Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-11-29 15:05:34 -0500 (Mon, 29 Nov 2021).

CHECK results for psichomics on tokay2

To the developers/maintainers of the psichomics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/psichomics.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 1480/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.20.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: RELEASE_3_14
git_last_commit: 84bcdbf
git_last_commit_date: 2021-10-26 12:30:49 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: psichomics
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:psichomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings psichomics_1.20.0.tar.gz
StartedAt: 2021-11-29 03:10:00 -0500 (Mon, 29 Nov 2021)
EndedAt: 2021-11-29 03:22:12 -0500 (Mon, 29 Nov 2021)
EllapsedTime: 731.7 seconds
RetCode: 0
Status:   OK  
CheckDir: psichomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:psichomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings psichomics_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/psichomics.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'psichomics/DESCRIPTION' ... OK
* this is package 'psichomics' version '1.20.0'
* 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 'psichomics' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.5Mb
    html   1.3Mb
    libs   2.1Mb
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/psichomics/libs/i386/psichomics.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/psichomics/libs/x64/psichomics.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
convertGeneIdentifiers  29.87   2.75   34.94
listSplicingAnnotations 26.08   1.63   29.14
loadAnnotation           6.90   0.39    7.64
listAllAnnotations       5.05   0.64    6.18
hchart.survfit           0.47   0.14    5.95
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
convertGeneIdentifiers  30.92   1.52   34.56
listSplicingAnnotations 24.77   1.22   27.44
loadAnnotation           6.33   0.30    7.01
listAllAnnotations       4.70   0.39    5.55
* 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-3.14-bioc/meat/psichomics.Rcheck/00check.log'
for details.



Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/psichomics_1.20.0.tar.gz && rm -rf psichomics.buildbin-libdir && mkdir psichomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=psichomics.buildbin-libdir psichomics_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL psichomics_1.20.0.zip && rm psichomics_1.20.0.tar.gz psichomics_1.20.0.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
 80 3828k   80 3099k    0     0  2949k      0  0:00:01  0:00:01 --:--:-- 2949k
100 3828k  100 3828k    0     0  3105k      0  0:00:01  0:00:01 --:--:-- 3105k

install for i386

* installing *source* package 'psichomics' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c progressBar.cpp -o progressBar.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c psiFastCalc.cpp -o psiFastCalc.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c vastToolsParser.cpp -o vastToolsParser.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o psichomics.dll tmp.def RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/psichomics.buildbin-libdir/00LOCK-psichomics/00new/psichomics/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'colSums' from package 'base' in package 'psichomics'
** help
*** installing help indices
  converting help for package 'psichomics'
    finding HTML links ... done
    HTMLfast                                html  
    addObjectAttrs                          html  
    addTCGAdata                             html  
    analysesTableSet                        html  
    appServer                               html  
    appUI                                   html  
    appendNewGroups                         html  
    areSplicingEvents                       html  
    articleUI                               html  
    assignColours                           html  
    assignValuePerSubject                   html  
    basicStats                              html  
    blendColours                            html  
    browseDownloadFolderInput               html  
    browserHistory                          html  
    calculateInclusionLevels                html  
    calculateLoadingsContribution           html  
    checkFileFormat                         html  
    checkFirebrowse                         html  
    checkGroupType                          html  
    checkIntegrity                          html  
    checkSurvivalInput                      html  
    clusterICAset                           html  
    clusterSet                              html  
    colSums-EList-method                    html  
    finding level-2 HTML links ... done

