[Debian-med-packaging] Help needed to update bowtie to new version

[Andreas Tille]

Hi,

there is a new release of bowtie (1.1).  I updated the quilt patches in SVN but
the package does not build.  The error is

g++ -O3 -DCOMPILER_OPTIONS="\"-O3  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro\""  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro  \
        -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -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 /usr/include/seqan -I third_party -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 blockwise_sa.h:13:0,
                 from ebwt.h:27,
                 from ebwt_build.cpp:11:
diff_sample.h: In member function 'void DifferenceCoverSample<T>::build()':
diff_sample.h:859:3: error: '_Context_LSS' was not declared in this scope
   _Context_LSS<TIndexOff> c;
   ^
diff_sample.h:859:25: error: expected primary-expression before '>' token
   _Context_LSS<TIndexOff> c;
                         ^
diff_sample.h:859:27: error: 'c' was not declared in this scope
   _Context_LSS<TIndexOff> c;
                           ^
Makefile:205: recipe for target 'bowtie-build-s' failed


Any help would be welcome.

Kind regards

      Andreas.


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