##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf Rbowtie.buildbin-libdir && mkdir Rbowtie.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rbowtie_1.16.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rbowtie.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rbowtie.buildbin-libdir Rbowtie_1.16.0.tar.gz'
>>>>>>>
* installing *source* package ‘Rbowtie’ ...
rm -f bowtie-build-s bowtie-align-s \
bowtie_prof \
bowtie-build-s.exe bowtie-align-s.exe bowtie_prof.exe \
bowtie-src.zip bowtie-bin.zip
rm -f core.*
rm -f SpliceMap/*.o SpliceMap/SpliceMap SpliceMap/amalgamateSAM SpliceMap/getSpliceMapUnmapped SpliceMap/fuseReorder SpliceMap/runSpliceMap_QuasR SpliceMap/sortsam
rm -f ../inst/bowtie ../inst/bowtie-build ../inst/SpliceMap ../inst/amalgamateSAM ../inst/getSpliceMapUnmapped ../inst/fuseReorder ../inst/runSpliceMap_QuasR ../inst/sortsam
** libs
** arch -
clang++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64 -stdlib=libstdc++ -Wall -g -O2 -Wall -g -O2 \"" -stdlib=libstdc++ -Wall -g -O2 -Wall -g -O2 \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
-I SeqAn-1.1 -I third_party \
-o bowtie-build-s ebwt_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp bowtie_build_main.cpp \
-lpthread
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:64:
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: unused typedef 'THostValue' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:38:
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: unused typedef 'TLeftValue' [-Wunused-local-typedef]
typedef typename Value<TLeft>::Type TLeftValue;
^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:53:
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: unused typedef 'TIterator' [-Wunused-local-typedef]
typedef typename Iterator<T, Standard>::Type TIterator;
^
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:27:
In file included from SeqAn-1.1/seqan/sequence.h:62:
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: unused typedef 'TId' [-Wunused-local-typedef]
typedef typename Id<TStringSet>::Type TId;
^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:82:
SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: unused typedef 'THValue' [-Wunused-local-typedef]
typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
^
SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: unused typedef 'THValue' [-Wunused-local-typedef]
typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
^
SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
^
SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: unused typedef 'THValue' [-Wunused-local-typedef]
typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
^
SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: unused typedef 'THValue' [-Wunused-local-typedef]
typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
^
SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: unused typedef 'THValue' [-Wunused-local-typedef]
typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
^
In file included from ebwt_build.cpp:5:
In file included from SeqAn-1.1/seqan/index.h:83:
SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: unused typedef 'THValue' [-Wunused-local-typedef]
typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
^
SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: unused typedef 'THValue' [-Wunused-local-typedef]
typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
^
SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: unused typedef 'THValue' [-Wunused-local-typedef]
typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
^
In file included from ebwt_build.cpp:7:
In file included from SeqAn-1.1/seqan/file.h:66:
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: unused typedef 'TPosition' [-Wunused-local-typedef]
typedef typename Position<TAlign>::Type TPosition;
^
In file included from ebwt_build.cpp:7:
In file included from SeqAn-1.1/seqan/file.h:69:
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
In file included from ebwt_build.cpp:11:
In file included from ./ebwt.h:27:
./blockwise_sa.h:380:37: warning: unused typedef 'TAlphabet' [-Wunused-local-typedef]
typedef typename Value<TStr>::Type TAlphabet;
^
./blockwise_sa.h:755:37: warning: unused typedef 'TAlphabet' [-Wunused-local-typedef]
typedef typename Value<TStr>::Type TAlphabet;
^
34 warnings generated.
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:64:
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: unused typedef 'THostValue' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:38:
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: unused typedef 'TLeftValue' [-Wunused-local-typedef]
typedef typename Value<TLeft>::Type TLeftValue;
^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:53:
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: unused typedef 'TIterator' [-Wunused-local-typedef]
typedef typename Iterator<T, Standard>::Type TIterator;
^
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:62:
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: unused typedef 'TId' [-Wunused-local-typedef]
typedef typename Id<TStringSet>::Type TId;
^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:12:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:66:
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: unused typedef 'TPosition' [-Wunused-local-typedef]
typedef typename Position<TAlign>::Type TPosition;
^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:12:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:69:
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
23 warnings generated.
