Package: gep2pep

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gep2pep_1.6.0.tar.gz

StartedAt: 2020-04-15 02:41:29 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:43:38 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 128.9 seconds

RetCode: 0

Status:  OK

CheckDir: gep2pep.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:gep2pep.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gep2pep_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/gep2pep.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 ‘gep2pep/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gep2pep’ version ‘1.6.0’
* package encoding: UTF-8
* 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 ‘gep2pep’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 gep2pep
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘gep2pep’ ...
** using staged installation
** R
** 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 (gep2pep)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(gep2pep)
> 
> test_check("gep2pep")
Chunk 1 of 2, 519 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 665 bytes (current file size: 12.3 Kb)
Chunk 1 of 2, 538 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 691 bytes (current file size: 12.3 Kb)
Chunk 1 of 2, 549 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 685 bytes (current file size: 12.3 Kb)
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 154 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 14.965   0.867  16.345 

name	user	system	elapsed
CategorizedCollection	0.146	0.017	0.163
CondSEA	1.065	0.116	1.238
PathSEA	0.795	0.058	0.900
addSingleGeneSets	0.743	0.033	0.779
as.CategorizedCollection	0.405	0.032	0.441
buildPEPs	0.620	0.039	0.775
checkRepository	0.249	0.022	0.339
clearCache	0.776	0.054	0.842
createMergedRepository	0.698	0.060	0.767
createRepository	0.179	0.020	0.200
exportSEA	0.617	0.038	0.661
gene2pathways	0.180	0.018	0.201
getCollections	0.166	0.018	0.185
getDetails	0.565	0.044	0.615
getResults	0.639	0.047	0.734
importFromRawMode	0.642	0.045	0.698
importMSigDB.xml	0.188	0.020	0.210
loadCollection	0.200	0.020	0.221
loadESmatrix	0.553	0.035	0.596
loadPVmatrix	0.535	0.038	0.583
loadSampleGEP	0.001	0.001	0.002
loadSamplePWS	0.001	0.000	0.001
makeCollectionIDs	0.058	0.001	0.059
openRepository	0.184	0.019	0.208
setId2setName	0.050	0.000	0.051