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This page was generated on 2021-10-15 15:06:22 -0400 (Fri, 15 Oct 2021).

INSTALL results for ShortRead on tokay2

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

Package 1753/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ShortRead 1.50.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/ShortRead
git_branch: RELEASE_3_13
git_last_commit: 31dea4d
git_last_commit_date: 2021-05-19 11:40:52 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  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: ShortRead
Version: 1.50.0
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ShortRead_1.50.0.tar.gz && rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ShortRead.buildbin-libdir ShortRead_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ShortRead_1.50.0.zip && rm ShortRead_1.50.0.tar.gz ShortRead_1.50.0.zip
StartedAt: 2021-10-14 08:46:31 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 08:48:51 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 140.2 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ShortRead_1.50.0.tar.gz && rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ShortRead.buildbin-libdir ShortRead_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ShortRead_1.50.0.zip && rm ShortRead_1.50.0.tar.gz ShortRead_1.50.0.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
 17 4894k   17  872k    0     0  1121k      0  0:00:04 --:--:--  0:00:04 1121k
 61 4894k   61 3012k    0     0  1707k      0  0:00:02  0:00:01  0:00:01 1706k
100 4894k  100 4894k    0     0  2061k      0  0:00:02  0:00:02 --:--:-- 2061k

install for i386

* installing *source* package 'ShortRead' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_ShortRead.c -o R_init_ShortRead.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c alphabet.c -o alphabet.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c count.c -o count.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c io.c -o io.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c io_bowtie.c -o io_bowtie.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c io_soap.c -o io_soap.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c readBfaToc.cc -o readBfaToc.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_maq_map.cc -o read_maq_map.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sampler.c -o sampler.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c trim.c -o trim.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c util.c -o util.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c xsnap.c -o xsnap.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/ShortRead.buildbin-libdir/00LOCK-ShortRead/00new/ShortRead/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ShortRead'
    finding HTML links ... done
    AlignedDataFrame-class                  html  
    AlignedDataFrame                        html  
    AlignedRead-class                       html  
    AlignedRead                             html  
    BowtieQA-class                          html  
    ExperimentPath-class                    html  
    FastqQA-class                           html  
    Intensity-class                         html  
    MAQMapQA-class                          html  
    QA-class                                html  
    QualityScore-class                      html  
    QualityScore                            html  
    RochePath-class                         html  
    RocheSet-class                          html  
    RtaIntensity-class                      html  
    RtaIntensity                            html  
    SRFilter-class                          html  
    SRFilterResult-class                    html  
    SRSet-class                             html  
    finding level-2 HTML links ... done

    SRUtil-class                            html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/ShortRead.buildbin-libdir/00LOCK-ShortRead/00new/ShortRead/help/srlist.html
    Sampler-class                           html  
    ShortRead-class                         html  
    ShortRead-deprecated                    html  
    ShortRead-package                       html  
    ShortReadQ-class                        html  
    Snapshot-class                          html  
    SnapshotFunction-class                  html  
    SolexaExportQA-class                    html  
    SolexaIntensity-class                   html  
    SolexaIntensity                         html  
    SolexaPath-class                        html  
    SolexaSet-class                         html  
    SpTrellis-class                         html  
    accessors                               html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/ShortRead.buildbin-libdir/00LOCK-ShortRead/00new/ShortRead/help/experimentPath.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/ShortRead.buildbin-libdir/00LOCK-ShortRead/00new/ShortRead/help/solexaPath.html
    alphabetByCycle                         html  
    alphabetScore                           html  
    clean                                   html  
    countLines                              html  
    deprecated                              html  
    dotQA-class                             html  
    dustyScore                              html  
    filterFastq                             html  
    polyn                                   html  
    qa                                      html  
    qa2                                     html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/ShortRead.buildbin-libdir/00LOCK-ShortRead/00new/ShortRead/help/QA.html
    readAligned                             html  
    readBaseQuality                         html  
    readBfaToc                              html  
    readFasta                               html  
    readFastq                               html  
    readIntensities                         html  
    readPrb                                 html  
    readQseq                                html  
    readXStringColumns                      html  
    renew                                   html  
    report                                  html  
    spViewPerFeature                        html  
    srFilter                                html  
    srdistance                              html  
    srduplicated                            html  
    tables                                  html  
    trimTails                               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 'ShortRead' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_ShortRead.c -o R_init_ShortRead.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c alphabet.c -o alphabet.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c count.c -o count.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c io.c -o io.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c io_bowtie.c -o io_bowtie.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c io_soap.c -o io_soap.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c readBfaToc.cc -o readBfaToc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_maq_map.cc -o read_maq_map.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sampler.c -o sampler.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c trim.c -o trim.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c util.c -o util.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c xsnap.c -o xsnap.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/ShortRead.buildbin-libdir/ShortRead/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ShortRead' as ShortRead_1.50.0.zip
* DONE (ShortRead)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ShortRead' successfully unpacked and MD5 sums checked