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CHECK report for psichomics on tokay1

This page was generated on 2020-04-15 12:27:27 -0400 (Wed, 15 Apr 2020).

Package 1325/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.12.1
Nuno Saraiva-Agostinho
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/psichomics
Branch: RELEASE_3_10
Last Commit: fac011f
Last Changed Date: 2020-01-29 17:27:21 -0400 (Wed, 29 Jan 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: psichomics
Version: 1.12.1
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:psichomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings psichomics_1.12.1.tar.gz
StartedAt: 2020-04-15 05:43:36 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:52:51 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 554.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: psichomics.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:psichomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings psichomics_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/psichomics.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.12.1'
* 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 'psichomics' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSkZRR2/R.INSTALL24bc71d514fc/psichomics/man/plot.GEandAScorrelation.Rd:71: file link 'loess.smooth' in package 'stats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSkZRR2/R.INSTALL24bc71d514fc/psichomics/man/plotDistribution.Rd:34: file link 'density.default' in package 'stats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSkZRR2/R.INSTALL24bc71d514fc/psichomics/man/plotDistribution.Rd:41: file link 'bw.nrd' in package 'stats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSkZRR2/R.INSTALL24bc71d514fc/psichomics/man/plotDistribution.Rd:89: file link 'approx' in package 'stats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSkZRR2/R.INSTALL24bc71d514fc/psichomics/man/reduceDimensionality.Rd:25: file link 'as.numeric' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSkZRR2/R.INSTALL24bc71d514fc/psichomics/man/reduceDimensionality.Rd:26: file link 'is.numeric' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSkZRR2/R.INSTALL24bc71d514fc/psichomics/man/renderDataTableSparklines.Rd:22: file link 'dataTableOutput' in package 'shiny' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSkZRR2/R.INSTALL24bc71d514fc/psichomics/man/styleModal.Rd:41: file link 'removeModal' in package 'shiny' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/psichomics.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    html   1.2Mb
    libs   1.5Mb
* 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-3.10-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-3.10-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
** running examples for arch 'x64' ... OK
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/psichomics.Rcheck/00check.log'
for details.



Installation output

psichomics.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/psichomics_1.12.1.tar.gz && rm -rf psichomics.buildbin-libdir && mkdir psichomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=psichomics.buildbin-libdir psichomics_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL psichomics_1.12.1.zip && rm psichomics_1.12.1.tar.gz psichomics_1.12.1.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 3784k  100 3784k    0     0  9602k      0 --:--:-- --:--:-- --:--:-- 9702k

