--- Begin Message ---
Package: src:pizzly
Version: 0.37.3+ds-11
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202601/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:pizzly, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
rm -f debian/pizzly.1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/pizzly.substvars debian/files
rm -fr -- debian/pizzly/ debian/tmp/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path
.\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o
-type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
[... snipped ...]
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:338:20: error: âseqanâ has not been
declared
338 | int ascore = seqan::globalAlignmentScore(read, ref,
seqan::MyersBitVector());
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:338:54: error: ârefâ was not declared in
this scope; did you mean âstd::refâ?
338 | int ascore = seqan::globalAlignmentScore(read, ref,
seqan::MyersBitVector());
| ^~~
| std::ref
In file included from /usr/include/c++/15/string:54,
from /usr/include/c++/15/bits/locale_classes.h:42,
from /usr/include/c++/15/bits/ios_base.h:43,
from /usr/include/c++/15/ios:46,
from /usr/include/c++/15/bits/ostream.h:43,
from /usr/include/c++/15/ostream:42,
from /usr/include/c++/15/iostream:43,
from /<<PKGBUILDDIR>>/main.cpp:1:
/usr/include/c++/15/bits/refwrap.h:448:5: note: âstd::refâ declared here
448 | ref(reference_wrapper<_Tp> __t) noexcept
| ^~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:338:59: error: âseqanâ has not been
declared
338 | int ascore = seqan::globalAlignmentScore(read, ref,
seqan::MyersBitVector());
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:332:13: warning: unused variable âtseqâ
[-Wunused-variable]
332 | auto& tseq = it.first;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function:
/<<PKGBUILDDIR>>/FilterFusions.hpp:403:9: error: âseqanâ has not been
declared
403 | seqan::CharString read(seq.c_str());
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:404:9: error: âseqanâ has not been
declared
404 | seqan::CharString splitref(tsplit.first.c_str()); //
inefficient, refactor at some point
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:405:9: error: âseqanâ has not been
declared
405 | seqan::CharString saferef(tsafe.first.c_str());
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:9: error: âseqanâ has not been
declared
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight,
splitRowLeft, safeRowRight;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:21: error: âseqanâ has not been
declared
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight,
splitRowLeft, safeRowRight;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:40: error: âreadRowLeftâ was not
declared in this scope
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight,
splitRowLeft, safeRowRight;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:53: error: âreadRowRightâ was not
declared in this scope
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight,
splitRowLeft, safeRowRight;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:67: error: âsplitRowLeftâ was not
declared in this scope
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight,
splitRowLeft, safeRowRight;
|
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:81: error: âsafeRowRightâ was not
declared in this scope
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight,
splitRowLeft, safeRowRight;
|
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:408:9: error: âseqanâ has not been
declared
408 | seqan::setSource(readRowLeft, read);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:409:9: error: âseqanâ has not been
declared
409 | seqan::setSource(readRowRight, read);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:410:9: error: âseqanâ has not been
declared
410 | seqan::setSource(splitRowLeft, splitref);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:410:40: error: âsplitrefâ was not
declared in this scope; did you mean âsplitrecâ?
410 | seqan::setSource(splitRowLeft, splitref);
| ^~~~~~~~
| splitrec
/<<PKGBUILDDIR>>/FilterFusions.hpp:411:9: error: âseqanâ has not been
declared
411 | seqan::setSource(safeRowRight, saferef);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:411:40: error: âsaferefâ was not
declared in this scope
411 | seqan::setSource(safeRowRight, saferef);
| ^~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:413:9: error: âseqanâ has not been
declared
413 | seqan::Score<int, seqan::Simple> scoringScheme(0,-1,-1);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:413:22: error: expected primary-expression
before âintâ
413 | seqan::Score<int, seqan::Simple> scoringScheme(0,-1,-1);
| ^~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:414:9: error: âseqanâ has not been
declared
414 | seqan::AlignConfig<false, true, true, false> config;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:414:54: error: âconfigâ was not declared
in this scope
414 | seqan::AlignConfig<false, true, true, false> config;
| ^~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:415:26: error: âseqanâ has not been
declared
415 | int splitScore = seqan::splitAlignment(readRowLeft,
splitRowLeft, readRowRight, safeRowRight, scoringScheme, config);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:415:103: error: âscoringSchemeâ was not
declared in this scope; did you mean âseqan2::scoringSchemeâ?
