Multiple platform build/check report for BioC 3.7 - CHECK report for gep2pep on malbec2

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### Running command:
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###   /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

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### Running command:
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###   /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


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

name	user	system	elapsed
CategorizedCollection	0.084	0.012	0.098
CondSEA	0.592	0.396	1.083
PathSEA	0.572	0.352	0.986
as.CategorizedCollection	0.316	0.220	0.578
buildPEPs	0.548	0.300	0.915
checkRepository	0.216	0.180	0.436
createRepository	0.164	0.204	0.406
exportSEA	0.536	0.328	0.928
gene2pathways	0.168	0.168	0.381
getCollections	0.144	0.172	0.355
getDetails	0.464	0.292	0.821
getResults	0.428	0.344	0.835
importMSigDB.xml	0.144	0.180	0.367
loadCollection	0.164	0.160	0.364
loadESmatrix	0.412	0.316	0.781
loadPVmatrix	0.468	0.296	0.826
loadSampleGEP	0.000	0.000	0.001
loadSamplePWS	0.008	0.004	0.014
makeCollectionIDs	0.044	0.004	0.048
openRepository	0.144	0.176	0.361

CHECK report for gep2pep on malbec2

Summary

Command output

Installation output

Tests output

Example timings