##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL Rbowtie2
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘Rbowtie2’ ...
** using staged installation
** libs
** arch -
mkdir -p ../inst
(cd adapterremoval && (make CXX="g++ -std=gnu++11" -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rbowtie2/src/adapterremoval'
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c adapterset.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c alignment.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c argparse.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c debug.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c demultiplex.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq_enc.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq_io.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c linereader.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c linereader_joined.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_adapter_id.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_adapter_rm.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_demultiplex.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c scheduler.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c strutils.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c threads.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c timer.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c trimmed_reads.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c userconfig.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main.cc
g++ -std=gnu++11 -O3 -pthread -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/
make[1]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rbowtie2/src/adapterremoval'
(cd bowtie2 && (make CXX="g++" -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/Rbowtie2/src/bowtie2'
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bt2_build.o bt2_build.cpp
In file included from blockwise_sa.h:34:0,
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;
^~~~~
In file included from bt2_build.cpp:27:0:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_build.cpp:27:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from bt2_build.cpp:27:0:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_build.cpp:27:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o ccnt_lut.o ccnt_lut.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o ref_read.o ref_read.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o alphabet.o alphabet.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o shmem.o shmem.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o edit.o edit.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bt2_idx.o bt2_idx.cpp
In file included from blockwise_sa.h:34:0,
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;
^~~~~
In file included from bt2_idx.cpp:25:0:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_idx.cpp:25:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from bt2_idx.cpp:25:0:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_idx.cpp:25:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bt2_io.o bt2_io.cpp
In file included from blockwise_sa.h:34:0,
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;
^~~~~
In file included from bt2_io.cpp:25:0:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_io.cpp:25:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from bt2_io.cpp:25:0:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_io.cpp:25:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bt2_util.o bt2_util.cpp
In file included from blockwise_sa.h:34:0,
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;
^~~~~
In file included from bt2_util.cpp:26:0:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_util.cpp:26:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from bt2_util.cpp:26:0:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_util.cpp:26:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o reference.o reference.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o ds.o ds.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o multikey_qsort.o multikey_qsort.cpp
In file included from multikey_qsort.h:27:0,
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;
^~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o limit.o limit.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o random_source.o random_source.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o tinythread.o tinythread.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bowtie_build_main.o bowtie_build_main.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o diff_sample.o diff_sample.cpp
In file included from diff_sample.cpp:20:0:
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;
^~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -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
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bt2_search.o bt2_search.cpp
In file included from blockwise_sa.h:34:0,
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;
^~~~~
In file included from bt2_search.cpp:33:0:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from bt2_search.cpp:33:0:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
bt2_search.cpp: In function ‘void parseOptions(int, const char**)’:
bt2_search.cpp:1458:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<Presets> presets(new PresetsV0());
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
bt2_search.cpp: In function ‘void multiseedSearchWorker(void*)’:
bt2_search.cpp:2840:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, pp, tid));
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
bt2_search.cpp:2841:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
bt2_search.cpp:2867:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
bt2_search.cpp: In function ‘void multiseedSearchWorker_2p5(void*)’:
bt2_search.cpp:3964:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, pp, tid));
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
bt2_search.cpp:3965:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
bt2_search.cpp:3977:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
bt2_search.cpp: In function ‘void multiseedSearch(Scoring&, const PatternParams&, PatternComposer&, AlnSink&, Ebwt&, Ebwt&, OutFileBuf*)’:
bt2_search.cpp:4300:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<BitPairReference> refs(
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o qual.o qual.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o pat.o pat.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o sam.o sam.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o read_qseq.o read_qseq.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_seed_policy.o aligner_seed_policy.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_seed.o aligner_seed.cpp
In file included from blockwise_sa.h:34:0,
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;
^~~~~
In file included from aligner_seed.cpp:23:0:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from aligner_seed.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from aligner_seed.cpp:23:0:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from aligner_seed.cpp:23:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_seed2.o aligner_seed2.cpp
In file included from blockwise_sa.h:34:0,
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;
^~~~~
In file included from aligner_seed2.h:103:0,
from aligner_seed2.cpp:22:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from aligner_seed2.h:103,
from aligner_seed2.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from aligner_seed2.h:103:0,
from aligner_seed2.cpp:22:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from aligner_seed2.h:103,
from aligner_seed2.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_sw.o aligner_sw.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_sw_driver.o aligner_sw_driver.cpp
In file included from blockwise_sa.h:34:0,
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;
^~~~~
In file included from group_walk.h:86:0,
from aligner_sw_driver.h:84,
from aligner_sw_driver.cpp:47:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from timer.h:26,
from reference.h:36,
from aligner_sw.h:78,
from aligner_sw_driver.h:81,
from aligner_sw_driver.cpp:47:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from group_walk.h:86:0,
from aligner_sw_driver.h:84,
from aligner_sw_driver.cpp:47:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from timer.h:26,
from reference.h:36,
from aligner_sw.h:78,
from aligner_sw_driver.h:81,
from aligner_sw_driver.cpp:47:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_cache.o aligner_cache.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_result.o aligner_result.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o ref_coord.o ref_coord.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o mask.o mask.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o pe.o pe.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aln_sink.o aln_sink.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o dp_framer.o dp_framer.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o scoring.o scoring.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o presets.o presets.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o unique.o unique.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o simple_func.o simple_func.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o random_util.o random_util.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_bt.o aligner_bt.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o sse_util.o sse_util.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_swsse.o aligner_swsse.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o outq.o outq.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_swsse_loc_i16.o aligner_swsse_loc_i16.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_swsse_ee_i16.o aligner_swsse_ee_i16.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_swsse_loc_u8.o aligner_swsse_loc_u8.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_swsse_ee_u8.o aligner_swsse_ee_u8.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_driver.o aligner_driver.cpp
In file included from blockwise_sa.h:34:0,
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;
^~~~~
In file included from aligner_seed2.h:103:0,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from aligner_seed2.h:103,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from aligner_seed2.h:103:0,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from bt2_idx.h:28,
from aligner_seed2.h:103,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bowtie_main.o bowtie_main.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -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 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -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
make[1]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/Rbowtie2/src/bowtie2'
g++ -shared -fPIC -o Rbowtie2.so version_info.cpp
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-Rbowtie2/00new/Rbowtie2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rbowtie2)