415 | int splitScore = seqan::splitAlignment(readRowLeft,
splitRowLeft, readRowRight, safeRowRight, scoringScheme, config);
|
^~~~~~~~~~~~~
|
seqan2::scoringScheme
In file included from /usr/include/seqan/find.h:93,
from /usr/include/seqan/index.h:46:
/usr/include/seqan/find/find_score.h:180:1: note: âseqan2::scoringSchemeâ
declared here
180 | scoringScheme(Pattern<TNeedle, DPSearch<TScore, TSpec,
TFindBeginPatternSpec> > & me)
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:426:24: error: âseqanâ has not been
declared
426 | splitPos = seqan::toSourcePosition(readRowLeft,
seqan::clippedEndPosition(readRowLeft));
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:426:61: error: âseqanâ has not been
declared
426 | splitPos = seqan::toSourcePosition(readRowLeft,
seqan::clippedEndPosition(readRowLeft));
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:433:27: error: âseqanâ has not been
declared
433 | int t2pos = seqan::toSourcePosition(safeRowRight, 0);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:434:27: error: âseqanâ has not been
declared
434 | int t2clip= seqan::toSourcePosition(readRowRight, 0);
//seqan::clippedBeginPosition(readRowRight));
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:436:39: error: âseqanâ has not been
declared
436 | t2copy.pos = t2.pos - seqan::length(saferef) + t2pos +
(seqan::length(splitref) - t2clip);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:436:73: error: âseqanâ has not been
declared
436 | t2copy.pos = t2.pos - seqan::length(saferef) + t2pos +
(seqan::length(splitref) - t2clip);
|
^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:438:39: error: âseqanâ has not been
declared
438 | t2copy.pos = t2.pos + seqan::length(saferef) - t2pos -1;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function:
/<<PKGBUILDDIR>>/FilterFusions.hpp:709:25: warning: comparison of integer
expressions of different signedness: âintâ and
âstd::vector<ExonModel>::size_typeâ {aka âlong unsigned intâ}
[-Wsign-compare]
709 | for (int i = 0; i < trm.exons.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function:
/<<PKGBUILDDIR>>/FilterFusions.hpp:738:25: warning: comparison of integer
expressions of different signedness: âintâ and
âstd::vector<ExonModel>::size_typeâ {aka âlong unsigned intâ}
[-Wsign-compare]
738 | for (int i = 0; i < trm.exons.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function:
/<<PKGBUILDDIR>>/FilterFusions.hpp:765:11: warning: unused variable âgapâ
[-Wunused-variable]
765 | int gap = d2 - d1;
| ^~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:781:21: warning: moving a local object in a
return statement prevents copy elision [-Wpessimizing-move]
781 | return std::move(ret);
| ~~~~~~~~~^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:781:21: note: remove âstd::moveâ call
/<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function:
/<<PKGBUILDDIR>>/FilterFusions.hpp:872:42: error: request for member âfindâ
in âtrx.Transcriptome::seqsâ, which is of non-class type âconst intâ
872 | const auto & seq1 = trx.seqs.find(sp.tr1)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:873:42: error: request for member âfindâ
in âtrx.Transcriptome::seqsâ, which is of non-class type âconst intâ
873 | const auto & seq2 = trx.seqs.find(sp.tr2)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:883:33: warning: comparison of integer
expressions of different signedness: âintâ and
âstd::vector<int>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare]
883 | for (int i = 0; i < v.size(); i++) {
| ~~^~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:907:145: error: âseqanâ has not been
declared
907 | std::string fasta_name = sp.tr1 + "_0:" +
std::to_string(tp1) + "_" + sp.tr2 + "_" + std::to_string(tp2) + ":" +
std::to_string(seqan::length(seq2));
|
