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BUILD BIN report for ORFik on tokay2

This page was generated on 2019-10-16 12:41:31 -0400 (Wed, 16 Oct 2019).

Package 1150/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.4.1
Kornel Labun
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ORFik
Branch: RELEASE_3_9
Last Commit: 3ae9f3b
Last Changed Date: 2019-06-06 08:36:37 -0400 (Thu, 06 Jun 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ORFik
Version: 1.4.1
Command: rm -rf ORFik.buildbin-libdir && mkdir ORFik.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ORFik.buildbin-libdir ORFik_1.4.1.tar.gz
StartedAt: 2019-10-16 09:50:00 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 09:51:46 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 105.4 seconds
RetCode: 0
Status:  OK  
PackageFile: ORFik_1.4.1.zip
PackageFileSize: 1.676 MiB

Command output

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###
### Running command:
###
###   rm -rf ORFik.buildbin-libdir && mkdir ORFik.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ORFik.buildbin-libdir ORFik_1.4.1.tar.gz
###
##############################################################################
##############################################################################



install for i386

* installing *source* package 'ORFik' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findORFsHelpers.cpp -o findORFsHelpers.o
findORFsHelpers.cpp: In function 'Rcpp::IntegerMatrix orfs_as_matrix(std::string&, std::string, std::string, int)':
findORFsHelpers.cpp:212:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i < uorfSize/2; i++) {
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findOrfs.cpp -o findOrfs.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findOrfsFasta.cpp -o findOrfsFasta.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o
pmapFromTranscripts.cpp: In function 'Rcpp::List pmapFromTranscriptsCPP(const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const char&, bool)':
pmapFromTranscripts.cpp:151:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0;i < xSize; i++){
                    ^
pmapFromTranscripts.cpp:155:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < indexSize; i++){
                     ^
pmapFromTranscripts.cpp:161:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 1; i < indexSize; i++){
                     ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ORFik.dll tmp.def RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/ORFik.buildbin-libdir/00LOCK-ORFik/00new/ORFik/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ORFik'
    finding HTML links ... done
    ORFik-package                           html  
    addCdsOnLeaderEnds                      html  
    addNewTSSOnLeaders                      html  
    allFeaturesHelper                       html  
    finding level-2 HTML links ... done

    asTX                                    html  
    assignAnnotations                       html  
    assignFirstExonsStartSite               html  
    assignLastExonsStopSite                 html  
    assignTSSByCage                         html  
    bedToGR                                 html  
    changePointAnalysis                     html  
    checkRFP                                html  
    checkRNA                                html  
    codonSumsPerGroup                       html  
    computeFeatures                         html  
    computeFeaturesCage                     html  
    convertToOneBasedRanges                 html  
    coverageGroupings                       html  
    coverageHeatMap                         html  
    coveragePerTiling                       html  
    coverageScorings                        html  
    defineIsoform                           html  
    defineTrailer                           html  
    detectRibosomeShifts                    html  
    disengagementScore                      html  
    distToCds                               html  
    distToTSS                               html  
    downstreamFromPerGroup                  html  
    downstreamN                             html  
    downstreamOfPerGroup                    html  
    entropy                                 html  
    extendLeaders                           html  
    extendsTSSexons                         html  
    filterCage                              html  
    filterTranscripts                       html  
    findFa                                  html  
    findMapORFs                             html  
    findMaxPeaks                            html  
    findNewTSS                              html  
    findORFs                                html  
    findORFsFasta                           html  
    firstEndPerGroup                        html  
    firstExonPerGroup                       html  
    firstStartPerGroup                      html  
    floss                                   html  
    fpkm                                    html  
    fpkm_calc                               html  
    fractionLength                          html  
    fread.bed                               html  
    gSort                                   html  
    gcContent                               html  
    groupGRangesBy                          html  
    groupings                               html  
    hasHits                                 html  
    initiationScore                         html  
    insideOutsideORF                        html  
    is.ORF                                  html  
    is.gr_or_grl                            html  
    is.grl                                  html  
    isInFrame                               html  
    isOverlapping                           html  
    isPeriodic                              html  
    kozakSequenceScore                      html  
    lastExonEndPerGroup                     html  
    lastExonPerGroup                        html  
    lastExonStartPerGroup                   html  
    loadRegion                              html  
    loadTxdb                                html  
    longestORFs                             html  
    makeExonRanks                           html  
    makeORFNames                            html  
    mapToGRanges                            html  
    matchNaming                             html  
    metaWindow                              html  
    numCodons                               html  
    numExonsPerGroup                        html  
    optimizeReads                           html  
    orfID                                   html  
    orfScore                                html  
    overlapsToCoverage                      html  
    pSitePlot                               html  
    parseCigar                              html  
    pmapFromTranscriptF                     html  
    rankOrder                               html  
    readWidths                              html  
    reassignTSSbyCage                       html  
    reassignTxDbByCage                      html  
    reduceKeepAttr                          html  
    remakeTxdbExonIds                       html  
    removeMetaCols                          html  
    removeTxdbExons                         html  
    removeTxdbTranscripts                   html  
    restrictTSSByUpstreamLeader             html  
    ribosomeReleaseScore                    html  
    ribosomeStallingScore                   html  
    savePlot                                html  
    scaledWindowPositions                   html  
    seqnamesPerGroup                        html  
    shiftFootprints                         html  
    sortPerGroup                            html  
    startCodons                             html  
    startDefinition                         html  
    startRegion                             html  
    startRegionCoverage                     html  
    startRegionString                       html  
    startSites                              html  
    stopCodons                              html  
    stopDefinition                          html  
    stopSites                               html  
    strandBool                              html  
    strandPerGroup                          html  
    subsetCoverage                          html  
    subsetToFrame                           html  
    tile1                                   html  
    translationalEff                        html  
    txNames                                 html  
    txSeqsFromFa                            html  
    uORFSearchSpace                         html  
    uniqueGroups                            html  
    uniqueOrder                             html  
    unlistGrl                               html  
    updateTxdbRanks                         html  
    updateTxdbStartSites                    html  
    upstreamFromPerGroup                    html  
    upstreamOfPerGroup                      html  
    validGRL                                html  
    validSeqlevels                          html  
    widthPerGroup                           html  
    windowCoveragePlot                      html  
    windowPerGroup                          html  
    windowPerReadLength                     html  
    windowPerTranscript                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ORFik' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findORFsHelpers.cpp -o findORFsHelpers.o
findORFsHelpers.cpp: In function 'Rcpp::IntegerMatrix orfs_as_matrix(std::string&, std::string, std::string, int)':
findORFsHelpers.cpp:212:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i < uorfSize/2; i++) {
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findOrfs.cpp -o findOrfs.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findOrfsFasta.cpp -o findOrfsFasta.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o
pmapFromTranscripts.cpp: In function 'Rcpp::List pmapFromTranscriptsCPP(const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const char&, bool)':
pmapFromTranscripts.cpp:151:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0;i < xSize; i++){
                    ^
pmapFromTranscripts.cpp:155:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < indexSize; i++){
                     ^
pmapFromTranscripts.cpp:161:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 1; i < indexSize; i++){
                     ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ORFik.dll tmp.def RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/ORFik.buildbin-libdir/ORFik/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ORFik' as ORFik_1.4.1.zip
* DONE (ORFik)