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CHECK report for Rbowtie2 on tokay1

This page was generated on 2019-04-13 11:28:14 -0400 (Sat, 13 Apr 2019).

Package 1258/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rbowtie2 1.4.0
Zheng Wei
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/Rbowtie2
Branch: RELEASE_3_8
Last Commit: e09f6d4
Last Changed Date: 2018-10-30 11:42:06 -0400 (Tue, 30 Oct 2018)
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: Rbowtie2
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Rbowtie2.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Rbowtie2_1.4.0.tar.gz
StartedAt: 2019-04-13 04:53:10 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:54:36 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 86.3 seconds
RetCode: 0
Status:  OK  
CheckDir: Rbowtie2.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Rbowtie2.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Rbowtie2_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/Rbowtie2.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rbowtie2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rbowtie2' version '1.4.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'Rbowtie2' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 51.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/Rbowtie2.Rcheck/00check.log'
for details.

Installation output

Rbowtie2.Rcheck/00install.out

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch Rbowtie2
###
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##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
* installing *source* package 'Rbowtie2' ...
** libs
  running 'src/Makefile.win' ...
mkdir -p ../inst
(cd	adapterremoval && (/cygdrive/c/Rtools/bin/make -f"C:/Users/biocbuild/bbs-3.8-bioc/R/etc/x64/Makeconf"  -fMakefile.win))
Makefile.win:46: warning: overriding commands for target `.cc.o'
C:/Users/biocbuild/bbs-3.8-bioc/R/etc/x64/Makeconf:213: warning: ignoring old commands for target `.cc.o'
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c adapterset.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c alignment.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c argparse.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c debug.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c demultiplex.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c fastq.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c fastq_enc.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c fastq_io.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c linereader.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c linereader_joined.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main_adapter_id.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main_adapter_rm.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main_demultiplex.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c scheduler.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c strutils.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c threads.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c timer.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c trimmed_reads.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c userconfig.cc 
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main.cc 
C:/Rtools/mingw_64/bin/g++  -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-3.8-bioc/R/etc/x64/Makeconf" -fMakefile.win))
Makefile.win:121: warning: overriding commands for target `.cc.o'
C:/Users/biocbuild/bbs-3.8-bioc/R/etc/x64/Makeconf:213: warning: ignoring old commands for target `.cc.o'
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -I"C:/Users/biocbuild/bbs-3.8-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++  -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
* DONE (Rbowtie2)
Making 'packages.html' ... done
In R CMD INSTALL

Tests output

Example timings

Rbowtie2.Rcheck/Rbowtie2-Ex.timings

nameusersystemelapsed
adapterremoval_usage0.000.030.27
adapterremoval_version0.000.000.12
bowtie2-build0.000.031.12
bowtie20.000.001.33
bowtie2_build_usage0.000.000.24
bowtie2_usage0.000.010.23
bowtie2_version0.000.000.22
identify_adapters0.000.002.73
remove_adapters0.000.000.44