^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:920:82: error: âseqanâ has not been
declared
920 | << ", \"endPos\" : " <<
std::to_string((sp.dir1) ? tp1 : seqan::length(seq1)) << ", \"edit\" : " <<
std::to_string(ed1)
|
^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:924:82: error: âseqanâ has not been
declared
924 | << ", \"endPos\" : " <<
std::to_string((sp.dir2) ? tp2 : seqan::length(seq2)) << ", \"edit\" : " <<
std::to_string(ed2)
|
^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:929:35: warning: comparison of integer
expressions of different signedness: âintâ and
âstd::vector<int>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare]
929 | for (int i = 0; i < readsInTr.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:940:29: error: âseqanâ has not been
declared
940 | << seqan::prefix(seq1, tp1)
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:941:29: error: âseqanâ has not been
declared
941 | << seqan::suffix(seq2, tp2)
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:867:17: warning: unused variable
âsplit_readsâ [-Wunused-variable]
867 | int split_reads = spp.second;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:961:33: error: âseqanâ has not been
declared
961 | int rlen1 = seqan::length(fr.seq1);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:962:33: error: âseqanâ has not been
declared
962 | int rlen2 = seqan::length(fr.seq2);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:964:50: error: request for member âfindâ
in âtrx.Transcriptome::seqsâ, which is of non-class type âconst intâ
964 | const auto & seq1 = trx.seqs.find(t1.tr)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:965:50: error: request for member âfindâ
in âtrx.Transcriptome::seqsâ, which is of non-class type âconst intâ
965 | const auto & seq2 = trx.seqs.find(t2.tr)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:971:72: error: âseqanâ has not been
declared
971 | int tp1 = (t1strand) ? std::min(t1.pos+rlen1,
(int)seqan::length(seq1)-1) : std::max(t1.pos-rlen1,0);
|
^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:972:72: error: âseqanâ has not been
declared
972 | int tp2 = (t2strand) ? std::min(t2.pos+rlen2,
(int)seqan::length(seq2)-1) : std::max(t2.pos-rlen2,0);
|
^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1033:29: warning: loop variable âpâ
creates a copy from type âconst std::pair<const SplitInfo,
std::vector<std::pair<int, int> > >â [-Wrange-loop-construct]
1033 | for (const auto p : trfmap) {
| ^
/<<PKGBUILDDIR>>/FilterFusions.hpp:1033:29: note: use reference type to prevent
copying
1033 | for (const auto p : trfmap) {
| ^
| &
/<<PKGBUILDDIR>>/FilterFusions.hpp:1037:44: error: request for member
âfindâ in âtrx.Transcriptome::seqsâ, which is of non-class type
âconst intâ
1037 | const auto & seq1 = trx.seqs.find(spi.tr1)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1038:44: error: request for member
âfindâ in âtrx.Transcriptome::seqsâ, which is of non-class type
âconst intâ
1038 | const auto & seq2 = trx.seqs.find(spi.tr2)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1080:145: error: âseqanâ has not been
declared
1080 | fasta_name = spi.tr1 + "_0:" + std::to_string(spi.pos1)
+ "_" + spi.tr2 + "_" + std::to_string(spi.pos2) + ":" +
std::to_string(seqan::length(seq2));
|
^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1083:88: error: âseqanâ has not been
declared
1083 | << ", \"endPos\" : " <<
std::to_string((spi.dir1) ? spi.pos1 : seqan::length(seq1))
|
^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1086:88: error: âseqanâ has not been
declared
1086 | << ", \"endPos\" : " <<
std::to_string((spi.dir2) ? spi.pos2 : seqan::length(seq2))
|
^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1091:35: warning: comparison of integer
expressions of different signedness: âintâ and