install for i386

* installing *source* package 'psichomics' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c psiFastCalc.cpp -o psiFastCalc.o
psiFastCalc.cpp: In function 'Rcpp::NumericMatrix psiFastCalc(const NumericMatrix&, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, int)':
psiFastCalc.cpp:30:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t col=0; col < mat.ncol(); col++) {
                            ^
psiFastCalc.cpp:31:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t idx=0; idx < incA.length(); idx++) {
                                ^
psiFastCalc.cpp: In function 'Rcpp::NumericMatrix psiFastCalc2(const NumericMatrix&, const List&, const List&, int)':
psiFastCalc.cpp:62:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t col=0; col < mat.ncol(); col++) {
                            ^
psiFastCalc.cpp:63:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t idx=0; idx < inc.length(); idx++) {
                                ^
psiFastCalc.cpp:66:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t k=0; k < incIdx.length(); k++)
                                ^
psiFastCalc.cpp:71:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t k=0; k < excIdx.length(); k++)
                                ^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o psichomics.dll tmp.def RcppExports.o psiFastCalc.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-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
    ASquantFileInput                        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  
    browserHistory                          html  
    bsModal2                                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  
    diagramSplicingEvent                    html  
    diffAnalyses                            html  
    diffExpressionSet                       html  
    diffSplicingSet                         html  
    disableTab                              html  
    discardOutsideSamplesFromGroups         html  
    display                                 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  
    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  
    getGtexTissues                          html  
    getHidden                               html  
    getHighlightedPoints                    html  
    getMatchingSamples                      html  
    getNumerics                             html  
    getServerFunctions                      html  
    getSplicingEventCoordinates             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  
    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  
    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  
    parseASeventNames                       html  
    parseCategoricalGroups                  html  
    parseDateResponse                       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  
    parseUniprotXML                         html  
    parseUrlsFromFirebrowseResponse         html  
    parseValidFile                          html  
    parseVastToolsEvent                     html  
    parseVastToolsSE                        html  
    performICA                              html  
    performPCA                              html  
    plot.GEandAScorrelation                 html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSkZRR2/R.INSTALL24bc71d514fc/psichomics/man/plot.GEandAScorrelation.Rd:71: file link 'loess.smooth' in package 'stats' does not exist and so has been treated as a topic
    plotClusters                            html  
    plotDistribution                        html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSkZRR2/R.INSTALL24bc71d514fc/psichomics/man/plotDistribution.Rd:34: file link 'density.default' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSkZRR2/R.INSTALL24bc71d514fc/psichomics/man/plotDistribution.Rd:41: file link 'bw.nrd' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSkZRR2/R.INSTALL24bc71d514fc/psichomics/man/plotDistribution.Rd:89: file link 'approx' in package 'stats' does not exist and so has been treated as a topic
    plotGeneExprPerSample                   html  
    plotGroupIndependence                   html  
    plotICA                                 html  
    plotPCA                                 html  
    plotPointsStyle                         html  
    plotProtein                             html  
    plotRowStats                            html  
    plotSingleICA                           html  
    plotSplicingEvent                       html  
    plotSurvivalCurves                      html  
    plotSurvivalPvaluesByCutoff             html  
    plotTranscripts                         html  
    plotVariance                            html  
    plottableXranges                        html  
    prepareAnnotationFromEvents             html  
    prepareEventPlotOptions                 html  
    prepareFileBrowser                      html  
    prepareFirebrowseArchives               html  
    prepareJunctionQuantSTAR                html  
    preparePreMadeGroupForSelection         html  
    prepareSRAmetadata                      html  
    prepareWordBreak                        html  
    print.geneList                          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  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSkZRR2/R.INSTALL24bc71d514fc/psichomics/man/reduceDimensionality.Rd:25: file link 'as.numeric' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSkZRR2/R.INSTALL24bc71d514fc/psichomics/man/reduceDimensionality.Rd:26: file link 'is.numeric' in package 'base' does not exist and so has been treated as a topic
    renameDuplicated                        html  
    renameGroups                            html  
    renderBoxplot                           html  
    renderDataTableSparklines               html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSkZRR2/R.INSTALL24bc71d514fc/psichomics/man/renderDataTableSparklines.Rd:22: file link 'dataTableOutput' in package 'shiny' does not exist and so has been treated as a topic
    renderGeneticInfo                       html  
    renderGroupInterface                    html  
    renderProteinInfo                       html  
    rm.null                                 html  
    roundDigits                             html  
    roundMinDown                            html  
    rowMeans                                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  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpSkZRR2/R.INSTALL24bc71d514fc/psichomics/man/styleModal.Rd:41: file link 'removeModal' in package 'shiny' does not exist and so has been treated as a topic
    subjectMultiMatchWarning                html  
    subsetGeneExpressionFromMatchingGenes   html  
    survdiffTerms                           html  
    survfit.survTerms                       html  
    tabDataset                              html  
    table2html                              html  
    tableRow                                html  
    testGroupIndependence                   html  
    testSingleIndependence                  html  
    testSurvival                            html  
    testSurvivalCutoff                      html  
    textSuggestions                         html  
    toJSarray                               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:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c psiFastCalc.cpp -o psiFastCalc.o
psiFastCalc.cpp: In function 'Rcpp::NumericMatrix psiFastCalc(const NumericMatrix&, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, int)':
psiFastCalc.cpp:30:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t col=0; col < mat.ncol(); col++) {
                            ^
psiFastCalc.cpp:31:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t idx=0; idx < incA.length(); idx++) {
                                ^
psiFastCalc.cpp: In function 'Rcpp::NumericMatrix psiFastCalc2(const NumericMatrix&, const List&, const List&, int)':
psiFastCalc.cpp:62:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t col=0; col < mat.ncol(); col++) {
                            ^
psiFastCalc.cpp:63:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t idx=0; idx < inc.length(); idx++) {
                                ^
psiFastCalc.cpp:66:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t k=0; k < incIdx.length(); k++)
                                ^
psiFastCalc.cpp:71:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t k=0; k < excIdx.length(); k++)
                                ^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o psichomics.dll tmp.def RcppExports.o psiFastCalc.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/psichomics.buildbin-libdir/psichomics/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'psichomics' as psichomics_1.12.1.zip
* DONE (psichomics)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'psichomics' successfully unpacked and MD5 sums checked

