[Debian-med-packaging] Bug#1125653: pizzly: FTBFS: /<<PKGBUILDDIR>>/GeneModel.hpp:92:35: error: 'seqan' was not declared in this scope; did you mean 'seqan2'?
Santiago Vila
sanvila at debian.org
Thu Jan 15 16:54:30 GMT 2026
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: ‘seqan’ has not been declared
338 | int ascore = seqan::globalAlignmentScore(read, ref, seqan::MyersBitVector());
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:338:54: error: ‘ref’ was not declared in this scope; did you mean ‘std::ref’?
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: ‘std::ref’ declared here
448 | ref(reference_wrapper<_Tp> __t) noexcept
| ^~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:338:59: error: ‘seqan’ has not been declared
338 | int ascore = seqan::globalAlignmentScore(read, ref, seqan::MyersBitVector());
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:332:13: warning: unused variable ‘tseq’ [-Wunused-variable]
332 | auto& tseq = it.first;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function:
/<<PKGBUILDDIR>>/FilterFusions.hpp:403:9: error: ‘seqan’ has not been declared
403 | seqan::CharString read(seq.c_str());
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:404:9: error: ‘seqan’ has not been declared
404 | seqan::CharString splitref(tsplit.first.c_str()); // inefficient, refactor at some point
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:405:9: error: ‘seqan’ has not been declared
405 | seqan::CharString saferef(tsafe.first.c_str());
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:9: error: ‘seqan’ has not been declared
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:21: error: ‘seqan’ has not been declared
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:40: error: ‘readRowLeft’ was not declared in this scope
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:53: error: ‘readRowRight’ was not declared in this scope
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:67: error: ‘splitRowLeft’ was not declared in this scope
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:407:81: error: ‘safeRowRight’ was not declared in this scope
407 | seqan::Gaps<seqan::CharString> readRowLeft, readRowRight, splitRowLeft, safeRowRight;
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:408:9: error: ‘seqan’ has not been declared
408 | seqan::setSource(readRowLeft, read);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:409:9: error: ‘seqan’ has not been declared
409 | seqan::setSource(readRowRight, read);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:410:9: error: ‘seqan’ has not been declared
410 | seqan::setSource(splitRowLeft, splitref);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:410:40: error: ‘splitref’ was not declared in this scope; did you mean ‘splitrec’?
410 | seqan::setSource(splitRowLeft, splitref);
| ^~~~~~~~
| splitrec
/<<PKGBUILDDIR>>/FilterFusions.hpp:411:9: error: ‘seqan’ has not been declared
411 | seqan::setSource(safeRowRight, saferef);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:411:40: error: ‘saferef’ was not declared in this scope
411 | seqan::setSource(safeRowRight, saferef);
| ^~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:413:9: error: ‘seqan’ has not been declared
413 | seqan::Score<int, seqan::Simple> scoringScheme(0,-1,-1);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:413:22: error: expected primary-expression before ‘int’
413 | seqan::Score<int, seqan::Simple> scoringScheme(0,-1,-1);
| ^~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:414:9: error: ‘seqan’ has not been declared
414 | seqan::AlignConfig<false, true, true, false> config;
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:414:54: error: ‘config’ was not declared in this scope
414 | seqan::AlignConfig<false, true, true, false> config;
| ^~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:415:26: error: ‘seqan’ has not been declared
415 | int splitScore = seqan::splitAlignment(readRowLeft, splitRowLeft, readRowRight, safeRowRight, scoringScheme, config);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:415:103: error: ‘scoringScheme’ was not declared in this scope; did you mean ‘seqan2::scoringScheme’?
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: ‘seqan2::scoringScheme’ declared here
180 | scoringScheme(Pattern<TNeedle, DPSearch<TScore, TSpec, TFindBeginPatternSpec> > & me)
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:426:24: error: ‘seqan’ has not been declared
426 | splitPos = seqan::toSourcePosition(readRowLeft, seqan::clippedEndPosition(readRowLeft));
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:426:61: error: ‘seqan’ has not been declared
426 | splitPos = seqan::toSourcePosition(readRowLeft, seqan::clippedEndPosition(readRowLeft));
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:433:27: error: ‘seqan’ has not been declared
433 | int t2pos = seqan::toSourcePosition(safeRowRight, 0);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:434:27: error: ‘seqan’ has not been declared
434 | int t2clip= seqan::toSourcePosition(readRowRight, 0); //seqan::clippedBeginPosition(readRowRight));
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:436:39: error: ‘seqan’ has not been declared
436 | t2copy.pos = t2.pos - seqan::length(saferef) + t2pos + (seqan::length(splitref) - t2clip);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:436:73: error: ‘seqan’ has not been declared
436 | t2copy.pos = t2.pos - seqan::length(saferef) + t2pos + (seqan::length(splitref) - t2clip);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:438:39: error: ‘seqan’ 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: ‘int’ and ‘std::vector<ExonModel>::size_type’ {aka ‘long unsigned int’} [-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: ‘int’ and ‘std::vector<ExonModel>::size_type’ {aka ‘long unsigned int’} [-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 ‘gap’ [-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 ‘std::move’ call
