############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch Rbowtie2 ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.13-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-3.13-bioc/R/etc/x64/Makeconf" -fMakefile.win)) Makefile.win:46: warning: overriding recipe for target '.cc.o' C:/Users/biocbuild/bbs-3.13-bioc/R/etc/x64/Makeconf:243: 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-3.13-bioc/R/etc/x64/Makeconf" -fMakefile.win)) Makefile.win:121: warning: overriding recipe for target '.cc.o' C:/Users/biocbuild/bbs-3.13-bioc/R/etc/x64/Makeconf:243: warning: ignoring old recipe for target '.cc.o' "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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