clang++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64 -stdlib=libstdc++ -Wall -g -O2 -Wall -g -O2 \"" -stdlib=libstdc++ -Wall -g -O2 -Wall -g -O2 \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
-I SeqAn-1.1 -I third_party \
-o bowtie-align-s ebwt_search.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
-lpthread
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:64:
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: unused typedef 'THostValue' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:38:
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: unused typedef 'TLeftValue' [-Wunused-local-typedef]
typedef typename Value<TLeft>::Type TLeftValue;
^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:53:
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: unused typedef 'TIterator' [-Wunused-local-typedef]
typedef typename Iterator<T, Standard>::Type TIterator;
^
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:31:
In file included from SeqAn-1.1/seqan/sequence.h:62:
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: unused typedef 'TId' [-Wunused-local-typedef]
typedef typename Id<TStringSet>::Type TId;
^
In file included from ebwt_search.cpp:8:
In file included from SeqAn-1.1/seqan/find.h:62:
SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: unused typedef 'TWord' [-Wunused-local-typedef]
typedef unsigned int TWord;
^
In file included from ebwt_search.cpp:11:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:66:
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: unused typedef 'TPosition' [-Wunused-local-typedef]
typedef typename Position<TAlign>::Type TPosition;
^
In file included from ebwt_search.cpp:11:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:69:
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:16:
In file included from SeqAn-1.1/seqan/index.h:82:
SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: unused typedef 'THValue' [-Wunused-local-typedef]
typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
^
SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: unused typedef 'THValue' [-Wunused-local-typedef]
typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
^
SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
^
SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: unused typedef 'THValue' [-Wunused-local-typedef]
typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
^
SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: unused typedef 'THValue' [-Wunused-local-typedef]
typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
^
SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: unused typedef 'THValue' [-Wunused-local-typedef]
typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:16:
In file included from SeqAn-1.1/seqan/index.h:83:
SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: unused typedef 'THValue' [-Wunused-local-typedef]
typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
^
SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: unused typedef 'THValue' [-Wunused-local-typedef]
typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
^
SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: unused typedef 'THValue' [-Wunused-local-typedef]
typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
^
In file included from ebwt_search.cpp:14:
In file included from ./ebwt.h:27:
./blockwise_sa.h:380:37: warning: unused typedef 'TAlphabet' [-Wunused-local-typedef]
typedef typename Value<TStr>::Type TAlphabet;
^
./blockwise_sa.h:755:37: warning: unused typedef 'TAlphabet' [-Wunused-local-typedef]
typedef typename Value<TStr>::Type TAlphabet;
^
In file included from ebwt_search.cpp:22:
./range_cache.h:338:11: warning: private field 'sanity_' is not used [-Wunused-private-field]
bool sanity_; /// do consistency checks?
^
In file included from ebwt_search.cpp:26:
./aligner_0mm.h:119:22: warning: private field 'ebwtBw_' is not used [-Wunused-private-field]
Ebwt<String<Dna> >* ebwtBw_;
^
./aligner_0mm.h:136:11: warning: private field 'seed_' is not used [-Wunused-private-field]
uint32_t seed_;
^
./aligner_0mm.h:351:22: warning: private field 'ebwtBw_' is not used [-Wunused-private-field]
Ebwt<String<Dna> >* ebwtBw_;
^
./aligner_0mm.h:379:17: warning: private field 'seed_' is not used [-Wunused-private-field]
const uint32_t seed_;
^
In file included from ebwt_search.cpp:27:
./aligner_1mm.h:173:11: warning: private field 'seed_' is not used [-Wunused-private-field]
uint32_t seed_;
^
./aligner_1mm.h:491:17: warning: private field 'seed_' is not used [-Wunused-private-field]
const uint32_t seed_;
^
In file included from ebwt_search.cpp:28:
./aligner_23mm.h:243:11: warning: private field 'seed_' is not used [-Wunused-private-field]
uint32_t seed_;
^
./aligner_23mm.h:688:17: warning: private field 'seed_' is not used [-Wunused-private-field]
const uint32_t seed_;
^
44 warnings generated.
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:64:
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: unused typedef 'THostValue' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:38:
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: unused typedef 'TLeftValue' [-Wunused-local-typedef]
typedef typename Value<TLeft>::Type TLeftValue;
^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:53:
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: unused typedef 'TIterator' [-Wunused-local-typedef]
typedef typename Iterator<T, Standard>::Type TIterator;
^
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:62:
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: unused typedef 'TId' [-Wunused-local-typedef]
typedef typename Id<TStringSet>::Type TId;
^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:12:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:66:
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: unused typedef 'TPosition' [-Wunused-local-typedef]
typedef typename Position<TAlign>::Type TPosition;
^
In file included from ref_read.cpp:1:
In file included from ./ref_read.h:12:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:69:
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
23 warnings generated.