/<<PKGBUILDDIR>>/FilterFusions.hpp: In lambda function:
/<<PKGBUILDDIR>>/FilterFusions.hpp:872:42: error: request for member ‘find’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘const int’
872 | const auto & seq1 = trx.seqs.find(sp.tr1)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:873:42: error: request for member ‘find’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘const int’
873 | const auto & seq2 = trx.seqs.find(sp.tr2)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:883:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
883 | for (int i = 0; i < v.size(); i++) {
| ~~^~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:907:145: error: ‘seqan’ 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: ‘seqan’ 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: ‘seqan’ 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: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
929 | for (int i = 0; i < readsInTr.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:940:29: error: ‘seqan’ has not been declared
940 | << seqan::prefix(seq1, tp1)
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:941:29: error: ‘seqan’ has not been declared
941 | << seqan::suffix(seq2, tp2)
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:867:17: warning: unused variable ‘split_reads’ [-Wunused-variable]
867 | int split_reads = spp.second;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:961:33: error: ‘seqan’ has not been declared
961 | int rlen1 = seqan::length(fr.seq1);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:962:33: error: ‘seqan’ has not been declared
962 | int rlen2 = seqan::length(fr.seq2);
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:964:50: error: request for member ‘find’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘const int’
964 | const auto & seq1 = trx.seqs.find(t1.tr)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:965:50: error: request for member ‘find’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘const int’
965 | const auto & seq2 = trx.seqs.find(t2.tr)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:971:72: error: ‘seqan’ 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: ‘seqan’ 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 ‘p’ creates a copy from type ‘const std::pair<const SplitInfo, std::vector<std::pair<int, int> > >’ [-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 ‘find’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘const int’
1037 | const auto & seq1 = trx.seqs.find(spi.tr1)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1038:44: error: request for member ‘find’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘const int’
1038 | const auto & seq2 = trx.seqs.find(spi.tr2)->second;
| ^~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1080:145: error: ‘seqan’ 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: ‘seqan’ has not been declared
1083 | << ", \"endPos\" : " << std::to_string((spi.dir1) ? spi.pos1 : seqan::length(seq1))
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1086:88: error: ‘seqan’ 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: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1091 | for (int i = 0; i < readsInTr.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1102:28: error: ‘seqan’ has not been declared
1102 | << seqan::prefix(seq1, spi.pos1)
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1103:28: error: ‘seqan’ has not been declared
1103 | << seqan::suffix(seq2, spi.pos2)
| ^~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1115:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1115 | for (int i = 0; i < v.size(); i++) {
| ~~^~~~~~~~~~
/<<PKGBUILDDIR>>/FilterFusions.hpp:1112:18: warning: unused variable ‘firstJsonRead’ [-Wunused-variable]
1112 | bool firstJsonRead = true;
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/main.cpp: At global scope:
/<<PKGBUILDDIR>>/main.cpp:11:1: error: ‘seqan’ does not name a type
11 | seqan::ArgumentParser::ParseResult
| ^~~~~
/<<PKGBUILDDIR>>/main.cpp: In function ‘int main(int, const char**)’:
/<<PKGBUILDDIR>>/main.cpp:79:5: error: ‘seqan’ has not been declared
79 | seqan::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
| ^~~~~
/<<PKGBUILDDIR>>/main.cpp:83:9: error: ‘res’ was not declared in this scope
83 | if (res != seqan::ArgumentParser::PARSE_OK)
| ^~~
/<<PKGBUILDDIR>>/main.cpp:83:16: error: ‘seqan’ has not been declared
83 | if (res != seqan::ArgumentParser::PARSE_OK)
| ^~~~~
/<<PKGBUILDDIR>>/main.cpp:84:23: error: ‘seqan’ has not been declared
84 | return res == seqan::ArgumentParser::PARSE_ERROR;
| ^~~~~
/<<PKGBUILDDIR>>/main.cpp:111:31: error: ‘begin’ 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: ‘std::begin’
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: ‘seqan2::begin’
460 | begin(
| ^~~~~
/<<PKGBUILDDIR>>/main.cpp:111:31: error: ‘end’ 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: ‘std::end’
122 | template<typename _Tp> const _Tp* end(const valarray<_Tp>&) noexcept;
| ^~~
/usr/include/seqan/index/index_pizzachili_string.h:480:1: note: ‘seqan2::end’
480 | end(
| ^~~
/<<PKGBUILDDIR>>/main.cpp:126:43: error: request for member ‘size’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘int’
126 | } else if (numTxpSeqFound != trx.seqs.size()) {
| ^~~~
/<<PKGBUILDDIR>>/main.cpp:127:78: error: request for member ‘size’ in ‘trx.Transcriptome::seqs’, which is of non-class type ‘int’
127 | std::cerr << "Warning: could not find annotations for " << (trx.seqs.size() - numTxpSeqFound) << " transcripts\n" << std::endl;
| ^~~~
/<<PKGBUILDDIR>>/GeneModel.hpp: In function ‘Strandedness operator~(const Strandedness&)’:
/<<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
--------------------------------------------------------------------------------
More information about the Debian-med-packaging
mailing list