BioC 3.5: CHECK report for Rbowtie on veracruz2

Package: Rbowtie

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rbowtie_1.16.0.tar.gz

StartedAt: 2017-10-18 07:55:29 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 07:57:45 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 135.9 seconds

RetCode: 0

Status:  OK

CheckDir: Rbowtie.Rcheck

Warnings: 0

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rbowtie_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Rbowtie.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rbowtie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rbowtie’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rbowtie’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
Package unavailable to check Rd xrefs: ‘QuasR’
* 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/Rbowtie.Rcheck/00check.log’
for details.

* installing *source* package ‘Rbowtie’ ...
** 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: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: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: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)

name	user	system	elapsed
Rbowtie-package	0.001	0.000	0.001
Rbowtie	0.931	0.141	1.093
SpliceMap	0.445	0.106	1.302