##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Rbowtie2.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Rbowtie2_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/Rbowtie2.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rbowtie2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rbowtie2' version '1.10.1'
* 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 whether package 'Rbowtie2' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 66.9Mb
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... OK
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/Rbowtie2.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch Rbowtie2
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
* installing *source* package 'Rbowtie2' ...
** using staged installation
** libs
  running 'src/Makefile.win' ...
mkdir -p ../inst
(cd	adapterremoval && (/usr/bin/make -f"C:/Users/biocbuild/bbs-3.11-bioc/R/etc/x64/Makeconf"  -fMakefile.win))
Makefile.win:46: warning: overriding recipe for target '.cc.o'
C:/Users/biocbuild/bbs-3.11-bioc/R/etc/x64/Makeconf:227: warning: ignoring old recipe for target '.cc.o'
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c adapterset.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c alignment.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c argparse.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c debug.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c demultiplex.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c fastq.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c fastq_enc.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c fastq_io.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c linereader.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c linereader_joined.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main_adapter_id.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main_adapter_rm.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main_demultiplex.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c scheduler.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c strutils.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c threads.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c timer.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c trimmed_reads.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c userconfig.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG   -o AdapterRemoval adapterset.o alignment.o argparse.o debug.o demultiplex.o fastq.o fastq_enc.o fastq_io.o linereader.o linereader_joined.o main_adapter_id.o main_adapter_rm.o main_demultiplex.o scheduler.o strutils.o threads.o timer.o trimmed_reads.o userconfig.o main.o
cp AdapterRemoval ../../inst/
(cd bowtie2 && (/usr/bin/make -f"C:/Users/biocbuild/bbs-3.11-bioc/R/etc/x64/Makeconf" -fMakefile.win))
Makefile.win:121: warning: overriding recipe for target '.cc.o'
C:/Users/biocbuild/bbs-3.11-bioc/R/etc/x64/Makeconf:227: warning: ignoring old recipe for target '.cc.o'
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c bt2_build.cpp -o bt2_build.o
In file included from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:27:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c ccnt_lut.cpp -o ccnt_lut.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c ref_read.cpp -o ref_read.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c alphabet.cpp -o alphabet.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c shmem.cpp -o shmem.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c edit.cpp -o edit.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c bt2_idx.cpp -o bt2_idx.o
In file included from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c bt2_io.cpp -o bt2_io.o
In file included from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c bt2_util.cpp -o bt2_util.o
In file included from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c reference.cpp -o reference.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c ds.cpp -o ds.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c multikey_qsort.cpp -o multikey_qsort.o
In file included from multikey_qsort.h:27,
                 from multikey_qsort.cpp:20:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c limit.cpp -o limit.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c random_source.cpp -o random_source.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c tinythread.cpp -o tinythread.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c bowtie_build_main.cpp -o bowtie_build_main.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c diff_sample.cpp -o diff_sample.o
In file included from diff_sample.cpp:20:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party   -o bowtie2-build-s bt2_build.o ccnt_lut.o ref_read.o alphabet.o shmem.o edit.o bt2_idx.o bt2_io.o bt2_util.o reference.o ds.o multikey_qsort.o limit.o random_source.o tinythread.o bowtie_build_main.o diff_sample.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c bt2_search.cpp -o bt2_search.o
In file included from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_search.cpp:33:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c qual.cpp -o qual.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c pat.cpp -o pat.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c sam.cpp -o sam.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c read_qseq.cpp -o read_qseq.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_seed_policy.cpp -o aligner_seed_policy.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_seed.cpp -o aligner_seed.o
In file included from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from aligner_seed.cpp:23:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_seed2.cpp -o aligner_seed2.o
In file included from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from aligner_seed2.h:103,
                 from aligner_seed2.cpp:22:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_sw.cpp -o aligner_sw.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_sw_driver.cpp -o aligner_sw_driver.o
In file included from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from group_walk.h:86,
                 from aligner_sw_driver.h:84,
                 from aligner_sw_driver.cpp:47:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_cache.cpp -o aligner_cache.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_result.cpp -o aligner_result.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c ref_coord.cpp -o ref_coord.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c mask.cpp -o mask.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c pe.cpp -o pe.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aln_sink.cpp -o aln_sink.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c dp_framer.cpp -o dp_framer.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c scoring.cpp -o scoring.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c presets.cpp -o presets.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c unique.cpp -o unique.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c simple_func.cpp -o simple_func.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c random_util.cpp -o random_util.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_bt.cpp -o aligner_bt.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c sse_util.cpp -o sse_util.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_swsse.cpp -o aligner_swsse.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c outq.cpp -o outq.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_swsse_loc_i16.cpp -o aligner_swsse_loc_i16.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_swsse_ee_i16.cpp -o aligner_swsse_ee_i16.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_swsse_loc_u8.cpp -o aligner_swsse_loc_u8.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_swsse_ee_u8.cpp -o aligner_swsse_ee_u8.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c aligner_driver.cpp -o aligner_driver.o
In file included from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from aligner_seed2.h:103,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:180:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party    -I"C:/extsoft/include"     -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -c bowtie_main.cpp -o bowtie_main.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -O3 -m64 -msse2 -funroll-loops -g3 -Wall -ansi -static -static-libgcc -static-libstdc++ -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -I third_party   -o bowtie2-align-s bt2_search.o qual.o pat.o sam.o read_qseq.o aligner_seed_policy.o aligner_seed.o aligner_seed2.o aligner_sw.o aligner_sw_driver.o aligner_cache.o aligner_result.o ref_coord.o mask.o pe.o aln_sink.o dp_framer.o scoring.o presets.o unique.o simple_func.o random_util.o aligner_bt.o sse_util.o aligner_swsse.o outq.o aligner_swsse_loc_i16.o aligner_swsse_ee_i16.o aligner_swsse_loc_u8.o aligner_swsse_ee_u8.o aligner_driver.o ccnt_lut.o ref_read.o alphabet.o shmem.o edit.o bt2_idx.o bt2_io.o bt2_util.o reference.o ds.o multikey_qsort.o limit.o random_source.o tinythread.o bowtie_main.o 
cp bowtie2-align-s ../../inst
cp bowtie2-build-s ../../inst
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Rbowtie2'
    finding HTML links ... done
    adapterremoval_usage                    html  
    adapterremoval_version                  html  
    bowtie2-build                           html  
    bowtie2                                 html  
    bowtie2_build_usage                     html  
    bowtie2_usage                           html  
    bowtie2_version                         html  
    identify_adapters                       html  
    remove_adapters                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rbowtie2)
Making 'packages.html' ... done