--- Begin Message ---
Source: bowtie2
Version: 2.2.9-2
Severity: serious
Tags: stretch sid
User: debian...@lists.debian.org
Usertags: qa-ftbfs-20160713 qa-ftbfs
Justification: FTBFS with GCC 6 on amd64
Hi,
During a rebuild of all packages in sid using the gcc-defaults package
available in experimental to make GCC default to version 6, your package failed
to build on amd64. For more information about GCC 6 and Stretch, see:
- https://wiki.debian.org/GCC6
- https://lists.debian.org/debian-devel-announce/2016/06/msg00007.html
Relevant part (hopefully):
> g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2
> -funroll-loops -g3 -fPIE -pie -Wl,-z,relro -Wl,-z,now -DPOPCNT_CAPABILITY
> -DWITH_TBB\"" -fPIE -pie -Wl,-z,relro -Wl,-z,now -DPOPCNT_CAPABILITY
> -DWITH_TBB \
> -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\""
> -DBUILD_HOST="\"\"" -DBUILD_TIME="\"\"" -DCOMPILER_VERSION="\"\""
> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM
> -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall \
> -I third_party \
> -o bowtie2-build-s bt2_build.cpp \
> ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp
> bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp
> random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
> -lpthread -ltbb -ltbbmalloc_proxy
> In file included from blockwise_sa.h:34:0,
> from bt2_idx.h:42,
> from bt2_build.cpp:27:
> diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
> diff_sample.h:180:6: warning: this ‘if’ clause does not guard...
> [-Wmisleading-indentation]
> if(!diffs[d1]) diffCnt++; diffs[d1] = true;
> ^~
> diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly
> indented as if it is guarded by the ‘if’
> if(!diffs[d1]) diffCnt++; diffs[d1] = true;
> ^~~~~
> diff_sample.h:181:6: warning: this ‘if’ clause does not guard...
> [-Wmisleading-indentation]
> if(!diffs[d2]) diffCnt++; diffs[d2] = true;
> ^~
> diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly
> indented as if it is guarded by the ‘if’
> if(!diffs[d2]) diffCnt++; diffs[d2] = true;
> ^~~~~
> In file included from bt2_idx.h:42:0,
> from bt2_build.cpp:27:
> blockwise_sa.h: In instantiation of ‘class
> KarkkainenBlockwiseSA<S2bDnaString>’:
> blockwise_sa.h:520:48: required from here
> blockwise_sa.h:218:5: error: looser throw specifier for
> ‘KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA() noexcept (false) [with
> TStr = S2bDnaString]’
> ~KarkkainenBlockwiseSA()
> ^
> In file included from bt2_idx.h:42:0,
> from bt2_build.cpp:27:
> blockwise_sa.h:178:7: error: overriding ‘virtual
> InorderBlockwiseSA<S2bDnaString>::~InorderBlockwiseSA() noexcept’
> class InorderBlockwiseSA : public BlockwiseSA<TStr> {
> ^~~~~~~~~~~~~~~~~~
> In file included from bt2_build.cpp:27:0:
> bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*>
> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int,
> int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU,
> TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
> bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated
> [-Wdeprecated-declarations]
> auto_ptr<stringstream> ss(new stringstream());
> ^~~~~~~~
> In file included from /usr/include/c++/6/memory:81:0,
> from bt2_idx.h:28,
> from bt2_build.cpp:27:
> /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
> template<typename> class auto_ptr;
> ^~~~~~~~
> In file included from bt2_build.cpp:27:0:
> bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated
> [-Wdeprecated-declarations]
> auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
> ^~~~~~~~
> In file included from /usr/include/c++/6/memory:81:0,
> from bt2_idx.h:28,
> from bt2_build.cpp:27:
> /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
> template<typename> class auto_ptr;
> ^~~~~~~~
> In file included from bt2_idx.h:42:0,
> from bt2_build.cpp:27:
> blockwise_sa.h: In instantiation of ‘class
> KarkkainenBlockwiseSA<SString<char> >’:
> bt2_idx.h:1062:66: required from ‘void
> Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const
> RefReadInParams&, std::ofstream&, std::ofstream&, const string&,
> std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU,
> TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU =
> unsigned int; std::ofstream = std::basic_ofstream<char>; std::__cxx11::string
> = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
> bt2_idx.h:655:23: required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t,
> int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU,
> TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const
> RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr
> = SString<char>; int32_t = int; std::__cxx11::string =
> std::__cxx11::basic_string<char>; TIndexOffU = unsigned int; uint32_t =
> unsigned int]’
> bt2_build.cpp:462:14: required from ‘void driver(const string&,
> EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with
> TStr = SString<char>; std::__cxx11::string =
> std::__cxx11::basic_string<char>]’
> bt2_build.cpp:618:78: required from here
> blockwise_sa.h:218:5: error: looser throw specifier for
> ‘KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA() noexcept (false) [with
> TStr = SString<char>]’
> ~KarkkainenBlockwiseSA()
> ^
> In file included from bt2_idx.h:42:0,
> from bt2_build.cpp:27:
> blockwise_sa.h:178:7: error: overriding ‘virtual
> InorderBlockwiseSA<SString<char> >::~InorderBlockwiseSA() noexcept’
> class InorderBlockwiseSA : public BlockwiseSA<TStr> {
> ^~~~~~~~~~~~~~~~~~
> In file included from blockwise_sa.h:34:0,
> from bt2_idx.h:42,
> from bt2_idx.cpp:25:
> diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
> diff_sample.h:180:6: warning: this ‘if’ clause does not guard...