    colourInputMod                          html  
    convertGeneIdentifiers                  html  
    correlateGEandAS                        html  
    createDataTab                           html  
    createDensitySparklines                 html  
    createEventPlotting                     html  
    createGroup                             html  
    createGroupByAttribute                  html  
    createGroupById                         html  
    createGroupFromInput                    html  
    createJunctionsTemplate                 html  
    createOptimalSurvData                   html  
    createSparklines                        html  
    customRowMeans                          html  
    diagramSplicingEvent                    html  
    diffAnalyses                            html  
    diffExpressionSet                       html  
    diffSplicingSet                         html  
    disableTab                              html  
    discardLowCoveragePSIvalues             html  
    discardOutsideSamplesFromGroups         html  
    display                                 html  
    dot-onAttach                            html  
    downloadFiles                           html  
    ensemblToUniprot                        html  
    escape                                  html  
    eventPlotOptions                        html  
    exportGroupsToFile                      html  
    export_highcharts                       html  
    fileBrowser                             html  
    fileBrowserInput                        html  
    filterGeneExpr                          html  
    filterGroups                            html  
    filterPSI                               html  
    findASeventsFromGene                    html  
    findEventData                           html  
    geNormalisationFilteringInterface       html  
    geneExprFileInput                       html  
    geneExprSurvSet                         html  
    getAttributesTime                       html  
    getClinicalDataForSurvival              html  
    getClinicalMatchFrom                    html  
    getData                                 html  
    getDataRows                             html  
    getDifferentialExpression               html  
    getDifferentialSplicing                 html  
    getDownloadsFolder                      html  
    getFirebrowseDateFormat                 html  
    getGeneList                             html  
    getGlobal                               html  
    getGroups                               html  
    getGtexDataTypes                        html  
    getGtexDataURL                          html  
    getGtexTissues                          html  
    getHidden                               html  
    getHighlightedPoints                    html  
    getNumerics                             html  
    getSampleFromSubject                    html  
    getSelectedDataPanel                    html  
    getServerFunctions                      html  
    getSplicingEventCoordinates             html  
    getSplicingEventData                    html  
    getSplicingEventFromGenes               html  
    getSplicingEventTypes                   html  
    getSubjectFromSample                    html  
    getTCGAdataTypes                        html  
    getUiFunctions                          html  
    getValidEvents                          html  
    ggplotServer                            html  
    ggplotTooltip                           html  
    ggplotUI                                html  
    globalSelectize                         html  
    groupByAttribute                        html  
    groupManipulation                       html  
    groupManipulationInput                  html  
    groupPerElem                            html  
    groupsServerOnce                        html  
    hc_scatter                              html  
    hchart.survfit                          html  
    importGroupsFrom                        html  
    inclusionLevelsFilterInterface          html  
    inclusionLevelsInterface                html  
    inlineDialog                            html  
    insideFile                              html  
    is.whole                                html  
    isFile                                  html  
    isFirebrowseUp                          html  
    isRStudioServer                         html  
    joinEventsPerType                       html  
    junctionString                          html  
    labelBasedOnCutoff                      html  
    leveneTest                              html  
    linkToArticles                          html  
    linkToRunJS                             html  
    listAllAnnotations                      html  
    listSplicingAnnotations                 html  
    loadAnnotation                          html  
    loadAnnotationHub                       html  
    loadBy                                  html  
    loadCustomSplicingAnnotationSet         html  
    loadFile                                html  
    loadFileFormats                         html  
    loadFirebrowseFolders                   html  
    loadGeneExpressionSet                   html  
    loadGtexData                            html  
    loadGtexDataShiny                       html  
    loadGtexFile                            html  
    loadLocalFiles                          html  
    loadSRAproject                          html  
    loadSplicingQuantificationSet           html  
    loadTCGAdata                            html  
    loadTCGAsampleMetadata                  html  
    loadedDataModal                         html  
    matchGroupASeventsAndGenes              html  
    matchGroupSubjectsAndSamples            html  
    matchSplicingEventsWithGenes            html  
    missingDataModal                        html  
    modTabPanel                             html  
    navSelectize                            html  
    normaliseGeneExpression                 html  
    operateOnGroups                         html  
    optimSurvDiffSet                        html  
    optimalSurvivalCutoff                   html  
    parseCategoricalGroups                  html  
    parseDateResponse                       html  
    parseFile                               html  
    parseFirebrowseMetadata                 html  
    parseMatsEvent                          html  
    parseMatsGeneric                        html  
    parseMisoAnnotation                     html  
