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.