Tests output

psichomics.Rcheck/tests_i386/spelling.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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 
   0.17    0.01    0.17 

psichomics.Rcheck/tests_x64/spelling.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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 
   0.17    0.03    0.18 

psichomics.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(psichomics)
Loading required package: shiny
Loading required package: shinyBS

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Start the visual interface by running the function psichomics()

Attaching package: 'psichomics'

The following object is masked from 'package:base':

    rowMeans

> 
> test_check("psichomics")
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Retrieving protein annotation from UniProt...

Plotting protein domains...

Retrieving rMATS annotation...

Parsing rMATS annotation...

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Parsing rMATS annotation...

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

Parsing SUPPA annotation...

Retrieving VAST-TOOLS annotation...

Parsing VAST-TOOLS annotation...

ALT3

ALT5

COMBI

IR

MERGE3m

MIC

EXSK

MULTI
== testthat results  ===========================================================
[ OK: 1240 | SKIPPED: 2 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  30.56    3.00   37.68 

psichomics.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(psichomics)
Loading required package: shiny
Loading required package: shinyBS

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Start the visual interface by running the function psichomics()

Attaching package: 'psichomics'

The following object is masked from 'package:base':

    rowMeans

> 
> test_check("psichomics")
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Retrieving protein annotation from UniProt...

Plotting protein domains...

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

IR

MERGE3m

MIC

EXSK

MULTI
== testthat results  ===========================================================
[ OK: 1240 | SKIPPED: 2 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  32.71    0.90   37.70 

Example timings

psichomics.Rcheck/examples_i386/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs000
assignValuePerSubject000
blendColours000
calculateLoadingsContribution0.010.000.02
convertGeneIdentifiers0.240.010.25
correlateGEandAS0.000.000.02
createGroupByAttribute000
createJunctionsTemplate0.020.000.02
diffAnalyses0.080.000.07
downloadFiles000
ensemblToUniprot0.030.030.54
filterGeneExpr0.010.000.01
filterGroups000
filterPSI0.020.000.02
getAttributesTime000
getDownloadsFolder000
getFirebrowseDateFormat000
getGeneList0.000.020.04
getGtexDataTypes000
getGtexTissues000
getMatchingSamples000
getNumerics0.020.000.02
getSplicingEventFromGenes0.010.000.01
getSplicingEventTypes000
getSubjectFromSample000
getTCGAdataTypes0.060.000.16
getValidEvents000
groupPerElem000
hchart.survfit0.330.063.50
isFirebrowseUp0.020.000.03
labelBasedOnCutoff000
leveneTest0.010.000.02
listAllAnnotations000
listSplicingAnnotations000
loadAnnotation000
loadGtexData000
loadLocalFiles000
loadTCGAdata000
missingDataModal000
normaliseGeneExpression0.020.000.01
optimalSurvivalCutoff0.110.000.11
parseCategoricalGroups000
parseFirebrowseMetadata0.030.020.14
parseMatsEvent0.000.010.02
parseMatsGeneric0.010.020.03
parseMisoAnnotation0.360.031.83
parseMisoEvent0.020.000.01
parseMisoEventID0.000.000.02
parseMisoGeneric0.030.000.03
parseMisoId000
parseSplicingEvent0.020.000.02
parseSuppaEvent000
parseSuppaGeneric0.010.000.01
parseTcgaSampleInfo000
parseUrlsFromFirebrowseResponse0.030.000.10
parseVastToolsEvent000
parseVastToolsSE0.020.000.01
performICA000
performPCA000
plot.GEandAScorrelation1.100.011.11
plotDistribution1.700.652.36
plotGeneExprPerSample0.130.090.21
plotGroupIndependence0.150.000.16
plotICA0.080.090.75
plotPCA0.310.100.41
plotProtein0.530.111.00
plotRowStats0.550.060.61
plotSingleICA0.270.080.50
plotSplicingEvent0.030.020.05
plotSurvivalCurves0.080.030.30
plotSurvivalPvaluesByCutoff0.480.050.81
plotTranscripts0.030.001.11
plotVariance0.050.000.25
prepareAnnotationFromEvents0.120.000.12
prepareFirebrowseArchives000
prepareJunctionQuantSTAR000
prepareSRAmetadata000
processSurvTerms0.020.000.02
psichomics000
quantifySplicing000
queryEnsembl0.030.001.11
queryEnsemblByGene0.090.003.22
queryFirebrowseData0.070.000.18
queryPubMed0.030.000.49
queryUniprot0.050.000.33
readFile000
renameDuplicated0.000.010.01
renderBoxplot0.100.030.14
rowMeans000
sidebar000
survdiffTerms000
survfit.survTerms0.020.000.07
testGroupIndependence000
testSurvival0.020.000.01
textSuggestions000
trimWhitespace000

