Package: gep2pep

Version: 1.2.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings gep2pep_1.2.0.tar.gz

StartedAt: 2019-04-16 00:16:37 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:18:30 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 113.3 seconds

RetCode: 0

Status:  OK

CheckDir: gep2pep.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings gep2pep_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/gep2pep.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.2.0’
* 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 ‘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-3.8-bioc/R/bin/R CMD INSTALL gep2pep
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘gep2pep’ ...
** 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
* DONE (gep2pep)

R version 3.5.3 (2019-03-11) -- "Great Truth"
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, 511 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 658 bytes (current file size: 11.8 Kb)
Chunk 1 of 2, 530 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 684 bytes (current file size: 11.8 Kb)
Chunk 1 of 2, 541 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 678 bytes (current file size: 11.8 Kb)
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 158 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 11.704   2.644  15.021 

name	user	system	elapsed
CategorizedCollection	0.136	0.008	0.141
CondSEA	0.968	0.400	1.481
PathSEA	0.74	0.36	1.15
as.CategorizedCollection	0.356	0.320	0.717
buildPEPs	0.684	0.360	1.119
checkRepository	0.292	0.240	0.565
clearCache	0.844	0.488	1.396
createMergedRepository	0.912	0.676	1.702
createRepository	0.216	0.256	0.534
exportSEA	0.692	0.420	1.179
gene2pathways	0.224	0.252	0.520
getCollections	0.204	0.212	0.459
getDetails	0.620	0.372	1.063
getResults	0.816	0.428	1.328
importFromRawMode	0.808	0.276	1.137
importMSigDB.xml	0.188	0.248	0.489
loadCollection	0.228	0.252	0.531
loadESmatrix	0.620	0.404	1.087
loadPVmatrix	0.648	0.400	1.120
loadSampleGEP	0.004	0.000	0.002
loadSamplePWS	0.000	0.000	0.002
makeCollectionIDs	0.072	0.004	0.075
openRepository	0.208	0.276	0.539
setId2setName	0.076	0.000	0.077