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CHECK report for gep2pep on malbec2

This page was generated on 2019-10-16 12:12:45 -0400 (Wed, 16 Oct 2019).

Package 671/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gep2pep 1.4.0
Francesco Napolitano
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/gep2pep
Branch: RELEASE_3_9
Last Commit: e083bac
Last Changed Date: 2019-05-02 11:54:09 -0400 (Thu, 02 May 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

Summary

Package: gep2pep
Version: 1.4.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings gep2pep_1.4.0.tar.gz
StartedAt: 2019-10-16 01:59:22 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:01:17 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 115.1 seconds
RetCode: 0
Status:  OK 
CheckDir: gep2pep.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings gep2pep_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/gep2pep.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL gep2pep
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘gep2pep’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gep2pep)

Tests output

gep2pep.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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, 521 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 666 bytes (current file size: 12.3 Kb)
Chunk 1 of 2, 540 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 692 bytes (current file size: 12.3 Kb)
Chunk 1 of 2, 550 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 686 bytes (current file size: 12.3 Kb)
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 154 | SKIPPED: 1 | WARNINGS: 9 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 12.897   0.468  14.094 

Example timings

gep2pep.Rcheck/gep2pep-Ex.timings

nameusersystemelapsed
CategorizedCollection0.1120.0040.116
CondSEA0.5630.0360.611
PathSEA0.5110.0360.548
addSingleGeneSets0.5460.0040.565
as.CategorizedCollection0.2640.0160.280
buildPEPs0.4150.0280.444
checkRepository0.1660.0000.167
clearCache0.7450.0311.028
createMergedRepository0.8300.0260.887
createRepository0.2340.0170.251
exportSEA0.6970.0260.723
gene2pathways0.2320.0100.243
getCollections0.2230.0030.226
getDetails0.5550.0270.583
getResults0.4330.0190.452
importFromRawMode0.4720.0180.489
importMSigDB.xml0.1480.0040.164
loadCollection0.1300.0100.141
loadESmatrix0.3660.0140.385
loadPVmatrix0.3820.0210.405
loadSampleGEP0.0000.0010.001
loadSamplePWS0.0000.0010.001
makeCollectionIDs0.0340.0010.036
openRepository0.1320.0050.138
setId2setName0.0320.0020.035