##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch Rbowtie2
###
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* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
* installing *source* package 'Rbowtie2' ...
** using staged installation
** libs
running 'src/Makefile.win' ...
mkdir -p ../inst
(cd adapterremoval && (/usr/bin/make -f"C:/Users/biocbuild/bbs-3.12-bioc/R/etc/x64/Makeconf" -fMakefile.win))
Makefile.win:46: warning: overriding recipe for target '.cc.o'
C:/Users/biocbuild/bbs-3.12-bioc/R/etc/x64/Makeconf:227: warning: ignoring old recipe for target '.cc.o'
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c adapterset.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c alignment.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c argparse.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c debug.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c demultiplex.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c fastq.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c fastq_enc.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c fastq_io.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c linereader.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c linereader_joined.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c main_adapter_id.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c main_adapter_rm.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c main_demultiplex.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c scheduler.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c strutils.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c threads.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c timer.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c trimmed_reads.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c userconfig.cc
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c main.cc
"C:/rtools40/mingw64/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 && (/usr/bin/make -f"C:/Users/biocbuild/bbs-3.12-bioc/R/etc/x64/Makeconf" -fMakefile.win))
Makefile.win:121: warning: overriding recipe for target '.cc.o'
C:/Users/biocbuild/bbs-3.12-bioc/R/etc/x64/Makeconf:227: warning: ignoring old recipe for target '.cc.o'
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from bt2_build.cpp:27:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from bt2_idx.cpp:25:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from bt2_io.cpp:25:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from bt2_util.cpp:26:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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
In file included from multikey_qsort.h:27,
from multikey_qsort.cpp:20:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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
In file included from diff_sample.cpp:20:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~~~~
"C:/rtools40/mingw64/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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from bt2_search.cpp:33:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from aligner_seed.cpp:23:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from aligner_seed2.h:103,
from aligner_seed2.cpp:22:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from group_walk.h:86,
from aligner_sw_driver.h:84,
from aligner_sw_driver.cpp:47:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from aligner_seed2.h:103,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/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
* DONE (Rbowtie2)
Making 'packages.html' ... done
