Package: Rbowtie2

Version: 1.5.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Rbowtie2.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Rbowtie2_1.5.0.tar.gz

StartedAt: 2019-04-09 03:01:45 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:02:09 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 24.5 seconds

RetCode: 0

Status:  OK

CheckDir: Rbowtie2.Rcheck

Warnings: 0

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Rbowtie2.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Rbowtie2_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Rbowtie2.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rbowtie2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rbowtie2’ version ‘1.5.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rbowtie2’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 18.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/Rbowtie2.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Rbowtie2
###
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* installing to library ‘/home/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/meat/Rbowtie2/src/adapterremoval'
(cd bowtie2 && (make CXX="g++" -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.9-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-3.9-bioc/meat/Rbowtie2/src/bowtie2'
g++ -shared -fPIC -o Rbowtie2.so  version_info.cpp
installing to /home/biocbuild/bbs-3.9-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)

name	user	system	elapsed
adapterremoval_usage	0.012	0.007	0.047
adapterremoval_version	0.008	0.000	0.032
bowtie2-build	0.721	0.368	1.469
bowtie2	0.722	0.197	1.072
bowtie2_build_usage	0.006	0.002	0.033
bowtie2_usage	0.000	0.013	0.029
bowtie2_version	0.010	0.000	0.032
identify_adapters	0.018	0.009	0.089
remove_adapters	0.021	0.020	0.131