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This page was generated on 2022-04-13 12:06:49 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

INSTALL results for maftools on tokay2


To the developers/maintainers of the maftools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maftools.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
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raw results

Package 1034/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maftools 2.10.05  (landing page)
Anand Mayakonda
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/maftools
git_branch: RELEASE_3_14
git_last_commit: 3e3625a
git_last_commit_date: 2022-02-23 23:37:39 -0400 (Wed, 23 Feb 2022)
nebbiolo2Linux (Ubuntu 20.04.4 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: maftools
Version: 2.10.05
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/maftools_2.10.05.tar.gz && rm -rf maftools.buildbin-libdir && mkdir maftools.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=maftools.buildbin-libdir maftools_2.10.05.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL maftools_2.10.05.zip && rm maftools_2.10.05.tar.gz maftools_2.10.05.zip
StartedAt: 2022-04-12 05:23:32 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 05:26:26 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 174.2 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/maftools_2.10.05.tar.gz && rm -rf maftools.buildbin-libdir && mkdir maftools.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=maftools.buildbin-libdir maftools_2.10.05.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL maftools_2.10.05.zip && rm maftools_2.10.05.tar.gz maftools_2.10.05.zip
###
##############################################################################
##############################################################################


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install for i386

* installing *source* package 'maftools' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ntcounts.c -o ntcounts.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c somaticfreq.c -o somaticfreq.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o maftools.dll tmp.def ntcounts.o somaticfreq.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -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/maftools.buildbin-libdir/00LOCK-maftools/00new/maftools/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'maftools'
    finding HTML links ... done
    GISTIC-class                            html  
    MAF-class                               html  
    MAF                                     html  
    OncogenicPathways                       html  
    PlotOncogenicPathways                   html  
    annovarToMaf                            html  
    bamreadcounts                           html  
    cancerhotspots                          html  
    clinicalEnrichment                      html  
    coBarplot                               html  
    coOncoplot                              html  
    compareSignatures                       html  
    drugInteractions                        html  
    estimateSignatures                      html  
    extractSignatures                       html  
    filterMaf                               html  
    forestPlot                              html  
    genesToBarcodes                         html  
    genotypeMatrix                          html  
    getClinicalData                         html  
    getCytobandSummary                      html  
    getFields                               html  
    getGeneSummary                          html  
    getSampleSummary                        html  
    gisticBubblePlot                        html  
    gisticChromPlot                         html  
    gisticOncoPlot                          html  
    icgcSimpleMutationToMAF                 html  
    inferHeterogeneity                      html  
    lollipopPlot                            html  
    lollipopPlot2                           html  
    maf2mae                                 html  
    mafCompare                              html  
    mafSummary                              html  
    mafSurvGroup                            html  
    mafSurvival                             html  
    mafbarplot                              html  
    math.score                              html  
    merge_mafs                              html  
    mutCountMatrix                          html  
    oncodrive                               html  
    oncoplot                                html  
    oncostrip                               html  
    pfamDomains                             html  
    plotApobecDiff                          html  
    plotCBSsegments                         html  
    plotClusters                            html  
    plotCophenetic                          html  
    plotEnrichmentResults                   html  
    plotOncodrive                           html  
    plotProtein                             html  
    plotSignatures                          html  
    plotTiTv                                html  
    plotVaf                                 html  
    plotmafSummary                          html  
    prepareMutSig                           html  
    rainfallPlot                            html  
    read.maf                                html  
    readGistic                              html  
    sampleSwaps                             html  
    setMaf                                  html  
    signatureEnrichment                     html  
    somaticInteractions                     html  
    subsetMaf                               html  
    finding level-2 HTML links ... done

    survGroup                               html  
    tcgaAvailable                           html  
    tcgaCompare                             html  
    tcgaDriverBP                            html  
    tcgaLoad                                html  
    titv                                    html  
    tmb                                     html  
    trinucleotideMatrix                     html  
    vafCompare                              html  
    write.GisticSummary                     html  
    write.mafSummary                        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 'maftools' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ntcounts.c -o ntcounts.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c somaticfreq.c -o somaticfreq.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o maftools.dll tmp.def ntcounts.o somaticfreq.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -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/maftools.buildbin-libdir/maftools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'maftools' as maftools_2.10.05.zip
* DONE (maftools)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'maftools' successfully unpacked and MD5 sums checked