> [-Wmisleading-indentation]
> if(!diffs[d1]) diffCnt++; diffs[d1] = true;
> ^~
> diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly
> indented as if it is guarded by the ‘if’
> if(!diffs[d1]) diffCnt++; diffs[d1] = true;
> ^~~~~
> diff_sample.h:181:6: warning: this ‘if’ clause does not guard...
> [-Wmisleading-indentation]
> if(!diffs[d2]) diffCnt++; diffs[d2] = true;
> ^~
> diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly
> indented as if it is guarded by the ‘if’
> if(!diffs[d2]) diffCnt++; diffs[d2] = true;
> ^~~~~
> In file included from bt2_idx.h:42:0,
> from bt2_idx.cpp:25:
> blockwise_sa.h: In instantiation of ‘class
> KarkkainenBlockwiseSA<S2bDnaString>’:
> blockwise_sa.h:520:48: required from here
> blockwise_sa.h:218:5: error: looser throw specifier for
> ‘KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA() noexcept (false) [with
> TStr = S2bDnaString]’
> ~KarkkainenBlockwiseSA()
> ^
> In file included from bt2_idx.h:42:0,
> from bt2_idx.cpp:25:
> blockwise_sa.h:178:7: error: overriding ‘virtual
> InorderBlockwiseSA<S2bDnaString>::~InorderBlockwiseSA() noexcept’
> class InorderBlockwiseSA : public BlockwiseSA<TStr> {
> ^~~~~~~~~~~~~~~~~~
> In file included from bt2_idx.cpp:25:0:
> bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*>
> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int,
> int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU,
> TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
> bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated
> [-Wdeprecated-declarations]
> auto_ptr<stringstream> ss(new stringstream());
> ^~~~~~~~
> In file included from /usr/include/c++/6/memory:81:0,
> from bt2_idx.h:28,
> from bt2_idx.cpp:25:
> /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
> template<typename> class auto_ptr;
> ^~~~~~~~
> In file included from bt2_idx.cpp:25:0:
> bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated
> [-Wdeprecated-declarations]
> auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
> ^~~~~~~~
> In file included from /usr/include/c++/6/memory:81:0,
> from bt2_idx.h:28,
> from bt2_idx.cpp:25:
> /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
> template<typename> class auto_ptr;
> ^~~~~~~~
> In file included from blockwise_sa.h:34:0,
> from bt2_idx.h:42,
> from bt2_io.cpp:25:
> diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
> diff_sample.h:180:6: warning: this ‘if’ clause does not guard...
> [-Wmisleading-indentation]
> if(!diffs[d1]) diffCnt++; diffs[d1] = true;
> ^~
> diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly
> indented as if it is guarded by the ‘if’
> if(!diffs[d1]) diffCnt++; diffs[d1] = true;
> ^~~~~
> diff_sample.h:181:6: warning: this ‘if’ clause does not guard...
> [-Wmisleading-indentation]
> if(!diffs[d2]) diffCnt++; diffs[d2] = true;
> ^~
> diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly
> indented as if it is guarded by the ‘if’
> if(!diffs[d2]) diffCnt++; diffs[d2] = true;
> ^~~~~
> In file included from bt2_idx.h:42:0,
> from bt2_io.cpp:25:
> blockwise_sa.h: In instantiation of ‘class
> KarkkainenBlockwiseSA<S2bDnaString>’:
> blockwise_sa.h:520:48: required from here
> blockwise_sa.h:218:5: error: looser throw specifier for
> ‘KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA() noexcept (false) [with
> TStr = S2bDnaString]’
> ~KarkkainenBlockwiseSA()
> ^
> In file included from bt2_idx.h:42:0,
> from bt2_io.cpp:25:
> blockwise_sa.h:178:7: error: overriding ‘virtual
> InorderBlockwiseSA<S2bDnaString>::~InorderBlockwiseSA() noexcept’
> class InorderBlockwiseSA : public BlockwiseSA<TStr> {
> ^~~~~~~~~~~~~~~~~~
> In file included from bt2_io.cpp:25:0:
> bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*>
> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int,
> int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU,
> TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
> bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated
> [-Wdeprecated-declarations]
> auto_ptr<stringstream> ss(new stringstream());
> ^~~~~~~~
> In file included from /usr/include/c++/6/memory:81:0,
> from bt2_idx.h:28,
> from bt2_io.cpp:25:
> /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
> template<typename> class auto_ptr;
> ^~~~~~~~
> In file included from bt2_io.cpp:25:0:
> bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated
> [-Wdeprecated-declarations]
> auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
> ^~~~~~~~
> In file included from /usr/include/c++/6/memory:81:0,
> from bt2_idx.h:28,
> from bt2_io.cpp:25:
> /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
> template<typename> class auto_ptr;
> ^~~~~~~~
> In file included from blockwise_sa.h:34:0,
> from bt2_idx.h:42,
> from bt2_util.cpp:26:
> diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
> diff_sample.h:180:6: warning: this ‘if’ clause does not guard...