âstd::vector<int>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare]
1091 | for (int i = 0; i < readsInTr.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1102:28: error: âseqanâ has not been
declared
1102 | << seqan::prefix(seq1, spi.pos1)
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1103:28: error: âseqanâ has not been
declared
1103 | << seqan::suffix(seq2, spi.pos2)
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1115:31: warning: comparison of integer
expressions of different signedness: âintâ and
âstd::vector<int>::size_typeâ {aka âlong unsigned intâ} [-Wsign-compare]
1115 | for (int i = 0; i < v.size(); i++) {
| ~~^~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1112:18: warning: unused variable
âfirstJsonReadâ [-Wunused-variable]
1112 | bool firstJsonRead = true;
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/main.cpp: At global scope:
/<<PKGBUILDDIR>>/main.cpp:11:1: error: âseqanâ does not name a type
11 | seqan::ArgumentParser::ParseResult
| ^~~~~
/<<PKGBUILDDIR>>/main.cpp: In function âint main(int, const char**)â:
/<<PKGBUILDDIR>>/main.cpp:79:5: error: âseqanâ has not been declared
79 | seqan::ArgumentParser::ParseResult res = parseCommandLine(options,
argc, argv);
| ^~~~~
/<<PKGBUILDDIR>>/main.cpp:83:9: error: âresâ was not declared in this scope
83 | if (res != seqan::ArgumentParser::PARSE_OK)
| ^~~
/<<PKGBUILDDIR>>/main.cpp:83:16: error: âseqanâ has not been declared
83 | if (res != seqan::ArgumentParser::PARSE_OK)
| ^~~~~
/<<PKGBUILDDIR>>/main.cpp:84:23: error: âseqanâ has not been declared
84 | return res == seqan::ArgumentParser::PARSE_ERROR;
| ^~~~~
/<<PKGBUILDDIR>>/main.cpp:111:31: error: âbeginâ was not declared in this
scope
111 | for (const auto &it : trx.seqs) {
| ^~~~
/<<PKGBUILDDIR>>/main.cpp:111:31: note: suggested alternatives:
In file included from /usr/include/c++/15/string:55:
/usr/include/c++/15/bits/range_access.h:120:37: note: âstd::beginâ
120 | template<typename _Tp> const _Tp* begin(const valarray<_Tp>&)
noexcept;
| ^~~~~
In file included from /usr/include/seqan/index/index_pizzachili.h:39,
from /usr/include/seqan/index.h:194:
/usr/include/seqan/index/index_pizzachili_string.h:460:1: note:
âseqan2::beginâ
460 | begin(
| ^~~~~
/<<PKGBUILDDIR>>/main.cpp:111:31: error: âendâ was not declared in this
scope
111 | for (const auto &it : trx.seqs) {
| ^~~~
/<<PKGBUILDDIR>>/main.cpp:111:31: note: suggested alternatives:
/usr/include/c++/15/bits/range_access.h:122:37: note: âstd::endâ
122 | template<typename _Tp> const _Tp* end(const valarray<_Tp>&) noexcept;
| ^~~
/usr/include/seqan/index/index_pizzachili_string.h:480:1: note:
âseqan2::endâ
480 | end(
| ^~~
/<<PKGBUILDDIR>>/main.cpp:126:43: error: request for member âsizeâ in
âtrx.Transcriptome::seqsâ, which is of non-class type âintâ
126 | } else if (numTxpSeqFound != trx.seqs.size()) {
| ^~~~
/<<PKGBUILDDIR>>/main.cpp:127:78: error: request for member âsizeâ in
âtrx.Transcriptome::seqsâ, which is of non-class type âintâ
127 | std::cerr << "Warning: could not find annotations for " <<
(trx.seqs.size() - numTxpSeqFound) << " transcripts\n" << std::endl;
|
^~~~
/<<PKGBUILDDIR>>/GeneModel.hpp: In function âStrandedness operator~(const
Strandedness&)â:
/<<PKGBUILDDIR>>/GeneModel.hpp:18:1: warning: control reaches end of non-void
function [-Wreturn-type]
18 | }
| ^
make[3]: *** [CMakeFiles/pizzly.dir/build.make:82:
CMakeFiles/pizzly.dir/main.cpp.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:90: CMakeFiles/pizzly.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:94: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j2 INSTALL="install
--strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:7: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit
status 2
--------------------------------------------------------------------------------
--- End Message ---
pgpXWQH0xDM1t.pgp
