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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