists	6.902	0.092	7.180
ngenes	2.853	0.028	2.937
omimIds	0.009	0.001	0.012
plotProfiles	6.300	0.078	6.415
printProfiles	6.060	0.087	6.190
prostateIds	0.007	0.002	0.009