Zheng Wei
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/Rbowtie2 |
| Branch: RELEASE_3_10 |
| Last Commit: 06e43e8 |
| Last Changed Date: 2019-10-29 13:10:42 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:28:59 -0400 (Wed, 15 Apr 2020).
| Package 1376/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rbowtie2 1.8.0 Zheng Wei
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Rbowtie2 |
| Version: 1.8.0 |
| Command: rm -rf Rbowtie2.buildbin-libdir && mkdir Rbowtie2.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch --build --library=Rbowtie2.buildbin-libdir Rbowtie2_1.8.0.tar.gz |
| StartedAt: 2020-04-15 09:29:29 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 09:33:02 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 213.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Rbowtie2_1.8.0.zip |
| PackageFileSize: 14.59 MiB |
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###
### Running command:
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### rm -rf Rbowtie2.buildbin-libdir && mkdir Rbowtie2.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch --build --library=Rbowtie2.buildbin-libdir Rbowtie2_1.8.0.tar.gz
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* installing *source* package 'Rbowtie2' ...
** using staged installation
** libs
running 'src/Makefile.win' ...
mkdir -p ../inst
(cd adapterremoval && (/cygdrive/c/Rtools/bin/make -f"C:/Users/biocbuild/bbs-3.10-bioc/R/etc/x64/Makeconf" -fMakefile.win))
Makefile.win:46: warning: overriding commands for target `.cc.o'
C:/Users/biocbuild/bbs-3.10-bioc/R/etc/x64/Makeconf:213: warning: ignoring old commands for target `.cc.o'
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c adapterset.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c alignment.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c argparse.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c debug.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c demultiplex.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c fastq.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c fastq_enc.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c fastq_io.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c linereader.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c linereader_joined.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c main_adapter_id.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c main_adapter_rm.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c main_demultiplex.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c scheduler.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c strutils.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c threads.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c timer.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c trimmed_reads.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c userconfig.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c main.cc
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -o AdapterRemoval adapterset.o alignment.o argparse.o debug.o demultiplex.o fastq.o fastq_enc.o fastq_io.o linereader.o linereader_joined.o main_adapter_id.o main_adapter_rm.o main_demultiplex.o scheduler.o strutils.o threads.o timer.o trimmed_reads.o userconfig.o main.o
cp AdapterRemoval ../../inst/
(cd bowtie2 && (/cygdrive/c/Rtools/bin/make -f"C:/Users/biocbuild/bbs-3.10-bioc/R/etc/x64/Makeconf" -fMakefile.win))
Makefile.win:121: warning: overriding commands for target `.cc.o'
C:/Users/biocbuild/bbs-3.10-bioc/R/etc/x64/Makeconf:213: warning: ignoring old commands for target `.cc.o'
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c bt2_build.cpp -o bt2_build.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c ccnt_lut.cpp -o ccnt_lut.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c ref_read.cpp -o ref_read.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c alphabet.cpp -o alphabet.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c shmem.cpp -o shmem.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c edit.cpp -o edit.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c bt2_idx.cpp -o bt2_idx.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c bt2_io.cpp -o bt2_io.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c bt2_util.cpp -o bt2_util.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c reference.cpp -o reference.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c ds.cpp -o ds.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c multikey_qsort.cpp -o multikey_qsort.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c limit.cpp -o limit.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c random_source.cpp -o random_source.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c tinythread.cpp -o tinythread.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c bowtie_build_main.cpp -o bowtie_build_main.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c diff_sample.cpp -o diff_sample.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -o bowtie2-build-s bt2_build.o ccnt_lut.o ref_read.o alphabet.o shmem.o edit.o bt2_idx.o bt2_io.o bt2_util.o reference.o ds.o multikey_qsort.o limit.o random_source.o tinythread.o bowtie_build_main.o diff_sample.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c bt2_search.cpp -o bt2_search.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c qual.cpp -o qual.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c pat.cpp -o pat.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c sam.cpp -o sam.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c read_qseq.cpp -o read_qseq.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_seed_policy.cpp -o aligner_seed_policy.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_seed.cpp -o aligner_seed.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_seed2.cpp -o aligner_seed2.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_sw.cpp -o aligner_sw.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_sw_driver.cpp -o aligner_sw_driver.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_cache.cpp -o aligner_cache.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_result.cpp -o aligner_result.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c ref_coord.cpp -o ref_coord.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c mask.cpp -o mask.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c pe.cpp -o pe.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aln_sink.cpp -o aln_sink.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c dp_framer.cpp -o dp_framer.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c scoring.cpp -o scoring.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c presets.cpp -o presets.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c unique.cpp -o unique.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c simple_func.cpp -o simple_func.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c random_util.cpp -o random_util.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_bt.cpp -o aligner_bt.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c sse_util.cpp -o sse_util.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_swsse.cpp -o aligner_swsse.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c outq.cpp -o outq.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_swsse_loc_i16.cpp -o aligner_swsse_loc_i16.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_swsse_ee_i16.cpp -o aligner_swsse_ee_i16.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_swsse_loc_u8.cpp -o aligner_swsse_loc_u8.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_swsse_ee_u8.cpp -o aligner_swsse_ee_u8.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_driver.cpp -o aligner_driver.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -I"C:/extsoft/include" -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c bowtie_main.cpp -o bowtie_main.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party -o bowtie2-align-s bt2_search.o qual.o pat.o sam.o read_qseq.o aligner_seed_policy.o aligner_seed.o aligner_seed2.o aligner_sw.o aligner_sw_driver.o aligner_cache.o aligner_result.o ref_coord.o mask.o pe.o aln_sink.o dp_framer.o scoring.o presets.o unique.o simple_func.o random_util.o aligner_bt.o sse_util.o aligner_swsse.o outq.o aligner_swsse_loc_i16.o aligner_swsse_ee_i16.o aligner_swsse_loc_u8.o aligner_swsse_ee_u8.o aligner_driver.o ccnt_lut.o ref_read.o alphabet.o shmem.o edit.o bt2_idx.o bt2_io.o bt2_util.o reference.o ds.o multikey_qsort.o limit.o random_source.o tinythread.o bowtie_main.o
cp bowtie2-align-s ../../inst
cp bowtie2-build-s ../../inst
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Rbowtie2'
finding HTML links ... done
adapterremoval_usage html
adapterremoval_version html
bowtie2-build html
bowtie2 html
bowtie2_build_usage html
bowtie2_usage html
bowtie2_version html
identify_adapters html
remove_adapters 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
* MD5 sums
packaged installation of 'Rbowtie2' as Rbowtie2_1.8.0.zip
* DONE (Rbowtie2)