[Debian-med-packaging] Bug#1126095: porechop: FTBFS porechop/include/alignment.h:10:17: error: ‘seqan’ is not a namespace-name
Emanuele Rocca
ema at debian.org
Wed Jan 21 18:58:24 GMT 2026
Source: porechop
Version: 0.2.4+dfsg-6
Severity: serious
Tags: ftbfs sid trixie
Justification: fails to build from source (but built successfully in the past)
Hi,
porechop currently fails to build from source on amd64 and arm64 (and probably
other architectures) with the following errors:
g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o porechop/src/adapter_align.o porechop/src/adapter_align.cpp
In file included from porechop/include/adapter_align.h:7,
from porechop/src/adapter_align.cpp:1:
porechop/include/alignment.h:10:17: error: ‘seqan’ is not a namespace-name
10 | using namespace seqan;
| ^~~~~
porechop/include/alignment.h:15:26: error: expected ‘)’ before ‘<’ token
15 | ScoredAlignment(Align<Dna5String, ArrayGaps> & alignment,
| ~ ^
| )
porechop/include/adapter_align.h:9:17: error: ‘seqan’ is not a namespace-name
9 | using namespace seqan;
| ^~~~~
porechop/src/adapter_align.cpp: In function ‘char* adapterAlignment(char*, char*, int, int, int, int)’:
porechop/src/adapter_align.cpp:15:5: error: ‘Dna5String’ was not declared in this scope; did you mean ‘seqan2::Dna5String’?
15 | Dna5String sequenceH = readSeq;
| ^~~~~~~~~~
| seqan2::Dna5String
In file included from /usr/include/seqan/sequence.h:112,
from porechop/include/adapter_align.h:4:
/usr/include/seqan/sequence/sequence_shortcuts.h:119:36: note: ‘seqan2::Dna5String’ declared here
119 | typedef String<Dna5, Alloc<void> > Dna5String;
| ^~~~~~~~~~
porechop/src/adapter_align.cpp:16:15: error: expected ‘;’ before ‘sequenceV’
16 | Dna5String sequenceV = adapterSeq;
| ^~~~~~~~~~
| ;
porechop/src/adapter_align.cpp:20:5: error: ‘Align’ was not declared in this scope; did you mean ‘seqan2::Align’?
20 | Align<Dna5String, ArrayGaps> alignment;
| ^~~~~
| seqan2::Align
In file included from /usr/include/seqan/file.h:65,
from /usr/include/seqan/stream.h:62,
from /usr/include/seqan/score.h:43,
from /usr/include/seqan/graph_align.h:45,
from /usr/include/seqan/align.h:59,
from porechop/include/alignment.h:8:
/usr/include/seqan/file/file_forwards.h:46:7: note: ‘seqan2::Align’ declared here
46 | class Align;
| ^~~~~
porechop/src/adapter_align.cpp:20:23: error: ‘ArrayGaps’ was not declared in this scope; did you mean ‘seqan2::ArrayGaps’?
20 | Align<Dna5String, ArrayGaps> alignment;
| ^~~~~~~~~
| seqan2::ArrayGaps
In file included from /usr/include/seqan/align.h:85:
/usr/include/seqan/align/gaps_array.h:75:25: note: ‘seqan2::ArrayGaps’ declared here
75 | typedef Tag<ArrayGaps_> ArrayGaps;
| ^~~~~~~~~
In file included from porechop/src/alignment.cpp:2:
porechop/include/alignment.h:10:17: error: ‘seqan’ is not a namespace-name
10 | using namespace seqan;
| ^~~~~
porechop/include/alignment.h:15:26: error: expected ‘)’ before ‘<’ token
15 | ScoredAlignment(Align<Dna5String, ArrayGaps> & alignment,
| ~ ^
| )
porechop/src/adapter_align.cpp:20:34: error: ‘alignment’ was not declared in this scope
20 | Align<Dna5String, ArrayGaps> alignment;
| ^~~~~~~~~
porechop/src/alignment.cpp:6:33: error: expected constructor, destructor, or type conversion before ‘(’ token
6 | ScoredAlignment::ScoredAlignment(Align<Dna5String, ArrayGaps> & alignment,
| ^
porechop/src/adapter_align.cpp:21:12: error: ‘rows’ was not declared in this scope; did you mean ‘seqan2::rows’?
21 | resize(rows(alignment), 2);
| ^~~~
| seqan2::rows
In file included from /usr/include/seqan/align.h:97:
/usr/include/seqan/align/align_base.h:341:1: note: ‘seqan2::rows’ declared here
341 | rows(Align<TSource, TSpec> const & me)
| ^~~~
porechop/src/adapter_align.cpp:21:5: error: ‘resize’ was not declared in this scope; did you mean ‘seqan2::resize’?
