Multiple platform build/check report for BioC 3.8 - CHECK report for gep2pep on merida1

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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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/gep2pep.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.2.0’
* 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

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/3.5/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 version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, 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 
 10.982   1.269  12.395

Example timings

name	user	system	elapsed
CategorizedCollection	0.141	0.016	0.156
CondSEA	1.048	0.199	1.274
PathSEA	0.862	0.147	1.023
as.CategorizedCollection	0.425	0.094	0.531
buildPEPs	0.755	0.137	0.904
checkRepository	0.265	0.078	0.362
clearCache	0.966	0.136	1.129
createMergedRepository	0.832	0.202	1.055
createRepository	0.226	0.073	0.307
exportSEA	0.657	0.125	0.808
gene2pathways	0.238	0.075	0.318
getCollections	0.212	0.074	0.290
getDetails	0.725	0.125	0.878
getResults	0.720	0.125	0.867
importFromRawMode	0.664	0.087	0.752
importMSigDB.xml	0.181	0.054	0.240
loadCollection	0.201	0.058	0.262
loadESmatrix	0.584	0.122	0.722
loadPVmatrix	0.639	0.126	0.787
loadSampleGEP	0.001	0.000	0.001
loadSamplePWS	0.001	0.001	0.001
makeCollectionIDs	0.044	0.000	0.043
openRepository	0.222	0.071	0.299
setId2setName	0.038	0.001	0.039

CHECK report for gep2pep on merida1

Summary

Command output

Installation output

Tests output

Example timings