Package: gep2pep

Version: 1.4.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings gep2pep_1.4.0.tar.gz

StartedAt: 2019-10-16 01:59:22 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:01:17 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 115.1 seconds

RetCode: 0

Status:  OK

CheckDir: gep2pep.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings gep2pep_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/gep2pep.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.0’
* 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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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL gep2pep
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 521 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 666 bytes (current file size: 12.3 Kb)
Chunk 1 of 2, 540 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 692 bytes (current file size: 12.3 Kb)
Chunk 1 of 2, 550 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 686 bytes (current file size: 12.3 Kb)
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 154 | SKIPPED: 1 | WARNINGS: 9 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 12.897   0.468  14.094 

name	user	system	elapsed
CategorizedCollection	0.112	0.004	0.116
CondSEA	0.563	0.036	0.611
PathSEA	0.511	0.036	0.548
addSingleGeneSets	0.546	0.004	0.565
as.CategorizedCollection	0.264	0.016	0.280
buildPEPs	0.415	0.028	0.444
checkRepository	0.166	0.000	0.167
clearCache	0.745	0.031	1.028
createMergedRepository	0.830	0.026	0.887
createRepository	0.234	0.017	0.251
exportSEA	0.697	0.026	0.723
gene2pathways	0.232	0.010	0.243
getCollections	0.223	0.003	0.226
getDetails	0.555	0.027	0.583
getResults	0.433	0.019	0.452
importFromRawMode	0.472	0.018	0.489
importMSigDB.xml	0.148	0.004	0.164
loadCollection	0.130	0.010	0.141
loadESmatrix	0.366	0.014	0.385
loadPVmatrix	0.382	0.021	0.405
loadSampleGEP	0.000	0.001	0.001
loadSamplePWS	0.000	0.001	0.001
makeCollectionIDs	0.034	0.001	0.036
openRepository	0.132	0.005	0.138
setId2setName	0.032	0.002	0.035