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CHECK report for gep2pep on malbec2

This page was generated on 2018-10-17 08:31:01 -0400 (Wed, 17 Oct 2018).

Package 609/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gep2pep 1.0.0
Francesco Napolitano
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/gep2pep
Branch: RELEASE_3_7
Last Commit: bc54ceb
Last Changed Date: 2018-04-30 10:35:48 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gep2pep
Version: 1.0.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings gep2pep_1.0.0.tar.gz
StartedAt: 2018-10-16 00:48:58 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 00:50:22 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 84.2 seconds
RetCode: 0
Status:  OK 
CheckDir: gep2pep.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings gep2pep_1.0.0.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/gep2pep.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.0.0’
* 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

gep2pep.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL gep2pep
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.7-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)

Tests output

gep2pep.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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")
       c3_TFT c3_MIR c4_CGN
c3_TFT      5      5      5
c3_MIR      5      5      5
c4_CGN      5      5      5
       c3_TFT c3_MIR c4_CGN
c3_TFT      5      5      5
c3_MIR      5      5      5
c4_CGN      5      5      5
       c3_TFT c3_MIR c4_CGN
c3_TFT      5      5      5
c3_MIR      5      5      5
c4_CGN      5      5      5
       c3_TFT c3_MIR c4_CGN
c3_TFT      5      5      5
c3_MIR      5      5      5
c4_CGN      5      5      5
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 86 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  4.824   1.072   6.071 

Example timings

gep2pep.Rcheck/gep2pep-Ex.timings

nameusersystemelapsed
CategorizedCollection0.0840.0120.098
CondSEA0.5920.3961.083
PathSEA0.5720.3520.986
as.CategorizedCollection0.3160.2200.578
buildPEPs0.5480.3000.915
checkRepository0.2160.1800.436
createRepository0.1640.2040.406
exportSEA0.5360.3280.928
gene2pathways0.1680.1680.381
getCollections0.1440.1720.355
getDetails0.4640.2920.821
getResults0.4280.3440.835
importMSigDB.xml0.1440.1800.367
loadCollection0.1640.1600.364
loadESmatrix0.4120.3160.781
loadPVmatrix0.4680.2960.826
loadSampleGEP0.0000.0000.001
loadSamplePWS0.0080.0040.014
makeCollectionIDs0.0440.0040.048
openRepository0.1440.1760.361