{"bugs":[{"bugid":715718,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/abyss-2.3.4 : Uncompress.cpp: error: redefinition of FILE* fopen(const char*, const char*)"},{"bugid":873022,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/abyss-2.3.4 fails to compile (MUSL): Timer.h:17:17: error: clock_t does not name a type"},{"bugid":898112,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/abyss-2.3.4 calls commands that do not exist (MUSL-CLANG-SYSTEM): :"},{"bugid":939044,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/abyss-2.3.4 - [gcc-15] Timer.cpp: error: m_start was not declared in this scope"}],"categories":[{"categoryid":429,"name":"dev-cpp","summary":"The dev-cpp category contains libraries and utilities relevant to the c++ programming language."},{"categoryid":452,"name":"dev-db","summary":"The dev-db category contains libraries and utilities for database related programming."},{"categoryid":450,"name":"dev-lang","summary":"The dev-lang category contains various programming language implementations and related tools."},{"categoryid":393,"name":"dev-libs","summary":"The dev-libs category contains various miscellaneous programming libraries."},{"categoryid":353,"name":"sci-biology","summary":"The sci-biology category contains software that can be used in biological and related scientific environments."},{"categoryid":361,"name":"sys-cluster","summary":"The sys-cluster category contains cluster-related software."}],"changelog":[{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"c38d55d6e7f840ae9e5d41a963b6979797d74290","committime":"2024-03-08T11:18:47","packageid":50240,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"eschwartz93@gmail.com","authorname":"Eli Schwartz","body":"Closes: https:\/\/bugs.gentoo.org\/862252\nSigned-off-by: Eli Schwartz \nSigned-off-by: Sam James ","commitid":"490ada295187ec9b28e867128b53f6bdf5f68f63","committime":"2024-03-08T01:20:48","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: mark as LTO-unsafe"},{"authoremail":"eschwartz93@gmail.com","authorname":"Eli Schwartz","body":"It seds out something that hasn't existed since 2012:\nhttps:\/\/github.com\/bcgsc\/abyss\/commit\/ded065d3b257e72ceb70ad3f6dd399019b00b46e\n\nSigned-off-by: Eli Schwartz \nSigned-off-by: Sam James ","commitid":"d0b8036f8b6c998f0cd1f5f975e04ec61d2cfe9f","committime":"2024-03-08T01:06:32","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: remove useless sed"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"a55cb1f4455e19d0b88ce121fde33388510d9b61","committime":"2022-01-13T11:36:53","packageid":50240,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"andrewammerlaan@gentoo.org","authorname":"Andrew Ammerlaan","body":"Closes: https:\/\/bugs.gentoo.org\/741154\nCloses: https:\/\/bugs.gentoo.org\/715718\nPackage-Manager: Portage-3.0.30, Repoman-3.0.3\nSigned-off-by: Andrew Ammerlaan ","commitid":"89ab6a3d9d32bcb93e27580298094a875a530685","committime":"2022-01-13T11:20:26","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: drop version 2.0.3"},{"authoremail":"andrewammerlaan@gentoo.org","authorname":"Andrew Ammerlaan","body":"Closes: https:\/\/bugs.gentoo.org\/646478\nPackage-Manager: Portage-3.0.30, Repoman-3.0.3\nSigned-off-by: Andrew Ammerlaan ","commitid":"03ada3844855dd1c9ff2627e7f9239d0248e7cc6","committime":"2022-01-13T11:19:37","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: add version 2.3.4"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"b83cbc544b4607e1911d267d5e3b66e0e2aade2b","committime":"2020-06-21T17:05:14","packageid":50240,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"slyfox@gentoo.org","authorname":"Sergei Trofimovich","body":"Package-Manager: Portage-2.3.101, Repoman-2.3.22\nSigned-off-by: Sergei Trofimovich ","commitid":"4499edbc478106c4f7a04062c8ee2f273474c8cb","committime":"2020-06-21T16:46:53","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: switch from virtual\/libffi"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"81fcfa43c528b384c35629e090dc70b1c8793737","committime":"2020-06-21T11:05:14","packageid":50240,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"slyfox@gentoo.org","authorname":"Sergei Trofimovich","body":"Package-Manager: Portage-2.3.101, Repoman-2.3.22\nSigned-off-by: Sergei Trofimovich ","commitid":"2007740170c55928a8e0d7f5f0628f58f3234c5b","committime":"2020-06-21T10:35:24","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: drop old"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"65adf3ee4286c28ca3754bc1121cc1e5f231937f","committime":"2020-05-25T11:05:12","packageid":50240,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"slyfox@gentoo.org","authorname":"Sergei Trofimovich","body":"GHC uses it's own native code generator. Portage's\nQA check generates false positive because it assumes\npresence of GCC-specific sections.\n\nWorkaround false positiove by disabling the check, bug #677600.