Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:01 -0400 (Fri, 15 Oct 2021).

CHECK results for cTRAP on tokay2

To the developers/maintainers of the cTRAP package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cTRAP.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 422/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cTRAP 1.10.1  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/cTRAP
git_branch: RELEASE_3_13
git_last_commit: 089d9ff
git_last_commit_date: 2021-10-04 12:40:46 -0400 (Mon, 04 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cTRAP
Version: 1.10.1
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cTRAP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings cTRAP_1.10.1.tar.gz
StartedAt: 2021-10-14 21:45:31 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 22:06:08 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 1236.7 seconds
RetCode: 0
Status:   OK  
CheckDir: cTRAP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cTRAP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings cTRAP_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/cTRAP.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.10.1'
* 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  5.5Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
* checking package 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 LazyData ... OK
* 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                    139.27   0.26  139.53
plot.referenceComparison                  17.57   0.24   17.82
plot.perturbationChanges                  14.55   1.03   15.59
analyseDrugSetEnrichment                  14.06   1.03   30.38
convertENSEMBLtoGeneSymbols               10.66   0.10   15.62
filterCMapMetadata                         7.86   0.52   11.14
prepareDrugSets                            6.71   1.46    8.16
plotTargetingDrugsVSsimilarPerturbations   5.75   0.07    5.81
prepareCMapPerturbations                   5.67   0.06    4.98
downloadENCODEknockdownMetadata            3.70   0.53   18.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                           user system elapsed
plotDrugSetEnrichment                    150.80   0.37  151.19
plot.referenceComparison                  15.57   0.54   16.11
plot.perturbationChanges                  13.71   0.45   14.15
analyseDrugSetEnrichment                  12.78   1.10   31.16
filterCMapMetadata                         7.26   0.53    9.87
prepareDrugSets                            6.19   1.50    7.68
convertENSEMBLtoGeneSymbols                7.05   0.00   10.33
plotTargetingDrugsVSsimilarPerturbations   6.25   0.20    6.49
downloadENCODEknockdownMetadata            3.63   0.48   18.54
loadCMapData                               3.50   0.30    5.65
* 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-3.13-bioc/meat/cTRAP.Rcheck/00check.log'
for details.



Installation output

cTRAP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/cTRAP_1.10.1.tar.gz && rm -rf cTRAP.buildbin-libdir && mkdir cTRAP.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cTRAP.buildbin-libdir cTRAP_1.10.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL cTRAP_1.10.1.zip && rm cTRAP_1.10.1.tar.gz cTRAP_1.10.1.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 40 3945k   40 1603k    0     0  1496k      0  0:00:02  0:00:01  0:00:01 1496k
100 3945k  100 3945k    0     0  1975k      0  0:00:01  0:00:01 --:--:-- 1975k

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  
    HTMLfast                                html  
    analyseDrugSetEnrichment                html  
    as.table.referenceComparison            html  
    cTRAP                                   html  
    calculateCellLineMean                   html  
    calculateEvenlyDistributedBins          html  
    checkColnames                           html  
    chunkColumns                            html  
    closeOpenHandles                        html  
    cmapMetadata                            html  
    cmapPerturbationsCompounds              html  
    cmapPerturbationsKD                     html  
    compareQuantile                         html  
    compareWithAllMethods                   html  
    convertENSEMBLtoGeneSymbols             html  
    counts                                  html  
    diffExprStat                            html  
    dimnames.expressionDrugSensitivityAssociation
                                            html  
    dot-plotBubbles                         html  
    dot-prepareNavPage                      html  
    downloadENCODEknockdownMetadata         html  
    downloadIfNotFound                      html  
    filterCMapMetadata                      html  
    findIntersectingCompounds               html  
    fix.datatypes                           html  
    getCMapConditions                       html  
    getCMapPerturbationTypes                html  
    getENCODEcontrols                       html  
    launchCMapDataLoader                    html  
    launchDiffExprLoader                    html  
    launchDrugSetEnrichmentAnalyser         html  
    launchMetadataViewer                    html  
    launchResultPlotter                     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  
    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  
    prepareSetsCompoundInfo                 html  
    prepareStatsCompoundInfo                html  
    prepareWordBreak                        html  
    print.similarPerturbations              html  
    processByChunks                         html  
    processIds                              html  
    rankAgainstReference                    html  
    rankColumns                             html  
    rankSimilarPerturbations                html  
    readGctxIds                             html  
    readGctxMeta                            html  
    stripStr                                html  
    subsetData                              html  
    subsetDim                               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_1.10.1.zip
* DONE (cTRAP)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'cTRAP' successfully unpacked and MD5 sums checked

Tests output

cTRAP.Rcheck/tests_i386/spelling.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 
   0.31    0.01    0.31 

cTRAP.Rcheck/tests_x64/spelling.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 
   0.26    0.04    0.28 

cTRAP.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 1616781 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

== Skipped tests ===============================================================
* On Bioconductor (1)
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 244 ]
> 
> proc.time()
   user  system elapsed 
  63.90    4.90  210.89 

cTRAP.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 1616781 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

== Skipped tests ===============================================================
* On Bioconductor (1)
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 244 ]
> 
> proc.time()
   user  system elapsed 
  67.18    5.71  225.15 

Example timings

cTRAP.Rcheck/examples_i386/cTRAP-Ex.timings

nameusersystemelapsed
analyseDrugSetEnrichment14.06 1.0330.38
convertENSEMBLtoGeneSymbols10.66 0.1015.62
downloadENCODEknockdownMetadata 3.70 0.5318.08
filterCMapMetadata 7.86 0.5211.14
getCMapConditions000
getCMapPerturbationTypes000
listExpressionDrugSensitivityAssociation000
loadCMapData2.570.153.19
loadCMapZscores3.370.142.78
loadDrugDescriptors0.090.060.16
loadENCODEsamples000
loadExpressionDrugSensitivityAssociation1.850.192.03
parseCMapID000
performDifferentialExpression000
plot.perturbationChanges14.55 1.0315.59
plot.referenceComparison17.57 0.2417.82
plotDrugSetEnrichment139.27 0.26139.53
plotTargetingDrugsVSsimilarPerturbations5.750.075.81
predictTargetingDrugs4.310.154.47
prepareCMapPerturbations5.670.064.98
prepareDrugSets6.711.468.16
prepareENCODEgeneExpression000
rankSimilarPerturbations1.590.011.61

cTRAP.Rcheck/examples_x64/cTRAP-Ex.timings

nameusersystemelapsed
analyseDrugSetEnrichment12.78 1.1031.16
convertENSEMBLtoGeneSymbols 7.05 0.0010.33
downloadENCODEknockdownMetadata 3.63 0.4818.54
filterCMapMetadata7.260.539.87
getCMapConditions0.020.000.02
getCMapPerturbationTypes000
listExpressionDrugSensitivityAssociation000
loadCMapData3.500.305.65
loadCMapZscores2.520.162.10
loadDrugDescriptors0.210.030.25
loadENCODEsamples000
loadExpressionDrugSensitivityAssociation1.570.201.76
parseCMapID0.010.000.02
performDifferentialExpression000
plot.perturbationChanges13.71 0.4514.15
plot.referenceComparison15.57 0.5416.11
plotDrugSetEnrichment150.80 0.37151.19
plotTargetingDrugsVSsimilarPerturbations6.250.206.49
predictTargetingDrugs3.840.133.96
prepareCMapPerturbations4.300.143.54
prepareDrugSets6.191.507.68
prepareENCODEgeneExpression000
rankSimilarPerturbations1.530.021.55