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This page was generated on 2021-10-15 15:05:49 -0400 (Fri, 15 Oct 2021).

INSTALL results for Rbowtie2 on nebbiolo1

To the developers/maintainers of the Rbowtie2 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rbowtie2.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 1512/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rbowtie2 1.14.0  (landing page)
Zheng Wei
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/Rbowtie2
git_branch: RELEASE_3_13
git_last_commit: f15bc6e
git_last_commit_date: 2021-05-19 12:29:56 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Rbowtie2
Version: 1.14.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL Rbowtie2
StartedAt: 2021-10-14 06:02:09 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 06:04:17 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 128.2 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL Rbowtie2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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-3.13-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-3.13-bioc/meat/Rbowtie2/src/adapterremoval'
(cd bowtie2 && (make CXX="g++" -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.13-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,
                 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]
  180 |      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’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      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’
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                ^~~~~
In file included from bt2_build.cpp:27:
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]
  827 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_build.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from bt2_build.cpp:27:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  831 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_build.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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,
                 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]
  180 |      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’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      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’
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                ^~~~~
In file included from bt2_idx.cpp:25:
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]
  827 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_idx.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from bt2_idx.cpp:25:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  831 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_idx.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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,
                 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]
  180 |      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’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      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’
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                ^~~~~
In file included from bt2_io.cpp:25:
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]
  827 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_io.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from bt2_io.cpp:25:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  831 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_io.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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,
                 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]
  180 |      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’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      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’
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                ^~~~~
In file included from bt2_util.cpp:26:
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]
  827 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_util.cpp:26:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from bt2_util.cpp:26:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  831 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_util.cpp:26:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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,
                 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]
  180 |      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’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      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’
  181 |      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:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  180 |      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’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      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’
  181 |      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,
                 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]
  180 |      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’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      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’
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                ^~~~~
In file included from bt2_search.cpp:33:
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]
  827 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from bt2_search.cpp:33:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  831 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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]
 1458 |  auto_ptr<Presets> presets(new PresetsV0());
      |  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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]
 2840 |  auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, pp, tid));
      |  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
bt2_search.cpp:2841:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 2841 |  auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
      |  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
bt2_search.cpp:2867:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 2867 |  auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
      |  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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]
 3964 |  auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, pp, tid));
      |  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
bt2_search.cpp:3965:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 3965 |  auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
      |  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
bt2_search.cpp:3977:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 3977 |  auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
      |  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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]
 4300 |  auto_ptr<BitPairReference> refs(
      |  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:31,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_search.cpp:33:
ds.h: In instantiation of ‘EMap<K, V>& EMap<K, V>::operator=(const EMap<K, V>&) [with K = DescentRedundancyKey; V = long int]’:
ds.h:973:12:   required from ‘void EList<T, S>::expandCopyExact(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
ds.h:958:3:   required from ‘void EList<T, S>::expandCopy(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
ds.h:569:4:   required from ‘void EList<T, S>::resize(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
aligner_seed2.h:482:31:   required from here
ds.h:2456:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair<DescentRedundancyKey, long int>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
 2456 |   memcpy(list_, o.list_, cur_ * sizeof(std::pair<K, V>));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algobase.h:64,
                 from /usr/include/c++/9/bits/char_traits.h:39,
                 from /usr/include/c++/9/ios:40,
                 from /usr/include/c++/9/ostream:38,
                 from /usr/include/c++/9/iostream:39,
                 from bt2_search.cpp:21:
/usr/include/c++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair<DescentRedundancyKey, long int>’ declared here
  208 |     struct pair
      |            ^~~~
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,
                 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]
  180 |      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’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      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’
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                ^~~~~
In file included from aligner_seed.cpp:23:
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]
  827 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from aligner_seed.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from aligner_seed.cpp:23:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  831 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from aligner_seed.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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,
                 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]
  180 |      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’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      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’
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                ^~~~~
In file included from aligner_seed2.h:103,
                 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]
  827 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from aligner_seed2.h:103,
                 from aligner_seed2.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from aligner_seed2.h:103,
                 from aligner_seed2.cpp:22:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  831 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from aligner_seed2.h:103,
                 from aligner_seed2.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from random_util.h:25,
                 from aligner_seed2.h:101,
                 from aligner_seed2.cpp:22:
ds.h: In instantiation of ‘EMap<K, V>& EMap<K, V>::operator=(const EMap<K, V>&) [with K = DescentRedundancyKey; V = long int]’:
ds.h:973:12:   required from ‘void EList<T, S>::expandCopyExact(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
ds.h:958:3:   required from ‘void EList<T, S>::expandCopy(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
ds.h:569:4:   required from ‘void EList<T, S>::resize(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
aligner_seed2.h:482:31:   required from here
ds.h:2456:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair<DescentRedundancyKey, long int>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
 2456 |   memcpy(list_, o.list_, cur_ * sizeof(std::pair<K, V>));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/utility:70,
                 from aligner_seed2.h:98,
                 from aligner_seed2.cpp:22:
/usr/include/c++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair<DescentRedundancyKey, long int>’ declared here
  208 |     struct pair
      |            ^~~~
aligner_seed2.cpp: In member function ‘size_t Descent::recalcOutgoing(const Read&, const Scoring&, TAlScore, TAlScore, DescentRedundancyChecker&, EFactory<DescentPos>&, const EList<DescentRoot>&, const EList<DescentConfig>&, PerReadMetrics&)’:
aligner_seed2.cpp:585:14: warning: ‘edge.DescentEdge::nex’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  585 |  DescentEdge edge;
      |              ^~~~
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,
                 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]
  180 |      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’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      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’
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                ^~~~~
In file included from group_walk.h:86,
                 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]
  827 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/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++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from group_walk.h:86,
                 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]
  831 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/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++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   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,
                 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]
  180 |      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’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      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’
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                ^~~~~
In file included from aligner_seed2.h:103,
                 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]
  827 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from aligner_seed2.h:103,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from aligner_seed2.h:103,
                 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]
  831 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from bt2_idx.h:28,
                 from aligner_seed2.h:103,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from random_util.h:25,
                 from aligner_seed2.h:101,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
ds.h: In instantiation of ‘EMap<K, V>& EMap<K, V>::operator=(const EMap<K, V>&) [with K = DescentRedundancyKey; V = long int]’:
ds.h:973:12:   required from ‘void EList<T, S>::expandCopyExact(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
ds.h:958:3:   required from ‘void EList<T, S>::expandCopy(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
ds.h:569:4:   required from ‘void EList<T, S>::resize(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
aligner_seed2.h:482:31:   required from here
ds.h:2456:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair<DescentRedundancyKey, long int>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
 2456 |   memcpy(list_, o.list_, cur_ * sizeof(std::pair<K, V>));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/utility:70,
                 from aligner_seed2.h:98,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
/usr/include/c++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair<DescentRedundancyKey, long int>’ declared here
  208 |     struct pair
      |            ^~~~
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-3.13-bioc/meat/Rbowtie2/src/bowtie2'
g++ -shared -fPIC -o Rbowtie2.so  version_info.cpp
installing to /home/biocbuild/bbs-3.13-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)