> [-Wmisleading-indentation]
> if(!diffs[d1]) diffCnt++; diffs[d1] = true;
> ^~
> diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly
> indented as if it is guarded by the ‘if’
> if(!diffs[d1]) diffCnt++; diffs[d1] = true;
> ^~~~~
> diff_sample.h:181:6: warning: this ‘if’ clause does not guard...
> [-Wmisleading-indentation]
> if(!diffs[d2]) diffCnt++; diffs[d2] = true;
> ^~
> diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly
> indented as if it is guarded by the ‘if’
> if(!diffs[d2]) diffCnt++; diffs[d2] = true;
> ^~~~~
> In file included from bt2_idx.h:42:0,
> from bt2_util.cpp:26:
> blockwise_sa.h: In instantiation of ‘class
> KarkkainenBlockwiseSA<S2bDnaString>’:
> blockwise_sa.h:520:48: required from here
> blockwise_sa.h:218:5: error: looser throw specifier for
> ‘KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA() noexcept (false) [with
> TStr = S2bDnaString]’
> ~KarkkainenBlockwiseSA()
> ^
> In file included from bt2_idx.h:42:0,
> from bt2_util.cpp:26:
> blockwise_sa.h:178:7: error: overriding ‘virtual
> InorderBlockwiseSA<S2bDnaString>::~InorderBlockwiseSA() noexcept’
> class InorderBlockwiseSA : public BlockwiseSA<TStr> {
> ^~~~~~~~~~~~~~~~~~
> In file included from bt2_util.cpp:26:0:
> bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*>
> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int,
> int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU,
> TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
> bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated
> [-Wdeprecated-declarations]
> auto_ptr<stringstream> ss(new stringstream());
> ^~~~~~~~
> In file included from /usr/include/c++/6/memory:81:0,
> from bt2_idx.h:28,
> from bt2_util.cpp:26:
> /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
> template<typename> class auto_ptr;
> ^~~~~~~~
> In file included from bt2_util.cpp:26:0:
> bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated
> [-Wdeprecated-declarations]
> auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
> ^~~~~~~~
> In file included from /usr/include/c++/6/memory:81:0,
> from bt2_idx.h:28,
> from bt2_util.cpp:26:
> /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
> template<typename> class auto_ptr;
> ^~~~~~~~
> In file included from multikey_qsort.h:27:0,
> from multikey_qsort.cpp:20:
> diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
> diff_sample.h:180:6: warning: this ‘if’ clause does not guard...
> [-Wmisleading-indentation]
> if(!diffs[d1]) diffCnt++; diffs[d1] = true;
> ^~
> diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly
> indented as if it is guarded by the ‘if’
> if(!diffs[d1]) diffCnt++; diffs[d1] = true;
> ^~~~~
> diff_sample.h:181:6: warning: this ‘if’ clause does not guard...
> [-Wmisleading-indentation]
> if(!diffs[d2]) diffCnt++; diffs[d2] = true;
> ^~
> diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly
> indented as if it is guarded by the ‘if’
> if(!diffs[d2]) diffCnt++; diffs[d2] = true;
> ^~~~~
> In file included from diff_sample.cpp:20:0:
> diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
> diff_sample.h:180:6: warning: this ‘if’ clause does not guard...
> [-Wmisleading-indentation]
> if(!diffs[d1]) diffCnt++; diffs[d1] = true;
> ^~
> diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly
> indented as if it is guarded by the ‘if’
> if(!diffs[d1]) diffCnt++; diffs[d1] = true;
> ^~~~~
> diff_sample.h:181:6: warning: this ‘if’ clause does not guard...
> [-Wmisleading-indentation]
> if(!diffs[d2]) diffCnt++; diffs[d2] = true;
> ^~
> diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly
> indented as if it is guarded by the ‘if’
> if(!diffs[d2]) diffCnt++; diffs[d2] = true;
> ^~~~~
> make[2]: *** [bowtie2-build-s] Error 1
The full build log is available from:
http://people.debian.org/~lucas/logs/2016/07/13/bowtie2_2.2.9-2_unstable_gcc6.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
--- End Message ---
