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CHECK report for cTRAP on tokay2

This page was generated on 2020-10-17 11:56:24 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE cTRAP PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 404/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cTRAP 1.6.1
Nuno Saraiva-Agostinho
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/cTRAP
Branch: RELEASE_3_11
Last Commit: 3570b03
Last Changed Date: 2020-08-17 13:06:31 -0400 (Mon, 17 Aug 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cTRAP
Version: 1.6.1
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cTRAP.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings cTRAP_1.6.1.tar.gz
StartedAt: 2020-10-17 03:05:52 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:27:43 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 1310.8 seconds
RetCode: 0
Status:  OK  
CheckDir: cTRAP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cTRAP.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings cTRAP_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/cTRAP.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cTRAP/DESCRIPTION' ... OK
* this is package 'cTRAP' version '1.6.1'
* 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 whether package 'cTRAP' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
plotDrugSetEnrichment           61.93   0.53   62.47
plot.referenceComparison        23.64   0.45   24.10
analyseDrugSetEnrichment        16.27   1.02   39.03
plot.perturbationChanges        16.19   0.36   16.54
predictTargetingDrugs           11.69   0.24   11.92
loadCMapData                     6.32   0.28    7.90
downloadENCODEknockdownMetadata  2.52   0.19   10.39
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
plotDrugSetEnrichment           67.38   0.21   67.61
plot.referenceComparison        27.75   0.40   28.25
plot.perturbationChanges        16.84   0.28   17.13
analyseDrugSetEnrichment        15.55   0.73   37.48
predictTargetingDrugs           13.71   0.16   13.87
loadCMapData                     7.42   0.48   17.86
downloadENCODEknockdownMetadata  2.11   0.14   23.46
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'spelling.R'
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'spelling.R'
  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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/cTRAP.Rcheck/00check.log'
for details.



Installation output

cTRAP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/cTRAP_1.6.1.tar.gz && rm -rf cTRAP.buildbin-libdir && mkdir cTRAP.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cTRAP.buildbin-libdir cTRAP_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL cTRAP_1.6.1.zip && rm cTRAP_1.6.1.tar.gz cTRAP_1.6.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3757k  100 3757k    0     0  16.0M      0 --:--:-- --:--:-- --:--:-- 16.4M

install for i386

* installing *source* package 'cTRAP' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cTRAP'
    finding HTML links ... done
    ENCODEmetadata                          html  
    GCT-class                               html  
    analyseDrugSetEnrichment                html  
    as.table.referenceComparison            html  
    cTRAP                                   html  
    calculateCellLineMean                   html  
    checkColnames                           html  
    chunkVector                             html  
    closeOpenHandles                        html  
    cmapMetadata                            html  
    cmapPerturbationsCompounds              html  
    cmapPerturbationsKD                     html  
    compareAgainstReference                 html  
    compareAgainstReferencePerMethod        html  
    compareQuantile                         html  
    convertENSEMBLtoGeneSymbols             html  
    correlateAgainstReference               html  
    counts                                  html  
    diffExprStat                            html  
    downloadENCODEknockdownMetadata         html  
    downloadIfNotFound                      html  
    filterCMapMetadata                      html  
    fix.datatypes                           html  
    getCMapConditions                       html  
    getCMapPerturbationTypes                html  
    getENCODEcontrols                       html  
    listExpressionDrugSensitivityAssociation
                                            html  
    loadCMapData                            html  
    loadCMapZscores                         html  
    loadCTRPgeneExpression                  html  
    loadDrugDescriptors                     html  
    loadENCODEsample                        html  
    loadENCODEsamples                       html  
    loadExpressionDrugSensitivityAssociation
                                            html  
    loadNCI60drugSensitivity                html  
    matchStatsWithDrugSetsID                html  
    parseCMapID                             html  
    performDifferentialExpression           html  
    performGSEA                             html  
    performGSEAagainstReference             html  
    plot.perturbationChanges                html  
    plot.referenceComparison                html  
    plotDrugSetEnrichment                   html  
    plotESplot                              html  
    plotGSEA                                html  
    plotMetricDistribution                  html  
    plotSingleCorr                          html  
    plotTargetingDrugsVSsimilarPerturbations
                                            html  
    predictTargetingDrugs                   html  
    prepareCMapPerturbations                html  
    prepareDrugSets                         html  
    prepareENCODEgeneExpression             html  
    prepareExpressionDrugSensitivityAssociation
                                            html  
    prepareGSEAgenesets                     html  
    print.similarPerturbations              html  
    processByChunks                         html  
    processIds                              html  
    rankColumns                             html  
    rankSimilarPerturbations                html  
    readGctxIds                             html  
    readGctxMeta                            html  
    stripStr                                html  
    subsetToIds                             html  
** 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

install for x64

* installing *source* package 'cTRAP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cTRAP' as cTRAP_1.6.1.zip
* DONE (cTRAP)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'cTRAP' successfully unpacked and MD5 sums checked

Tests output

cTRAP.Rcheck/tests_i386/spelling.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.34    0.10    0.42 

cTRAP.Rcheck/tests_x64/spelling.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.23    0.04    0.28 

cTRAP.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 249 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 103.90    4.25  297.07 

cTRAP.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: 249 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 109.64    4.48  320.59 

Example timings

cTRAP.Rcheck/examples_i386/cTRAP-Ex.timings

nameusersystemelapsed
analyseDrugSetEnrichment16.27 1.0239.03
downloadENCODEknockdownMetadata 2.52 0.1910.39
filterCMapMetadata000
getCMapConditions000
getCMapPerturbationTypes000
listExpressionDrugSensitivityAssociation000
loadCMapData6.320.287.90
loadCMapZscores000
loadDrugDescriptors0.280.000.28
loadENCODEsamples000
loadExpressionDrugSensitivityAssociation2.250.272.52
parseCMapID000
performDifferentialExpression000
plot.perturbationChanges16.19 0.3616.54
plot.referenceComparison23.64 0.4524.10
plotDrugSetEnrichment61.93 0.5362.47
predictTargetingDrugs11.69 0.2411.92
prepareCMapPerturbations000
prepareDrugSets1.150.611.76
prepareENCODEgeneExpression000
rankSimilarPerturbations3.240.013.25

cTRAP.Rcheck/examples_x64/cTRAP-Ex.timings

nameusersystemelapsed
analyseDrugSetEnrichment15.55 0.7337.48
downloadENCODEknockdownMetadata 2.11 0.1423.46
filterCMapMetadata0.000.020.01
getCMapConditions000
getCMapPerturbationTypes000
listExpressionDrugSensitivityAssociation000
loadCMapData 7.42 0.4817.86
loadCMapZscores000
loadDrugDescriptors0.260.000.27
loadENCODEsamples000
loadExpressionDrugSensitivityAssociation1.210.201.40
parseCMapID000
performDifferentialExpression000
plot.perturbationChanges16.84 0.2817.13
plot.referenceComparison27.75 0.4028.25
plotDrugSetEnrichment67.38 0.2167.61
predictTargetingDrugs13.71 0.1613.87
prepareCMapPerturbations000
prepareDrugSets0.820.381.19
prepareENCODEgeneExpression000
rankSimilarPerturbations3.360.033.39