--- Begin Message ---
Package: src:pbdagcon
Version: 0.3+git20180411.c14c422+dfsg-10
Severity: important
Tags: sid forky ftbfs
User: [email protected]
Usertags: ftbfs-gcc-16
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
--- End Message ---
pgpz3CCQ5ya2a.pgp
