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CHECK report for cTRAP on merida1

This page was generated on 2019-04-16 12:13:52 -0400 (Tue, 16 Apr 2019).

Package 354/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cTRAP 1.0.3
Nuno Saraiva-Agostinho
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/cTRAP
Branch: RELEASE_3_8
Last Commit: e97c3f1
Last Changed Date: 2018-12-03 11:02:57 -0400 (Mon, 03 Dec 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cTRAP
Version: 1.0.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cTRAP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cTRAP_1.0.3.tar.gz
StartedAt: 2019-04-15 23:18:32 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:21:04 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 152.1 seconds
RetCode: 0
Status:  OK 
CheckDir: cTRAP.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:cTRAP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cTRAP_1.0.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/cTRAP.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 ‘cTRAP/DESCRIPTION’ ... OK
* this is package ‘cTRAP’ version ‘1.0.3’
* 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 ‘cTRAP’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
downloadL1000data               16.899 13.905   7.184
plotL1000comparison             16.279  8.738  11.183
compareAgainstL1000              7.186  9.568   2.207
downloadENCODEknockdownMetadata  3.143  1.123  12.438
* 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

cTRAP.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cTRAP
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘cTRAP’ ...
** R
** data
*** moving datasets to lazyload DB
** 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 (cTRAP)

Tests output

cTRAP.Rcheck/tests/testthat.Rout


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(cTRAP)
> 
> test_check("cTRAP")
Comparing with cell line HepG2
Comparing with cell line HepG2
Performing GSA using perturbation signatures...
Comparing with cell line HEPG2
Comparing with cell line HEPG2
Performing GSA using perturbation signatures...
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 23 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 33.298  10.169  25.158 

Example timings

cTRAP.Rcheck/cTRAP-Ex.timings

nameusersystemelapsed
compareAgainstL10007.1869.5682.207
downloadENCODEknockdownMetadata 3.143 1.12312.438
downloadENCODEsamples0.0010.0000.000
downloadL1000data16.89913.905 7.184
filterL1000metadata0.0650.0820.021
getL1000Conditions0.0150.0230.005
getL1000PerturbationTypes0.0050.0070.002
loadL1000perturbations0.0050.0070.002
performDifferentialExpression0.0600.0780.018
plotL1000comparison16.279 8.73811.183
prepareENCODEgeneExpression0.0050.0010.006