\n\nBug: https:\/\/bugs.gentoo.org\/677600\nPackage-Manager: Portage-2.3.100, Repoman-2.3.22\nSigned-off-by: Sergei Trofimovich ","commitid":"caf207dd9d6bdc71885f9f459625856665972df1","committime":"2020-05-25T10:55:52","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: disable CFLAGS QA check on samtobreak"},{"authoremail":"slyfox@gentoo.org","authorname":"Sergei Trofimovich","body":"Use AM_PROG_AR to default to standard AR discovery\ninstead of make's 'ar'.\n\nReported-by: Agostino Sarubbo\nCloses: https:\/\/bugs.gentoo.org\/725300\nPackage-Manager: Portage-2.3.100, Repoman-2.3.22\nSigned-off-by: Sergei Trofimovich ","commitid":"363526d4663d10660c2c593d11a9ab3707443572","committime":"2020-05-25T10:51:11","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: respect AR override, bug #725300"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"658b8384937dcf0e7dc0dc31793a64d7c11ded54","committime":"2018-03-15T23:42:40","packageid":50240,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"slyfox@gentoo.org","authorname":"Sergei Trofimovich","body":"Package-Manager: Portage-2.3.24, Repoman-2.3.6","commitid":"42bcef7f16f3999182b38951f69ce0e15d1ef58a","committime":"2018-03-15T23:30:40","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: bump up to 2.0.3"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"25093d6359f778b8d1052f66ba9e26fc29ded21a","committime":"2017-02-28T20:35:29","packageid":50240,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"robbat2@gentoo.org","authorname":"Robin H. Johnson","body":"Signed-off-by: Robin H. Johnson ","commitid":"61b861acd7b49083dab687e133f30f3331cb7480","committime":"2017-02-28T19:47:27","packageid":50240,"repoid":1,"summary":"Drop $Id$ per council decision in bug #611234."},{"authoremail":"malfatti@neuro.ufrn.br","authorname":"T. Malfatti","commitid":"8457ba6f9fd6f0dbafcca1fb375788eeea02aae1","committime":"2017-01-26T18:44:34","packageid":50240,"repoid":1,"summary":"media-libs\/portaudio: Version bump"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"ac1e9190947a812528bc47250909c9429abb2d42","committime":"2017-01-15T18:33:21","packageid":50240,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mmokrejs@gmail.com","authorname":"Martin Mokrejš","body":"Closes: https:\/\/github.com\/gentoo\/gentoo\/pull\/3414","commitid":"6764ffe099c90b89117afeb0087258ec76f3136f","committime":"2017-01-10T13:32:37","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: only openmpi is supported"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"05aa9b363fa1c5c36739755fb0a23120d24bd0b5","committime":"2016-12-20T17:42:53","packageid":50240,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-2.3.3, Repoman-2.3.1\nCloses: https:\/\/github.com\/gentoo\/gentoo\/pull\/3183","commitid":"159437c4bc58b8fcd12cc33bb11d8a4fef437f1b","committime":"2016-12-20T15:47:48","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: Remove old"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"fb3df0829a5ea4d4447735840019725cc74e9fe3","committime":"2016-11-06T13:21:50","packageid":50240,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"slyfox@gentoo.org","authorname":"Sergei Trofimovich","body":"Fixes gcc-6 and boost-1.62 build failures.\n\nReported-by: Toralf Förster\nBug: https:\/\/bugs.gentoo.org\/596018\n\nPackage-Manager: portage-2.3.2","commitid":"4c8a5799cd9b07143e1c1b9ba865c3e9bbbf5f3e","committime":"2016-11-06T13:12:25","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: bump up to 2.0.2, bug #596018"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"65904781a395b07123c907813a0b055289df21e6","committime":"2016-09-18T23:03:10","packageid":50240,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"slyfox@gentoo.org","authorname":"Sergei Trofimovich","body":"Package-Manager: portage-2.3.0","commitid":"3602af844edaa72d2e2e62018e61466fa3117a51","committime":"2016-09-18T22:51:40","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: pin boost subslot, noticed by Soap"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"661e511c237e3ef7c2be593371b52f07ebf7ea6c","committime":"2016-09-18T21:46:48","packageid":50240,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"slyfox@gentoo.org","authorname":"Sergei Trofimovich","body":"On gcc-6 build failed as:\n```\n In file included from AssemblyAlgorithms.cpp:4:0:\n ..\/DataLayer\/FastaReader.h: In member function ‘FastaReader::operator void*() const’:\n ..\/DataLayer\/FastaReader.h:49:35: error: cannot convert ‘std::istream {aka std::basic_istream}’ to ‘void*’ ...\n operator void*() const { return m_in; }\n ^~~~\n```\n\nIn the following source:\n```c++\n static bool existFile(const char* f)\n {\n ifstream file(f);\n return file;\n }\n\n```\n\nc++98 provides file->operator void*()\nc++11 provides file->explicit operator bool()\n\nHence the failure on c++11.\n\nThe change adds explicit casts around ifstream.