    parseMisoEvent                          html  
    parseMisoEventID                        html  
    parseMisoGeneric                        html  
    parseMisoId                             html  
    parseSplicingEvent                      html  
    parseSuppaEvent                         html  
    parseSuppaGeneric                       html  
    parseTcgaSampleInfo                     html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/psichomics.buildbin-libdir/00LOCK-psichomics/00new/psichomics/help/parseTcgaSampleInfo.html
    parseUniprotXML                         html  
    parseUrlsFromFirebrowseResponse         html  
    parseVastToolsEvent                     html  
    parseVastToolsSE                        html  
    performICA                              html  
    performPCA                              html  
    plot.GEandAScorrelation                 html  
    plotClusters                            html  
    plotDistribution                        html  
    plotGeneExprPerSample                   html  
    plotGroupIndependence                   html  
    plotICA                                 html  
    plotLibrarySize                         html  
    plotPCA                                 html  
    plotPCAvariance                         html  
    plotPointsStyle                         html  
    plotProtein                             html  
    plotRowStats                            html  
    plotSingleICA                           html  
    plotSplicingEvent                       html  
    plotSurvivalCurves                      html  
    plotSurvivalPvaluesByCutoff             html  
    plotTranscripts                         html  
    plottableXranges                        html  
    prepareAnnotationFromEvents             html  
    prepareEventPlotOptions                 html  
    prepareFileBrowser                      html  
    prepareFirebrowseArchives               html  
    prepareGenePresentation                 html  
    prepareJunctionQuantSTAR                html  
    preparePreMadeGroupForSelection         html  
    prepareSRAmetadata                      html  
    prepareWordBreak                        html  
    preserveAttributes                      html  
    processButton                           html  
    processDatasetNames                     html  
    processSRAdata                          html  
    processSurvData                         html  
    processSurvTerms                        html  
    processSurvival                         html  
    psichomics                              html  
    pubmedUI                                html  
    quantifySplicing                        html  
    quantifySplicingSet                     html  
    queryEnsembl                            html  
    queryEnsemblByGene                      html  
    queryFirebrowseData                     html  
    queryPubMed                             html  
    queryUniprot                            html  
    readAnnot                               html  
    readFile                                html  
    reduceDimensionality                    html  
    renameDuplicated                        html  
    renameGroups                            html  
    renderBoxplot                           html  
    renderDataTableSparklines               html  
    renderGeneticInfo                       html  
    renderGroupInterface                    html  
    renderProteinInfo                       html  
    replaceStrInList                        html  
    rm.null                                 html  
    roundDigits                             html  
    roundMinDown                            html  
    saveProcessedSRAdata                    html  
    selectGroupsUI                          html  
    selectPreMadeGroup                      html  
    selectizeGeneInput                      html  
    setFirebrowseData                       html  
    setLocalData                            html  
    setOperation                            html  
    setOperationIcon                        html  
    showAlert                               html  
    showGroupsTable                         html  
    sidebar                                 html  
    signifDigits                            html  
    singleDiffAnalyses                      html  
    sortCoordinates                         html  
    startProcess                            html  
    startProgress                           html  
    styleModal                              html  
    subjectMultiMatchWarning                html  
    subsetGeneExpressionFromMatchingGenes   html  
    survdiffTerms                           html  
    survfit.survTerms                       html  
    t.sticky                                html  
    tabDataset                              html  
    table2html                              html  
    tableRow                                html  
    testGroupIndependence                   html  
    testSingleIndependence                  html  
    testSurvival                            html  
    testSurvivalCutoff                      html  
    textSuggestions                         html  
    toJSarray                               html  
    traceInList                             html  
    transformData                           html  
    transformOptions                        html  
    transformValues                         html  
    trimWhitespace                          html  
    uniqueBy                                html  
    updateClinicalParams                    html  
    updateFileBrowserInput                  html  
    vennEvents                              html  
    wilcox                                  html  
*** copying figures
** 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 'psichomics' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c progressBar.cpp -o progressBar.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c psiFastCalc.cpp -o psiFastCalc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c vastToolsParser.cpp -o vastToolsParser.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o psichomics.dll tmp.def RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/psichomics.buildbin-libdir/psichomics/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'psichomics' as psichomics_1.20.0.zip
* DONE (psichomics)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'psichomics' successfully unpacked and MD5 sums checked

