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INSTALL report for ORFik on tokay1

This page was generated on 2019-04-13 11:29:19 -0400 (Sat, 13 Apr 2019).

Package 1101/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.2.1
Kornel Labun
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/ORFik
Branch: RELEASE_3_8
Last Commit: 2e3a8c6
Last Changed Date: 2019-01-04 13:42:32 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  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: ORFik
Version: 1.2.1
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/ORFik_1.2.1.tar.gz && rm -rf ORFik.buildbin-libdir && mkdir ORFik.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ORFik.buildbin-libdir ORFik_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ORFik_1.2.1.zip && rm ORFik_1.2.1.tar.gz ORFik_1.2.1.zip
StartedAt: 2019-04-12 19:56:58 -0400 (Fri, 12 Apr 2019)
EndedAt: 2019-04-12 19:59:43 -0400 (Fri, 12 Apr 2019)
EllapsedTime: 165.5 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/ORFik_1.2.1.tar.gz && rm -rf ORFik.buildbin-libdir && mkdir ORFik.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ORFik.buildbin-libdir ORFik_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ORFik_1.2.1.zip && rm ORFik_1.2.1.tar.gz ORFik_1.2.1.zip
###
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install for i386

* installing *source* package 'ORFik' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findORFsHelpers.cpp -o findORFsHelpers.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-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++ -shared -s -static-libgcc -o ORFik.dll tmp.def RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/ORFik.buildbin-libdir/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  
    asTX                                    html  
    finding level-2 HTML links ... done

    assignAnnotations                       html  
    assignFirstExonsStartSite               html  
    assignLastExonsStopSite                 html  
    assignTSSByCage                         html  
    bedToGR                                 html  
    changePointAnalysis                     html  
    checkRFP                                html  
    checkRNA                                html  
    codonSumsPerGroup                       html  
    computeFeatures                         html  
    computeFeaturesCage                     html  
    convertToOneBasedRanges                 html  
    coverageByWindow                        html  
    coveragePerTiling                       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  
    findCageUTRFivelen                      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  
    getStartStopWindows                     html  
    groupGRangesBy                          html  
    hasHits                                 html  
    initiationScore                         html  
    insideOutsideORF                        html  
    is.gr_or_grl                            html  
    is.grl                                  html  
    isInFrame                               html  
    isOverlapping                           html  
    isPeriodic                              html  
    kozakSequenceScore                      html  
    lastExonEndPerGroup                     html  
    lastExonPerGroup                        html  
    lastExonStartPerGroup                   html  
    longestORFs                             html  
    makeExonRanks                           html  
    makeORFNames                            html  
    mapToGRanges                            html  
    matchNaming                             html  
    metaWindow                              html  
    numExonsPerGroup                        html  
    orfID                                   html  
    orfScore                                html  
    overlapsToCoverage                      html  
    parseCigar                              html  
    pmapFromTranscriptF                     html  
    rankOrder                               html  
    readWidths                              html  
    reassignTSSbyCage                       html  
    reassignTxDbByCage                      html  
    reduceKeepAttr                          html  
    regroupRleList                          html  
    remakeTxdbExonIds                       html  
    removeMetaCols                          html  
    removeTxdbExons                         html  
    restrictTSSByUpstreamLeader             html  
    riboTISCoverageProportion               html  
    ribosomeReleaseScore                    html  
    ribosomeStallingScore                   html  
    seqnamesPerGroup                        html  
    shiftFootprints                         html  
    sortPerGroup                            html  
    startCodons                             html  
    startDefinition                         html  
    startRegionString                       html  
    startSites                              html  
    stopCodons                              html  
    stopDefinition                          html  
    stopSites                               html  
    strandBool                              html  
    strandPerGroup                          html  
    subsetCoverage                          html  
    subset_to_frame                         html  
    tile1                                   html  
    translationalEff                        html  
    txLen                                   html  
    txNames                                 html  
    txNamesWithLeaders                      html  
    txSeqsFromFa                            html  
    uORFSearchSpace                         html  
    uniqueGroups                            html  
    uniqueOrder                             html  
    unlistGrl                               html  
    updateTxdbRanks                         html  
    updateTxdbStartSites                    html  
    upstreamFromPerGroup                    html  
    upstreamOfPerGroup                      html  
    validGRL                                html  
    widthPerGroup                           html  
    windowPerGroup                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ORFik' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findORFsHelpers.cpp -o findORFsHelpers.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-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++ -shared -s -static-libgcc -o ORFik.dll tmp.def RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/ORFik.buildbin-libdir/ORFik/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ORFik' as ORFik_1.2.1.zip
* DONE (ORFik)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'ORFik' successfully unpacked and MD5 sums checked
In R CMD INSTALL