\n\nReported-by: Toralf Förster\nBug: https:\/\/bugs.gentoo.org\/594254\n\nPackage-Manager: portage-2.3.0","commitid":"e5fd69e7be7b26a7b7481453553393865d823906","committime":"2016-09-18T21:41:58","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: bump up to 1.9.0, tweak for gcc-6, bug #594254"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"9d43f6610d39072cd401a4ee4df5076e0ac1a4f6","committime":"2016-05-15T08:42:13","packageid":50240,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"slyfox@gentoo.org","authorname":"Sergei Trofimovich","body":"Package-Manager: portage-2.2.28","commitid":"f5f3cc796d91c55aaba42ad00ffb441379848a3b","committime":"2016-05-15T08:25:43","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: add missing dev-libs\/boost dependency"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"0152aa5b9692f16558ee3d70f1e1bd465e56ef9f","committime":"2016-04-03T18:22:06","packageid":50240,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: portage-2.2.28","commitid":"61b63e5e683cf45cb9f52dca6b4f5462a472dc84","committime":"2016-04-03T18:00:32","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: Remove old"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"* EAPI=6\n\nPackage-Manager: portage-2.2.28","commitid":"f462f85a318159798956f27b851268e7fd0c2a16","committime":"2016-04-03T17:57:05","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: Latest ebuild from science-overlay"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"b92cc3e30c4278aa40a3deca9448346eeb84a313","committime":"2016-02-08T23:41:48","packageid":50240,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"slyfox@gentoo.org","authorname":"Sergei Trofimovich","body":"Reported-by: Toralf Förster\nBug: https:\/\/bugs.gentoo.org\/534412\n\nPackage-Manager: portage-2.2.27","commitid":"a50e1769e82e28dedb16083ac9136f17f9af2297","committime":"2016-02-08T23:33:45","packageid":50240,"repoid":1,"summary":"sci-biology\/abyss: fix automagic haskell deps, bug #534412"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"945f0d2a26da4f944fd06ad6a874f69d37ce1e06","committime":"2015-08-09T09:26:46","packageid":50240,"repoid":1,"summary":"2015-08-09 09:26:21 UTC"},{"authoremail":"robbat2@gentoo.org","authorname":"Robin H. Johnson","body":"This commit represents a new era for Gentoo:\nStoring the gentoo-x86 tree in Git, as converted from CVS.\n\nThis commit is the start of the NEW history.\nAny historical data is intended to be grafted onto this point.\n\nCreation process:\n1. Take final CVS checkout snapshot\n2. Remove ALL ChangeLog* files\n3. Transform all Manifests to thin\n4. Remove empty Manifests\n5. Convert all stale $Header$\/$Id$ CVS keywords to non-expanded Git $Id$\n5.1. Do not touch files with -kb\/-ko keyword flags.\n\nSigned-off-by: Robin H. Johnson \nX-Thanks: Alec Warner - did the GSoC 2006 migration tests\nX-Thanks: Robin H. Johnson - infra guy, herding this project\nX-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration\nX-Thanks: Brian Harring - wrote much python to improve cvs2svn\nX-Thanks: Rich Freeman - validation scripts\nX-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration\nX-Thanks: Michał Górny - scripts, QA, nagging\nX-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed","commitid":"56bd759df1d0c750a065b8c845e93d5dfa6b549d","committime":"2015-08-08T20:49:04","packageid":50240,"repoid":1,"summary":"proj\/gentoo: Initial commit"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"a637bd65b7fef8e2be4e7fc6e9097479372e0e2e","committime":"2015-06-19T16:38:33","packageid":50240,"repoid":1,"summary":"2015-06-19 16:35:30 UTC"}],"dependencies":[{"block":false,"categoryid":393,"description":"Boost Libraries for C++","ebuildids":[736385],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"cpp@gentoo.org","maintainername":"Gentoo C++ Project","name":"boost","packageid":45155},{"block":false,"categoryid":452,"description":"SQL database engine","ebuildids":[736385],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"arfrever.fta@gmail.com","maintainername":"Arfrever Frehtes Taifersar Arahesis","name":"sqlite","packageid":50388},{"block":false,"categoryid":393,"description":"Portable, high level programming interface to various calling conventions","ebuildids":[736385],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"toolchain@gentoo.org","maintainername":"Gentoo Toolchain Project","name":"libffi","packageid":52280,"summary":"Compilers for high level languages generate code that follow certain conventions. These conventions are necessary, in part, for separate compilation to work. One such convention is the \"calling convention\". The \"calling convention\" is essentially a set of assumptions made by the compiler about where function arguments will be found on entry to a function. A \"calling convention\" also specifies where the return value for a function is found. Some programs may not know at the time of compilation what arguments are to be passed to a function. For instance, an interpreter may be told at run-time about the number and types of arguments used to call a given function. Libffi can be used in such programs to provide a bridge from the interpreter program to compiled code. The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run time. Ffi stands for Foreign Function Interface. A foreign function interface is the popular name for the interface that allows code written in one language to call code written in another language. The libffi library really only provides the lowest, machine dependent layer of a fully featured foreign function interface. A layer must exist above libffi that handles type conversions for values passed between the two languages."