Multiple platform build/check report for BioC 3.9 - CHECK report for gep2pep on merida2

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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_1.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/gep2pep.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.3.1’
* 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

Installation output

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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’ ...
** 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)

Tests output


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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: 163 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 14.360   0.891  15.597

Example timings

name	user	system	elapsed
CategorizedCollection	0.161	0.016	0.178
CondSEA	1.060	0.145	1.226
PathSEA	0.822	0.070	0.900
addSingleGeneSets	0.834	0.030	0.870
as.CategorizedCollection	0.398	0.036	0.448
buildPEPs	0.719	0.054	0.789
checkRepository	0.215	0.026	0.243
clearCache	0.860	0.070	0.985
createMergedRepository	0.767	0.083	0.868
createRepository	0.204	0.025	0.232
exportSEA	0.672	0.050	0.802
gene2pathways	0.179	0.024	0.206
getCollections	0.192	0.024	0.219
getDetails	0.581	0.046	0.677
getResults	0.550	0.044	0.608
importFromRawMode	0.641	0.049	0.730
importMSigDB.xml	0.142	0.020	0.167
loadCollection	0.167	0.022	0.198
loadESmatrix	0.474	0.045	0.552
loadPVmatrix	0.481	0.048	0.555
loadSampleGEP	0.001	0.000	0.002
loadSamplePWS	0.002	0.001	0.002
makeCollectionIDs	0.061	0.001	0.064
openRepository	0.202	0.025	0.229
setId2setName	0.068	0.001	0.068

CHECK report for gep2pep on merida2

Summary

Command output

Installation output

Tests output

Example timings