In file included from pat.cpp:5:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:64:
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: unused typedef 'THostValue' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
^
In file included from pat.cpp:5:
In file included from SeqAn-1.1/seqan/sequence.h:38:
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: unused typedef 'TLeftValue' [-Wunused-local-typedef]
typedef typename Value<TLeft>::Type TLeftValue;
^
In file included from pat.cpp:5:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
In file included from pat.cpp:5:
In file included from SeqAn-1.1/seqan/sequence.h:53:
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from pat.cpp:5:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: unused typedef 'TIterator' [-Wunused-local-typedef]
typedef typename Iterator<T, Standard>::Type TIterator;
^
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from pat.cpp:5:
In file included from SeqAn-1.1/seqan/sequence.h:62:
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: unused typedef 'TId' [-Wunused-local-typedef]
typedef typename Id<TStringSet>::Type TId;
^
In file included from pat.cpp:6:
In file included from SeqAn-1.1/seqan/file.h:66:
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: unused typedef 'TPosition' [-Wunused-local-typedef]
typedef typename Position<TAlign>::Type TPosition;
^
In file included from pat.cpp:6:
In file included from SeqAn-1.1/seqan/file.h:69:
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
23 warnings generated.
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:64:
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: unused typedef 'THostValue' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:38:
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: unused typedef 'TLeftValue' [-Wunused-local-typedef]
typedef typename Value<TLeft>::Type TLeftValue;
^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:53:
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: unused typedef 'TIterator' [-Wunused-local-typedef]
typedef typename Iterator<T, Standard>::Type TIterator;
^
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
In file included from SeqAn-1.1/seqan/sequence.h:62:
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: unused typedef 'TId' [-Wunused-local-typedef]
typedef typename Id<TStringSet>::Type TId;
^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:9:
In file included from ./hit.h:12:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:66:
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: unused typedef 'TPosition' [-Wunused-local-typedef]
typedef typename Position<TAlign>::Type TPosition;
^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:9:
In file included from ./hit.h:12:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:69:
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
23 warnings generated.
In file included from hit_set.cpp:10:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:64:
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: unused typedef 'THostValue' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
^
In file included from hit_set.cpp:10:
In file included from SeqAn-1.1/seqan/sequence.h:38:
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: unused typedef 'TLeftValue' [-Wunused-local-typedef]
typedef typename Value<TLeft>::Type TLeftValue;
^
In file included from hit_set.cpp:10:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
In file included from hit_set.cpp:10:
In file included from SeqAn-1.1/seqan/sequence.h:53:
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from hit_set.cpp:10:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: unused typedef 'TIterator' [-Wunused-local-typedef]
typedef typename Iterator<T, Standard>::Type TIterator;
^
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from hit_set.cpp:10:
In file included from SeqAn-1.1/seqan/sequence.h:62:
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: unused typedef 'TId' [-Wunused-local-typedef]
typedef typename Id<TStringSet>::Type TId;
^
In file included from hit_set.cpp:11:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:66:
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: unused typedef 'TPosition' [-Wunused-local-typedef]
typedef typename Position<TAlign>::Type TPosition;
^
In file included from hit_set.cpp:11:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:69:
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
23 warnings generated.
In file included from sam.cpp:11:
In file included from ./pat.h:12:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:64:
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: unused typedef 'THostValue' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
^
In file included from sam.cpp:11:
In file included from ./pat.h:12:
In file included from SeqAn-1.1/seqan/sequence.h:38:
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: unused typedef 'TLeftValue' [-Wunused-local-typedef]
typedef typename Value<TLeft>::Type TLeftValue;
^
In file included from sam.cpp:11:
In file included from ./pat.h:12:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
In file included from sam.cpp:11:
In file included from ./pat.h:12:
In file included from SeqAn-1.1/seqan/sequence.h:53:
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from sam.cpp:11:
In file included from ./pat.h:12:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: unused typedef 'TIterator' [-Wunused-local-typedef]
typedef typename Iterator<T, Standard>::Type TIterator;
^
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from sam.cpp:11:
In file included from ./pat.h:12:
In file included from SeqAn-1.1/seqan/sequence.h:62:
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: unused typedef 'TId' [-Wunused-local-typedef]
typedef typename Id<TStringSet>::Type TId;
^
In file included from sam.cpp:11:
In file included from ./pat.h:13:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:66:
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: unused typedef 'TPosition' [-Wunused-local-typedef]
typedef typename Position<TAlign>::Type TPosition;
^
In file included from sam.cpp:11:
In file included from ./pat.h:13:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:69:
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
23 warnings generated.
