Your message dated Tue, 05 May 2026 06:19:08 +0000
with message-id <[email protected]>
and subject line Bug#1126095: fixed in porechop 0.2.4+dfsg-9
has caused the Debian Bug report #1126095,
regarding porechop: FTBFS porechop/include/alignment.h:10:17: error: ‘seqan’ is
not a namespace-name
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1126095: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1126095
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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'
--- End Message ---
--- Begin Message ---
Source: porechop
Source-Version: 0.2.4+dfsg-9
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
porechop, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated porechop package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 05 May 2026 07:55:42 +0200
Source: porechop
Architecture: source
Version: 0.2.4+dfsg-9
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1126095
Changes:
porechop (0.2.4+dfsg-9) unstable; urgency=medium
.
* Standards-Version: 4.7.4 (routine-update)
* Reflow Uploaders field (cme)
* Remove Priority field (cme)
* Drop default 'Rules-Requires-Root: no' from d/control (routine-
update)
* SeqAn-2.5.0 patch from experimental Closes: #1126095
* DEP3 dates
* d/watch: version=5
Checksums-Sha1:
444bedff29648af3c3299e26aac3206c38ee374d 2102 porechop_0.2.4+dfsg-9.dsc
93768bf2b6d0f35a08c2b9423a453ec97cef8c39 7428
porechop_0.2.4+dfsg-9.debian.tar.xz
f6e915b085839d64afaadb21e9500ca9d51a0553 7132
porechop_0.2.4+dfsg-9_amd64.buildinfo
Checksums-Sha256:
ade4e7ab10a42ed135e64c92586f096f4f39c1b1b0968787fe1befdb39525c22 2102
porechop_0.2.4+dfsg-9.dsc
1d21109b037232a5f28faa07f47d68735061fe174579846a3081f34ab85f179a 7428
porechop_0.2.4+dfsg-9.debian.tar.xz
2ceb9660e5d8e84acc6c54f569a5de566be046cd863d2383ccbeb4ffb2e02ad2 7132
porechop_0.2.4+dfsg-9_amd64.buildinfo
Files:
a62bb8e8f175d74ac1ae6ac770a4436e 2102 science optional
porechop_0.2.4+dfsg-9.dsc
4e196b8f33a53fb3cec9587e024a13a0 7428 science optional
porechop_0.2.4+dfsg-9.debian.tar.xz
f97273d6a52316c6f459c065bbff0bcb 7132 science optional
porechop_0.2.4+dfsg-9_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=ltbF
-----END PGP SIGNATURE-----
pgps2DUvCN4OO.pgp
Description: PGP signature
--- End Message ---
