[Debian-med-packaging] Bug#906341: bowtie: FTBFS in buster/sid

Santiago Vila sanvila at debian.org
Fri Aug 17 12:19:09 BST 2018


Package: src:bowtie
Version: 1.2.2+dfsg-3
Severity: serious
Tags: ftbfs

Dear maintainer:

I tried to build this package in buster but it failed:

--------------------------------------------------------------------------------
[...]
 debian/rules build-indep
dh build-indep
   dh_update_autotools_config -i
   dh_autoreconf -i
   dh_auto_configure -i
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/bowtie-1.2.2+dfsg'
/usr/bin/make allall
make[2]: Entering directory '/<<BUILDDIR>>/bowtie-1.2.2+dfsg'
g++ -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 -std=c++03 -Wl,-z,relro -Wl,-z,now\""  -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security  -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -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++ -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 -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \
	-isystem /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 \

[... snipped ...]

ebwt.h:826:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_ftab    != NULL) delete[] _ftab;    _ftab    = NULL;
                                            ^~~~~
ebwt.h:827:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_eftab   != NULL) delete[] _eftab;   _eftab   = NULL;
    ^~
ebwt.h:827:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_eftab   != NULL) delete[] _eftab;   _eftab   = NULL;
                                            ^~~~~~
ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_isa     != NULL) delete[] _isa;     _isa     = NULL;
    ^~
ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_isa     != NULL) delete[] _isa;     _isa     = NULL;
                                            ^~~~
ebwt.h:834:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_plen    != NULL) delete[] _plen;    _plen    = NULL;
    ^~
ebwt.h:834:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_plen    != NULL) delete[] _plen;    _plen    = NULL;
                                            ^~~~~
ebwt.h:835:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
    if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
    ^~
ebwt.h:835:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
                                            ^~~~~~~~
ebwt.h: In member function 'uint32_t* Ebwt<TStr>::isa() const':
ebwt.h:865:44: error: cannot convert 'TIndexOffU* const' {aka 'long unsigned int* const'} to 'uint32_t*' {aka 'unsigned int*'} in return
  uint32_t*   isa() const          { return _isa; } /* check */
                                            ^~~~
In file included from ebwt.h:27,
                 from ebwt_build.cpp:11:
blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA<TStr>::nextSuffix() [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> >; TIndexOffU = long unsigned int]':
blockwise_sa.h:287:23:   required from here
blockwise_sa.h:297:26: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size<seqan::String<long unsigned int, seqan::Alloc<> > >::Type' {aka 'long unsigned int'} [-Wsign-compare]
        for (int i = 0; i < length(_sampleSuffs) + 1; i++) {
                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA<TStr>::nextSuffix() [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Packed<> >; TIndexOffU = long unsigned int]':
blockwise_sa.h:287:23:   required from here
blockwise_sa.h:297:26: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size<seqan::String<long unsigned int, seqan::Alloc<> > >::Type' {aka 'long unsigned int'} [-Wsign-compare]
make[2]: *** [Makefile:273: bowtie-build-l] Error 1
make[2]: Leaving directory '/<<BUILDDIR>>/bowtie-1.2.2+dfsg'
make[1]: *** [debian/rules:17: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<BUILDDIR>>/bowtie-1.2.2+dfsg'
make: *** [debian/rules:14: build-indep] Error 2
dpkg-buildpackage: error: debian/rules build-indep subprocess returned exit status 2
--------------------------------------------------------------------------------

The build was made with "dpkg-buildpackage -A" in my autobuilder.
Most probably, it also fails here in reproducible builds:

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/bowtie.html

where you can get a full build log if you need it.

If this is really a bug in one of the build-depends, please use reassign and affects,
so that this is still visible in the BTS web page for this package.

Thanks.



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