In file included from color_dec.cpp:11:
In file included from ./alphabet.h:6:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:64:
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: unused typedef 'THostValue' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
^
In file included from color_dec.cpp:11:
In file included from ./alphabet.h:6:
In file included from SeqAn-1.1/seqan/sequence.h:38:
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: unused typedef 'TLeftValue' [-Wunused-local-typedef]
typedef typename Value<TLeft>::Type TLeftValue;
^
In file included from color_dec.cpp:11:
In file included from ./alphabet.h:6:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
In file included from color_dec.cpp:11:
In file included from ./alphabet.h:6:
In file included from SeqAn-1.1/seqan/sequence.h:53:
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from color_dec.cpp:11:
In file included from ./alphabet.h:6:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: unused typedef 'TIterator' [-Wunused-local-typedef]
typedef typename Iterator<T, Standard>::Type TIterator;
^
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from color_dec.cpp:11:
In file included from ./alphabet.h:6:
In file included from SeqAn-1.1/seqan/sequence.h:62:
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: unused typedef 'TId' [-Wunused-local-typedef]
typedef typename Id<TStringSet>::Type TId;
^
In file included from color_dec.cpp:11:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:66:
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: unused typedef 'TPosition' [-Wunused-local-typedef]
typedef typename Position<TAlign>::Type TPosition;
^
In file included from color_dec.cpp:11:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:69:
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
23 warnings generated.
In file included from hit.cpp:1:
In file included from ./hit.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:27:
In file included from SeqAn-1.1/seqan/basic.h:64:
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: unused typedef 'THolderType' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: unused typedef 'THostValue' [-Wunused-local-typedef]
typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
^
In file included from hit.cpp:1:
In file included from ./hit.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:38:
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: unused typedef 'TLeftValue' [-Wunused-local-typedef]
typedef typename Value<TLeft>::Type TLeftValue;
^
In file included from hit.cpp:1:
In file included from ./hit.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:51:
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: unused typedef 'TTarget' [-Wunused-local-typedef]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
In file included from hit.cpp:1:
In file included from ./hit.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:53:
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from hit.cpp:1:
In file included from ./hit.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:57:
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: unused typedef 'TIterator' [-Wunused-local-typedef]
typedef typename Iterator<T, Standard>::Type TIterator;
^
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: unused typedef 'TSize' [-Wunused-local-typedef]
typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
^
In file included from hit.cpp:1:
In file included from ./hit.h:11:
In file included from SeqAn-1.1/seqan/sequence.h:62:
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: unused typedef 'TId' [-Wunused-local-typedef]
typedef typename Id<TStringSet>::Type TId;
^
In file included from hit.cpp:1:
In file included from ./hit.h:12:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:66:
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: unused typedef 'TPosition' [-Wunused-local-typedef]
typedef typename Position<TAlign>::Type TPosition;
^
In file included from hit.cpp:1:
In file included from ./hit.h:12:
In file included from ./alphabet.h:7:
In file included from SeqAn-1.1/seqan/file.h:69:
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: unused typedef 'TRow' [-Wunused-local-typedef]
typedef typename Row<TAlign>::Type TRow;
^
23 warnings generated.
mkdir -p ../inst
cp bowtie-align-s ../inst/bowtie
cp bowtie-build-s ../inst/bowtie-build
cd SpliceMap; \
make -f Makefile; \
echo "MAKE of SpliceMap DONE"
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp
SpliceMap_utils_QuasR.cpp:364:15: warning: taking the absolute value of unsigned type 'bool' has no effect [-Wabsolute-value]
direc_type = abs(direc_type);
^
SpliceMap_utils_QuasR.cpp:364:15: note: remove the call to 'abs' since unsigned values cannot be negative
direc_type = abs(direc_type);
^˜˜
1 warning generated.
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c params.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o
runSpliceMap_QuasR.cpp:108:31: warning: unused variable 'chr_file_list_it' [-Wunused-variable]
vector<string>::iterator chr_file_list_it = chr_file_list.begin();
^
runSpliceMap_QuasR.cpp:191:27: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if (head_clip_length < 0) {
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^ ˜
2 warnings generated.
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o
MAKE of SpliceMap DONE
mkdir -p ../inst
cp SpliceMap/SpliceMap ../inst/SpliceMap
cp SpliceMap/amalgamateSAM ../inst/amalgamateSAM
cp SpliceMap/getSpliceMapUnmapped ../inst/getSpliceMapUnmapped
cp SpliceMap/fuseReorder ../inst/fuseReorder
cp SpliceMap/runSpliceMap_QuasR ../inst/runSpliceMap_QuasR
cp SpliceMap/sortsam ../inst/sortsam
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rbowtie)