Tests output

psichomics.Rcheck/tests_i386/spelling.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
   0.28    0.03    0.28 

psichomics.Rcheck/tests_x64/spelling.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
   0.20    0.07    0.26 

psichomics.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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(psichomics)
Loading required package: shiny
Loading required package: shinyBS
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

psichomics 1.20.0: start the visual interface by running psichomics()
Full documentation and tutorials at https://nuno-agostinho.github.io/psichomics
> 
> test_check("psichomics")
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Retrieving rMATS annotation...

Parsing rMATS annotation...

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Parsing rMATS annotation...

Retrieving MISO annotation...

Parsing MISO annotation...
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Retrieving SUPPA annotation...

Parsing SUPPA annotation...

Retrieving VAST-TOOLS annotation...

Parsing VAST-TOOLS annotation...

ALT3

ALT5

COMBI

EXSK

IR

MERGE3m

MIC

MULTI
== Skipped tests ===============================================================
* On Bioconductor (2)
* On CRAN (1)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 1396 ]
> 
> proc.time()
   user  system elapsed 
  21.20    2.43   33.00 

psichomics.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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(psichomics)
Loading required package: shiny
Loading required package: shinyBS
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

psichomics 1.20.0: start the visual interface by running psichomics()
Full documentation and tutorials at https://nuno-agostinho.github.io/psichomics
> 
> test_check("psichomics")
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Retrieving rMATS annotation...

Parsing rMATS annotation...

Retrieving rMATS annotation...

Parsing rMATS annotation...

Retrieving MISO annotation...

Parsing MISO annotation...
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Retrieving SUPPA annotation...

Parsing SUPPA annotation...

Retrieving VAST-TOOLS annotation...

Parsing VAST-TOOLS annotation...

ALT3

ALT5

COMBI

EXSK

IR

MERGE3m

MIC

MULTI
== Skipped tests ===============================================================
* On Bioconductor (2)
* On CRAN (1)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 1396 ]
> 
> proc.time()
   user  system elapsed 
  22.57    1.03   32.82 

Example timings

psichomics.Rcheck/examples_i386/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs000
assignValuePerSubject0.030.000.04
blendColours000
calculateLoadingsContribution0.000.010.03
convertGeneIdentifiers29.87 2.7534.94
correlateGEandAS0.000.020.01
createGroupByAttribute000
createJunctionsTemplate0.020.000.02
customRowMeans000
diffAnalyses0.070.000.07
downloadFiles000
ensemblToUniprot0.150.000.68
filterGeneExpr0.000.010.01
filterGroups000
filterPSI0.030.000.03
getAttributesTime000
getDownloadsFolder0.000.020.02
getFirebrowseDateFormat000
getGeneList0.010.000.01
getGtexDataTypes0.100.000.44
getGtexTissues000
getNumerics000
getSampleFromSubject000
getSplicingEventFromGenes0.020.000.01
getSplicingEventTypes000
getSubjectFromSample000
getTCGAdataTypes0.120.000.33
getValidEvents000
groupPerElem000
hchart.survfit0.470.145.95
isFirebrowseUp0.020.000.10
labelBasedOnCutoff000
leveneTest0.010.000.01
listAllAnnotations5.050.646.18
listSplicingAnnotations26.08 1.6329.14
loadAnnotation6.900.397.64
loadGtexData000
loadLocalFiles000
loadSRAproject000
loadTCGAdata0.030.000.11
missingDataModal000
normaliseGeneExpression0.050.000.04
optimalSurvivalCutoff0.160.000.16
parseCategoricalGroups000
parseFirebrowseMetadata0.040.000.28
parseMatsEvent000
parseMatsGeneric0.030.000.03
parseMisoAnnotation0.240.000.26
parseMisoEvent0.010.000.02
parseMisoEventID000
parseMisoGeneric0.060.000.06
parseMisoId000
parseSplicingEvent000
parseSuppaEvent000
parseSuppaGeneric0.030.000.03
parseTcgaSampleInfo000
parseUrlsFromFirebrowseResponse0.050.010.22
parseVastToolsEvent000
parseVastToolsSE0.010.020.03
performICA0.020.000.01
performPCA0.010.000.02
plot.GEandAScorrelation0.50.00.5
plotDistribution1.660.081.80
plotGeneExprPerSample0.160.040.20
plotGroupIndependence0.150.000.16
plotICA0.170.030.44
plotLibrarySize0.310.040.34
plotPCA0.330.140.47
plotPCAvariance0.050.040.10
plotProtein0.920.083.32
plotRowStats0.450.000.45
plotSingleICA0.350.201.11
plotSplicingEvent0.040.020.06
plotSurvivalCurves0.110.040.16
plotSurvivalPvaluesByCutoff0.520.020.53
plotTranscripts0.010.000.91
prepareAnnotationFromEvents0.250.010.27
prepareFirebrowseArchives000
prepareJunctionQuantSTAR000
prepareSRAmetadata000
processSurvTerms000
psichomics000
quantifySplicing0.010.000.02
queryEnsembl0.060.000.67
queryEnsemblByGene0.160.032.85
queryFirebrowseData0.050.000.34
queryPubMed0.080.000.84
queryUniprot0.090.021.70
readFile000
renameDuplicated000
renderBoxplot0.110.050.17
survdiffTerms0.020.000.02
survfit.survTerms0.030.000.03
testGroupIndependence000
testSurvival0.030.000.03
textSuggestions000
trimWhitespace000

