[From nobody Tue May 5 07:21:07 2026 Received: (at submit) by bugs.debian.org; 21 Jan 2026 18:58:27 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-105.3 required=4.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,DKIM_VALID_AU,DKIM_VALID_EF,FROMDEVELOPER, SPF_HELO_NONE,SPF_NONE,UNPARSEABLE_RELAY,USER_IN_DKIM_WELCOMELIST autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 70; hammy, 150; neutral, 157; spammy, 0. spammytokens: hammytokens:0.000-+--Hx-spam-relays-external:sk:stravin, 0.000-+--H*RT:sk:stravin, 0.000-+--Hx-spam-relays-external:311, 0.000-+--H*RT:311, 0.000-+--H*RT:108 Return-path: <ema@debian.org> Received: from stravinsky.debian.org ([2001:41b8:202:deb::311:108]:56280) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <ema@debian.org>) id 1vidPP-005U7P-2D for submit@bugs.debian.org; Wed, 21 Jan 2026 18:58:27 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debian.org; s=smtpauto.stravinsky; h=X-Debian-User:Content-Transfer-Encoding:Content-Type :MIME-Version:Message-ID:Subject:To:From:Date:Reply-To:Cc:Content-ID: Content-Description:In-Reply-To:References; bh=OywbqQo2CSMVteXKdCp09xtx5Gh7H0rdLMz5YJF1kkc=; b=fG5V9p18cCRwcHMkAxi+xIyoR8 7oMOXj/kfhqIZFpfoODsskX2/1KluzfzIHMsj4eLWH+aCd0PzQzRPTxaeXxo/suzVEtF8FvNfyvPz UM/21RMcTL5VEM23UEdF2U4jmMx1/aP+FrKCmZ0OcUm6puzZj6tUIfVExKorfPpA/CDWSakFgyIxb 2OxAtoFJmZIXs1mCTY3UB2q0XVkb15m0xC6h2DBn7l43vyqCRDc30zEfS6BB3tm/Bzp8IjqL+2J0H 2K6w57YlLlYVW5ySaSNLBQTK3KkF6WmMrXEXZo/zuw6o6NumNCJ1POZWo/l5EY+F4Zb8GUi4MBVoz WwSly2JQ==; Received: from authenticated user by stravinsky.debian.org with esmtpsa (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.94.2) (envelope-from <ema@debian.org>) id 1vidPN-00CPSU-Qm for submit@bugs.debian.org; Wed, 21 Jan 2026 18:58:26 +0000 Date: Wed, 21 Jan 2026 19:58:24 +0100 From: Emanuele Rocca <ema@debian.org> To: submit@bugs.debian.org Subject: porechop: FTBFS =?utf-8?Q?porechop=2Finclu?= =?utf-8?B?ZGUvYWxpZ25tZW50Lmg6MTA6MTc6IGVycm9yOiDigJhzZXFhbg==?= =?utf-8?B?4oCZ?= is not a namespace-name Message-ID: <aXEh0AdwfkuQhscD@ariel.home> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-Debian-User: ema Delivered-To: submit@bugs.debian.org 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' ]