psichomics.Rcheck/examples_x64/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs000
assignValuePerSubject0.010.000.03
blendColours000
calculateLoadingsContribution0.000.010.02
convertGeneIdentifiers0.340.050.39
correlateGEandAS0.000.020.01
createGroupByAttribute000
createJunctionsTemplate000
diffAnalyses0.060.000.06
downloadFiles000
ensemblToUniprot0.020.000.44
filterGeneExpr0.010.000.01
filterGroups000
filterPSI0.020.000.02
getAttributesTime000
getDownloadsFolder000
getFirebrowseDateFormat000
getGeneList000
getGtexDataTypes000
getGtexTissues000
getMatchingSamples000
getNumerics000
getSplicingEventFromGenes000
getSplicingEventTypes000
getSubjectFromSample000
getTCGAdataTypes0.030.000.13
getValidEvents0.020.000.02
groupPerElem000
hchart.survfit1.280.091.37
isFirebrowseUp0.000.000.02
labelBasedOnCutoff0.010.000.01
leveneTest000
listAllAnnotations0.020.000.02
listSplicingAnnotations000
loadAnnotation000
loadGtexData000
loadLocalFiles000
loadTCGAdata000
missingDataModal000
normaliseGeneExpression0.030.000.03
optimalSurvivalCutoff0.130.000.12
parseCategoricalGroups000
parseFirebrowseMetadata0.040.000.14
parseMatsEvent0.020.000.02
parseMatsGeneric0.010.000.02
parseMisoAnnotation0.280.020.29
parseMisoEvent000
parseMisoEventID0.020.000.02
parseMisoGeneric0.030.000.03
parseMisoId000
parseSplicingEvent000
parseSuppaEvent0.020.000.01
parseSuppaGeneric0.010.000.02
parseTcgaSampleInfo000
parseUrlsFromFirebrowseResponse0.070.000.11
parseVastToolsEvent000
parseVastToolsSE0.030.000.03
performICA0.020.000.01
performPCA000
plot.GEandAScorrelation0.590.030.63
plotDistribution1.910.122.04
plotGeneExprPerSample0.230.020.25
plotGroupIndependence0.140.000.14
plotICA0.140.000.15
plotPCA0.360.090.70
plotProtein0.630.101.55
plotRowStats0.780.040.82
plotSingleICA0.320.100.41
plotSplicingEvent0.040.000.04
plotSurvivalCurves0.100.010.11
plotSurvivalPvaluesByCutoff0.540.050.60
plotTranscripts0.020.000.81
plotVariance0.080.050.12
prepareAnnotationFromEvents0.230.000.24
prepareFirebrowseArchives000
prepareJunctionQuantSTAR000
prepareSRAmetadata000
processSurvTerms0.010.000.02
psichomics000
quantifySplicing000
queryEnsembl0.100.000.95
queryEnsemblByGene0.190.003.60
queryFirebrowseData0.070.000.18
queryPubMed0.070.010.50
queryUniprot0.090.000.36
readFile000
renameDuplicated000
renderBoxplot0.200.050.25
rowMeans000
sidebar000
survdiffTerms000
survfit.survTerms0.020.000.01
testGroupIndependence0.010.000.02
testSurvival0.020.000.01
textSuggestions000
trimWhitespace000