Hi,
pbdagcon fails to build in a test rebuild on at least amd64 and arm64 with
gcc-16/g++-16, but builds properly with gcc-15/g++-15. The severity of this
report will be raised before the forky release.
The full build log can be found at:
https://people.debian.org/~ema/gcc-16-rebuilds/output-1/pbdagcon_arm64.build.xz
The last lines of the build log are at the end of this report.
To build with GCC 16, either set CC=gcc-16 CXX=g++-16 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures include unused (but set) variables, array subscripts
partly outside array bounds, and new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-16/porting_to.html
Please only close this issue after double-checking that the package can be
built correctly with GCC 16.
Please do not reassign this bug to another package. If a fix in another package
is required, then file a bug for the other package (or clone), and mark this
bug as blocked by the bug in the other package.
[...]
402 | SWAlign(qFragment, tFragment, fragScoreMat, fragPathMat, frontAlignment,
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
403 | scoreFn, EndAnchored);
| ~~~~~~~~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/alignment/SDPAlignImpl.hpp:41:20: required from ‘int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; DNALength = unsigned int]’
41 | return SDPAlign(query, target, scoreFn, wordSize, sdpIns, sdpDel, indelRate, alignment,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
42 | fragmentSet, prefixFragmentSet, suffixFragmentSet, targetTupleList,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
43 | targetPrefixTupleList, targetSuffixTupleList, maxFragmentChain, alignType,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
44 | detailedAlignment, extendFrontByLocalAlignment, noRecurseUnder, fastSDP,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
45 | minFragmentsToUseGraphPaper);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SimpleAligner.cpp:35:13: required from here
35 | SDPAlign(query, target, distScoreFn_, tupleMetrics_.tupleSize,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
36 | config_.sdpIndel, config_.sdpIndel, config_.indelRate*2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | initialAln, Local);
| ~~~~~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/alignment/SWAlignImpl.hpp:135:10: warning: variable ‘matchScorePtr’ set but not used [-Wunused-but-set-variable=]
135 | int *matchScorePtr = &scoreMat[0];
| ^~~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/alignment/SWAlignImpl.hpp:136:10: warning: variable ‘gapQScorePtr’ set but not used [-Wunused-but-set-variable=]
136 | int *gapQScorePtr = &scoreMat[1];
| ^~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/alignment/SWAlignImpl.hpp:137:10: warning: variable ‘gapTScorePtr’ set but not used [-Wunused-but-set-variable=]
137 | int *gapTScorePtr = &scoreMat[tSeq.length + 1];
| ^~~~~~~~~~~~
In file included from /usr/include/pbseq/alignment/tuples/TupleList.hpp:64,
from /usr/include/pbseq/alignment/tuples/DNATuple.hpp:13,
from /usr/include/pbseq/alignment/tuples/TupleMatching.hpp:5:
/usr/include/pbseq/alignment/tuples/TupleListImpl.hpp: In instantiation of ‘void TupleList<T>::FindAll(T&, typename std::vector<T>::const_iterator&, typename std::vector<T>::const_iterator&) [with T = PositionDNATuple; typename std::vector<T>::const_iterator = std::vector<PositionDNATuple, std::allocator<PositionDNATuple> >::const_iterator]’:
/usr/include/pbseq/alignment/tuples/TupleMatchingImpl.hpp:51:40: required from ‘int StoreMatchingPositions(TSequence&, TupleMetrics&, T_TupleList&, std::vector<CharType>&) [with TSequence = DNASequence; TMatch = Fragment; T_TupleList = TupleList<PositionDNATuple>]’
51 | targetTupleList.FindAll(queryTuple, curIt, endIt);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/alignment/SDPAlignImpl.hpp:163:27: required from ‘int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>; DNALength = unsigned int]’
163 | StoreMatchingPositions(qPrefix, tmSmall, targetPrefixTupleList, prefixFragmentSet);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/alignment/SDPAlignImpl.hpp:41:20: required from ‘int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; DNALength = unsigned int]’
41 | return SDPAlign(query, target, scoreFn, wordSize, sdpIns, sdpDel, indelRate, alignment,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
42 | fragmentSet, prefixFragmentSet, suffixFragmentSet, targetTupleList,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
43 | targetPrefixTupleList, targetSuffixTupleList, maxFragmentChain, alignType,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
44 | detailedAlignment, extendFrontByLocalAlignment, noRecurseUnder, fastSDP,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
45 | minFragmentsToUseGraphPaper);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SimpleAligner.cpp:35:13: required from here
35 | SDPAlign(query, target, distScoreFn_, tupleMetrics_.tupleSize,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
36 | config_.sdpIndel, config_.sdpIndel, config_.indelRate*2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | initialAln, Local);
| ~~~~~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/tuples/TupleListImpl.hpp:107:21: error: return type of ‘int PositionDNATuple::operator==(const PositionDNATuple&) const’ is not ‘bool’
107 | if (*endPos != tuple) {
| ~~~~~~~~^~~~~~~~
/usr/include/pbseq/alignment/tuples/TupleListImpl.hpp:107:21: note: used as rewritten candidate for comparison of ‘const PositionDNATuple’ and ‘PositionDNATuple’
make[2]: *** [<builtin>: SimpleAligner.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp'
make[1]: *** [makefile:34: cpp] Error 2
make[1]: Leaving directory '/build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+dfsg'
dh_auto_build: error: make -j128 INSTALL="install --strip-program=true" returned exit code 2
make: *** [debian/rules:21: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2