},{"block":false,"categoryid":361,"description":"A high-performance message passing library (MPI)","ebuildids":[736385],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"jsbronder@gentoo.org","maintainername":"Gentoo Cluster Project","name":"openmpi","packageid":53053},{"block":false,"categoryid":429,"description":"An extremely memory-efficient hash_map implementation","ebuildids":[736385],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"cpp@gentoo.org","maintainername":"Gentoo C++ Project","name":"sparsehash","packageid":55213},{"block":false,"categoryid":393,"description":"Library for arbitrary-precision arithmetic on different type of numbers","ebuildids":[736385],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"toolchain@gentoo.org","maintainername":"Gentoo Toolchain Project","name":"gmp","packageid":55512},{"block":false,"categoryid":450,"description":"The Glasgow Haskell Compiler","ebuildids":[736385],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"haskell@gentoo.org","maintainername":"Gentoo Haskell","name":"ghc","packageid":55607}],"depending":[],"ebuilds":[{"archs":["~amd64","~x86"],"ebuildid":736385,"firstseen":"2022-01-13T11:49:10.092622","license":"GPL-3","moddate":"2026-03-22T20:20:57","packageid":50240,"repoid":1,"slot":"0","uses":["misc-haskell","openmp"],"version":"2.3.4"}],"masks":[],"package":{"categoryid":353,"description":"Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"abyss","packageid":50240},"rdependencies":[{"block":false,"categoryid":393,"description":"Boost Libraries for C++","ebuildids":[736385],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"cpp@gentoo.org","maintainername":"Gentoo C++ Project","name":"boost","packageid":45155},{"block":false,"categoryid":452,"description":"SQL database engine","ebuildids":[736385],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"arfrever.fta@gmail.com","maintainername":"Arfrever Frehtes Taifersar Arahesis","name":"sqlite","packageid":50388},{"block":false,"categoryid":393,"description":"Portable, high level programming interface to various calling conventions","ebuildids":[736385],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"toolchain@gentoo.org","maintainername":"Gentoo Toolchain Project","name":"libffi","packageid":52280,"summary":"Compilers for high level languages generate code that follow certain conventions. These conventions are necessary, in part, for separate compilation to work. One such convention is the \"calling convention\". The \"calling convention\" is essentially a set of assumptions made by the compiler about where function arguments will be found on entry to a function. A \"calling convention\" also specifies where the return value for a function is found. Some programs may not know at the time of compilation what arguments are to be passed to a function. For instance, an interpreter may be told at run-time about the number and types of arguments used to call a given function. Libffi can be used in such programs to provide a bridge from the interpreter program to compiled code. The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run time. Ffi stands for Foreign Function Interface. A foreign function interface is the popular name for the interface that allows code written in one language to call code written in another language. The libffi library really only provides the lowest, machine dependent layer of a fully featured foreign function interface. A layer must exist above libffi that handles type conversions for values passed between the two languages."},{"block":false,"categoryid":361,"description":"A high-performance message passing library (MPI)","ebuildids":[736385],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"jsbronder@gentoo.org","maintainername":"Gentoo Cluster Project","name":"openmpi","packageid":53053},{"block":false,"categoryid":429,"description":"An extremely memory-efficient hash_map implementation","ebuildids":[736385],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"cpp@gentoo.org","maintainername":"Gentoo C++ Project","name":"sparsehash","packageid":55213},{"block":false,"categoryid":393,"description":"Library for arbitrary-precision arithmetic on different type of numbers","ebuildids":[736385],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"toolchain@gentoo.org","maintainername":"Gentoo Toolchain Project","name":"gmp","packageid":55512}],"repos":[{"branch":"master","lastcommit":"52197549fd3431fa256b8edbafdcd3702dd0e134","name":"gentoo","path":"\/usr\/portage","repoid":1,"upstream":"origin"}],"tracked":false,"urls":["https:\/\/www.bcgsc.ca\/resources\/software\/abyss\/"],"uses":[{"description":"build abyss-samtobreak tool, pull in haskell toolchain","isdefault":false,"packageid":50240,"use":"misc-haskell"},{"description":"Build support for the OpenMP (support parallel computing), requires >=sys-devel\/gcc-4.2 built with USE=\"openmp\"","isdefault":false,"use":"openmp"}]}