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Issue with new version of Bowtie

Hi,

I've moved bowtie from SVN to Git[1] and injected the packaging for the
latest upstream version.  Unfortunately the build ended in:

...
g++ -w -O3 -DCOMPILER_OPTIONS="\"-O3  -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security  -g -O2 -fdebug-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now\""  -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/bowtie-1.2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security  -g -O2 -fdebug-prefix-map=/build/bowtie-1.2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now  \
        -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian-reproducible\"" -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" -DCOMPILER_VERSION="\"`g++ -w -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" -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 \
        -o bowtie-build-s ebwt_build.cpp \
        ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp  bowtie_build_main.cpp \
        -Wl,-z,relro -Wl,-z,now -lz -lpthread -ltbb -ltbbmalloc_proxy 
In file included from ebwt.h:27:0,
                 from ebwt_build.cpp:11:
blockwise_sa.h: In instantiation of 'class KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Packed<> > >':
blockwise_sa.h:502:52:   required from here
blockwise_sa.h:203:3: error: looser throw specifier for 'KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA() noexcept (false) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Packed<> >]'
   ~KarkkainenBlockwiseSA() {
   ^
In file included from ebwt.h:27:0,
                 from ebwt_build.cpp:11:
blockwise_sa.h:165:7: error:   overriding 'virtual InorderBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Packed<> > >::~InorderBlockwiseSA() noexcept'
 class InorderBlockwiseSA : public BlockwiseSA<TStr> {
       ^~~~~~~~~~~~~~~~~~
In file included from ebwt.h:27:0,
                 from ebwt_build.cpp:11:
blockwise_sa.h: In instantiation of 'class KarkkainenBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> > >':
ebwt.h:752:66:   required from 'void Ebwt<TStr>::initFromVector(std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> >; TIndexOffU = unsigned int; std::ofstream = std::basic_ofstream<char>; std::__cxx11::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
ebwt.h:509:17:   required from 'Ebwt<TStr>::Ebwt(int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> >; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string<char>; TIndexOffU = unsigned int; uint32_t = unsigned int]'
ebwt_build.cpp:451:13:   required from 'void driver(const string&, std::vector<std::__cxx11::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> >; std::__cxx11::string = std::__cxx11::basic_string<char>]'
ebwt_build.cpp:625:61:   required from here
blockwise_sa.h:203:3: error: looser throw specifier for 'KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA() noexcept (false) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> >]'
   ~KarkkainenBlockwiseSA() {
   ^
In file included from ebwt.h:27:0,
                 from ebwt_build.cpp:11:
blockwise_sa.h:165:7: error:   overriding 'virtual InorderBlockwiseSA<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> > >::~InorderBlockwiseSA() noexcept'
 class InorderBlockwiseSA : public BlockwiseSA<TStr> {
       ^~~~~~~~~~~~~~~~~~
Makefile:264: recipe for target 'bowtie-build-s' failed
make[2]: *** [bowtie-build-s] Error 1
make[2]: Leaving directory '/build/bowtie-1.2.1.1+dfsg'
debian/rules:17: recipe for target 'override_dh_auto_build' failed
make[1]: *** [override_dh_auto_build] Error 2
make[1]: Leaving directory '/build/bowtie-1.2.1.1+dfsg'
debian/rules:14: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
I: copying local configuration
E: Failed autobuilding of package
...


Could somebody more educated in bowtie (seqan) please have a look?

Kind regards

       Andreas.


[1] https://anonscm.debian.org/git/debian-med/bowtie.git

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http://fam-tille.de
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