21 | resize(rows(alignment), 2);
| ^~~~~~
| seqan2::resize
In file included from /usr/include/seqan/align.h:146:
/usr/include/seqan/align/dp_matrix_sparse.h:95:1: note: ‘seqan2::resize’ declared here
95 | resize(DPMatrix_<TValue, SparseDPMatrix, THost> & dpMatrix,
| ^~~~~~
porechop/src/adapter_align.cpp:22:18: error: ‘row’ was not declared in this scope; did you mean ‘seqan2::row’?
22 | assignSource(row(alignment, 0), sequenceH);
| ^~~
| seqan2::row
/usr/include/seqan/align/align_base.h:372:1: note: ‘seqan2::row’ declared here
372 | row(Align<TSource, TSpec> const & me,
| ^~~
porechop/src/adapter_align.cpp:22:37: error: ‘sequenceH’ was not declared in this scope
22 | assignSource(row(alignment, 0), sequenceH);
| ^~~~~~~~~
porechop/src/adapter_align.cpp:22:5: error: ‘assignSource’ was not declared in this scope; did you mean ‘seqan2::assignSource’?
22 | assignSource(row(alignment, 0), sequenceH);
| ^~~~~~~~~~~~
| seqan2::assignSource
In file included from /usr/include/seqan/align.h:89:
/usr/include/seqan/align/gaps_anchor.h:672:1: note: ‘seqan2::assignSource’ declared here
672 | assignSource(Gaps<TSequence, AnchorGaps<TGapAnchor> > & gaps, TSequence2 const & source)
| ^~~~~~~~~~~~
porechop/src/adapter_align.cpp:23:37: error: ‘sequenceV’ was not declared in this scope
23 | assignSource(row(alignment, 1), sequenceV);
| ^~~~~~~~~
porechop/src/adapter_align.cpp:24:5: error: ‘Score’ was not declared in this scope; did you mean ‘seqan2::Score’?
24 | Score<int, Simple> scoringScheme(matchScore, mismatchScore, gapExtensionScore, gapOpenScore);
| ^~~~~
| seqan2::Score
In file included from /usr/include/seqan/score.h:45:
/usr/include/seqan/score/score_base.h:68:7: note: ‘seqan2::Score’ declared here
68 | class Score;
| ^~~~~
porechop/src/adapter_align.cpp:24:11: error: expected primary-expression before ‘int’
24 | Score<int, Simple> scoringScheme(matchScore, mismatchScore, gapExtensionScore, gapOpenScore);
| ^~~
porechop/src/adapter_align.cpp:26:5: error: ‘AlignConfig’ was not declared in this scope; did you mean ‘seqan2::AlignConfig’?
26 | AlignConfig<true, true, true, true> alignConfig;
| ^~~~~~~~~~~
| seqan2::AlignConfig
In file included from /usr/include/seqan/align.h:70:
/usr/include/seqan/align/align_config.h:93:7: note: ‘seqan2::AlignConfig’ declared here
93 | class AlignConfig
| ^~~~~~~~~~~
porechop/src/adapter_align.cpp:26:41: error: ‘alignConfig’ was not declared in this scope
26 | AlignConfig<true, true, true, true> alignConfig;
| ^~~~~~~~~~~
porechop/src/adapter_align.cpp:27:44: error: ‘scoringScheme’ was not declared in this scope
27 | int score = globalAlignment(alignment, scoringScheme, alignConfig);
| ^~~~~~~~~~~~~
porechop/src/adapter_align.cpp:27:17: error: ‘globalAlignment’ was not declared in this scope; did you mean ‘seqan2::globalAlignment’?
27 | int score = globalAlignment(alignment, scoringScheme, alignConfig);
| ^~~~~~~~~~~~~~~
| seqan2::globalAlignment
In file included from /usr/include/seqan/align.h:218:
/usr/include/seqan/align/global_alignment_specialized.h:121:5: note: ‘seqan2::globalAlignment’ declared here
121 | int globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
| ^~~~~~~~~~~~~~~
porechop/src/adapter_align.cpp:29:48: error: ‘length’ was not declared in this scope; did you mean ‘seqan2::length’?
29 | ScoredAlignment scoredAlignment(alignment, length(readSeq), length(adapterSeq), score);
| ^~~~~~
| seqan2::length
In file included from /usr/include/seqan/align.h:145:
/usr/include/seqan/align/dp_matrix.h:419:1: note: ‘seqan2::length’ declared here
419 | length(DPMatrix_<TValue, TMatrixSpec, THost> const & dpMatrix)
| ^~~~~~
make[1]: *** [Makefile:56: porechop/src/alignment.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: *** [Makefile:56: porechop/src/adapter_align.o] Error 1
make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg'
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