Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-15 11:07:21 -0500 (Sat, 15 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4160
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4055
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3997
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4114
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for cTRAP on riesling1


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 431/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cTRAP 1.13.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2022-01-14 13:55:18 -0500 (Fri, 14 Jan 2022)
git_url: https://git.bioconductor.org/packages/cTRAP
git_branch: master
git_last_commit: df90b00
git_last_commit_date: 2021-10-26 12:47:45 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'AnnotationDbi' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'fgsea' which is not available

Summary

Package: cTRAP
Version: 1.13.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cTRAP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cTRAP_1.13.0.tar.gz
StartedAt: 2022-01-14 18:42:39 -0500 (Fri, 14 Jan 2022)
EndedAt: 2022-01-14 18:54:00 -0500 (Fri, 14 Jan 2022)
EllapsedTime: 680.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: cTRAP.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cTRAP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cTRAP_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/cTRAP.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.13.0'
* 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 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 ... WARNING
Warning in file 'R/shinyInterface.R':
  unable to translate 'For data with <U+2265> 2 cell lines' to native encoding
* 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 ... NOTE
taskAsyncApply: no visible global function definition for 'prepareArgs'
Undefined global functions or variables:
  prepareArgs
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                           user system elapsed
plotDrugSetEnrichment                    148.69   1.11  159.58
convertGeneIdentifiers                    23.85   1.56   27.72
plot.referenceComparison                  14.39   1.91   16.31
plot.perturbationChanges                  14.02   0.84   14.86
filterCMapMetadata                         7.36   7.40   16.03
loadCMapData                               4.32  10.24   15.19
analyseDrugSetEnrichment                  12.11   1.81   35.16
prepareDrugSets                            6.18   2.25    8.44
plotTargetingDrugsVSsimilarPerturbations   4.57   0.69    5.27
downloadENCODEknockdownMetadata            2.42   0.35   15.30
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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: 1 WARNING, 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/cTRAP.Rcheck/00check.log'
for details.



Installation output

cTRAP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL cTRAP
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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  
    convertGeneIdentifiers                  html  
    counts                                  html  
    diffExprStat                            html  
    dimnames.expressionDrugSensitivityAssociation
                                            html  
    dot-plotBubbles                         html  
    dot-prepareNavPage                      html  
    dot-traceInList                         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
* DONE (cTRAP)
Making 'packages.html' ... done

Tests output

cTRAP.Rcheck/tests/spelling.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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 
   0.10    0.06    0.14 

cTRAP.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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://compbio.imm.medicina.ulisboa.pt/public/cTRAP/expressionDrugSensitivityCorGDSC7.qs'
downloaded 31.6 MB

trying URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/compound_descriptors_NCI60_2D.qs'
downloaded 2.1 MB

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

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 244 ]
> 
> proc.time()
   user  system elapsed 
  56.45    6.35  199.43 

Example timings

cTRAP.Rcheck/cTRAP-Ex.timings

nameusersystemelapsed
analyseDrugSetEnrichment12.11 1.8135.16
convertGeneIdentifiers23.85 1.5627.72
downloadENCODEknockdownMetadata 2.42 0.3515.30
filterCMapMetadata 7.36 7.4016.03
getCMapConditions000
getCMapPerturbationTypes000
listExpressionDrugSensitivityAssociation000
loadCMapData 4.3210.2415.19
loadCMapZscores2.710.412.53
loadDrugDescriptors0.070.000.06
loadENCODEsamples000
loadExpressionDrugSensitivityAssociation0.760.341.11
parseCMapID000
performDifferentialExpression000
plot.perturbationChanges14.02 0.8414.86
plot.referenceComparison14.39 1.9116.31
plotDrugSetEnrichment148.69 1.11159.58
plotTargetingDrugsVSsimilarPerturbations4.570.695.27
predictTargetingDrugs3.650.534.18
prepareCMapPerturbations4.250.254.01
prepareDrugSets6.182.258.44
prepareENCODEgeneExpression000
rankSimilarPerturbations1.740.051.78