psichomics.Rcheck/examples_x64/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs000
assignValuePerSubject0.010.000.02
blendColours000
calculateLoadingsContribution0.020.000.03
convertGeneIdentifiers30.92 1.5234.56
correlateGEandAS0.020.000.02
createGroupByAttribute000
createJunctionsTemplate0.010.000.01
customRowMeans0.000.000.02
diffAnalyses0.110.010.12
downloadFiles000
ensemblToUniprot0.030.000.50
filterGeneExpr0.020.000.02
filterGroups000
filterPSI0.010.020.05
getAttributesTime000
getDownloadsFolder0.020.000.01
getFirebrowseDateFormat000
getGeneList000
getGtexDataTypes0.050.000.35
getGtexTissues000
getNumerics000
getSampleFromSubject0.010.000.01
getSplicingEventFromGenes000
getSplicingEventTypes000
getSubjectFromSample000
getTCGAdataTypes0.050.000.25
getValidEvents000
groupPerElem000
hchart.survfit0.400.090.48
isFirebrowseUp0.000.000.05
labelBasedOnCutoff000
leveneTest0.010.000.01
listAllAnnotations4.700.395.55
listSplicingAnnotations24.77 1.2227.44
loadAnnotation6.330.307.01
loadGtexData000
loadLocalFiles0.010.000.02
loadSRAproject000
loadTCGAdata0.020.000.09
missingDataModal000
normaliseGeneExpression0.030.000.03
optimalSurvivalCutoff0.170.000.18
parseCategoricalGroups000
parseFirebrowseMetadata0.080.000.28
parseMatsEvent0.020.000.01
parseMatsGeneric0.030.000.03
parseMisoAnnotation0.260.000.27
parseMisoEvent0.020.000.02
parseMisoEventID000
parseMisoGeneric0.050.000.05
parseMisoId000
parseSplicingEvent000
parseSuppaEvent000
parseSuppaGeneric0.020.000.02
parseTcgaSampleInfo0.010.000.01
parseUrlsFromFirebrowseResponse0.050.000.21
parseVastToolsEvent0.010.000.01
parseVastToolsSE0.040.000.03
performICA0.010.000.02
performPCA000
plot.GEandAScorrelation0.530.020.55
plotDistribution0.750.060.81
plotGeneExprPerSample0.080.050.12
plotGroupIndependence0.160.000.16
plotICA0.110.030.14
plotLibrarySize0.220.020.24
plotPCA0.350.100.53
plotPCAvariance0.100.050.14
plotProtein0.980.064.45
plotRowStats0.520.000.52
plotSingleICA0.300.080.37
plotSplicingEvent0.040.000.05
plotSurvivalCurves0.100.020.11
plotSurvivalPvaluesByCutoff0.480.030.53
plotTranscripts0.030.001.01
prepareAnnotationFromEvents0.30.00.3
prepareFirebrowseArchives000
prepareJunctionQuantSTAR000
prepareSRAmetadata000
processSurvTerms0.010.000.02
psichomics000
quantifySplicing0.040.000.03
queryEnsembl0.040.000.67
queryEnsemblByGene0.220.003.08
queryFirebrowseData0.080.000.40
queryPubMed0.060.010.68
queryUniprot0.080.001.23
readFile000
renameDuplicated0.020.000.02
renderBoxplot0.180.040.22
survdiffTerms0.020.000.01
survfit.survTerms0.010.000.02
testGroupIndependence000
testSurvival0.020.000.02
textSuggestions000
trimWhitespace000