Package: cTRAP

Version: 1.5.0

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_1.5.0.tar.gz

StartedAt: 2020-01-16 03:23:54 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 03:33:24 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 570.5 seconds

RetCode: 0

Status:  OK

CheckDir: cTRAP.Rcheck

Warnings: 0

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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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/cTRAP.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.5.0’
* 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 ‘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 ... NOTE
  Note: found 1 marked UTF-8 string
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
plotDrugSetEnrichment           113.777 23.668  81.869
predictTargetingDrugs            54.712 23.607  23.079
analyseDrugSetEnrichment         56.920 19.689  35.627
loadCMapData                     20.944  9.512  12.972
plot.perturbationChanges         22.972  4.075  22.056
plot.referenceComparison         10.326  2.453   5.299
rankSimilarPerturbations          8.360  2.747   4.173
prepareDrugSets                   4.440  3.341   6.196
downloadENCODEknockdownMetadata   3.542  1.742  12.806
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/cTRAP.Rcheck/00check.log’
for details.

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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/4.0/Resources/library’
* installing *source* package ‘cTRAP’ ...
** using staged installation
** 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 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 (cTRAP)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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")
trying URL 'https://www.dropbox.com/s/5q0dazbtnpojw2m/expressionDrugSensitivityCorGDSC7.rds?raw=1'
Content type 'application/octet-stream' length 36160847 bytes (34.5 MB)
==================================================
downloaded 34.5 MB

trying URL 'https://www.dropbox.com/s/599ok2w9ahysdga/compound_descriptors_NCI60_2D.rds?raw=1'
Content type 'application/octet-stream' length 1616106 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 155 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
202.099  78.064 114.663 

name	user	system	elapsed
analyseDrugSetEnrichment	56.920	19.689	35.627
downloadENCODEknockdownMetadata	3.542	1.742	12.806
filterCMapMetadata	0.075	0.063	0.025
getCMapConditions	0.019	0.012	0.006
getCMapPerturbationTypes	0.004	0.003	0.001
loadCMapData	20.944	9.512	12.972
loadCMapZscores	0.001	0.001	0.000
loadDrugDescriptors	0.449	0.173	0.297
loadENCODEsamples	0.003	0.002	0.002
loadExpressionDrugSensitivityAssociation	1.948	1.109	2.833
parseCMapID	0.001	0.000	0.001
performDifferentialExpression	0.004	0.001	0.005
plot.perturbationChanges	22.972	4.075	22.056
plot.referenceComparison	10.326	2.453	5.299
plotDrugSetEnrichment	113.777	23.668	81.869
predictTargetingDrugs	54.712	23.607	23.079
prepareCMapPerturbations	0	0	0
prepareDrugSets	4.440	3.341	6.196
prepareENCODEgeneExpression	0.001	0.001	0.001
rankSimilarPerturbations	8.360	2.747	4.173