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CHECK report for gep2pep on merida2

This page was generated on 2019-04-09 13:36:09 -0400 (Tue, 09 Apr 2019).

Package 662/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gep2pep 1.3.1
Francesco Napolitano
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/gep2pep
Branch: master
Last Commit: 0782762
Last Changed Date: 2019-03-30 19:16:16 -0400 (Sat, 30 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: gep2pep
Version: 1.3.1
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_1.3.1.tar.gz
StartedAt: 2019-04-09 01:12:31 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:14:45 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 133.8 seconds
RetCode: 0
Status:  OK 
CheckDir: gep2pep.Rcheck
Warnings: 0

Command output

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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

gep2pep.Rcheck/00install.out

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###
### Running command:
###
###   /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

gep2pep.Rcheck/tests/testthat.Rout


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

gep2pep.Rcheck/gep2pep-Ex.timings

nameusersystemelapsed
CategorizedCollection0.1610.0160.178
CondSEA1.0600.1451.226
PathSEA0.8220.0700.900
addSingleGeneSets0.8340.0300.870
as.CategorizedCollection0.3980.0360.448
buildPEPs0.7190.0540.789
checkRepository0.2150.0260.243
clearCache0.8600.0700.985
createMergedRepository0.7670.0830.868
createRepository0.2040.0250.232
exportSEA0.6720.0500.802
gene2pathways0.1790.0240.206
getCollections0.1920.0240.219
getDetails0.5810.0460.677
getResults0.5500.0440.608
importFromRawMode0.6410.0490.730
importMSigDB.xml0.1420.0200.167
loadCollection0.1670.0220.198
loadESmatrix0.4740.0450.552
loadPVmatrix0.4810.0480.555
loadSampleGEP0.0010.0000.002
loadSamplePWS0.0020.0010.002
makeCollectionIDs0.0610.0010.064
openRepository0.2020.0250.229
setId2setName0.0680.0010.068