{"bugs":[{"bugid":806067,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/bowtie-2.4.4 fails tests"},{"bugid":952649,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/bowtie: needs porting to Python 3.13"}],"categories":[{"categoryid":450,"name":"dev-lang","summary":"The dev-lang category contains various programming language implementations and related tools."},{"categoryid":353,"name":"sci-biology","summary":"The sci-biology category contains software that can be used in biological and related scientific environments."},{"categoryid":396,"name":"virtual","summary":"The virtual category contains packages which satisfy virtual dependencies."}],"changelog":[{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"00b4cc6bb3b864fbeaa6dca1da399c3716afed16","committime":"2025-11-04T09:50:46","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Done via:\n\n```\ngit grep -l virtual\/zlib$ | xargs sed -i -e 's@virtual\/zlib$@&:=@'\n```\n\nSigned-off-by: Michał Górny ","commitid":"6a3644bf2f9aace46ad9bbab2e4f3bccd747079e","committime":"2025-11-04T09:36:27","packageid":51612,"repoid":1,"summary":"*\/*: Add := to virtual\/zlib deps, part 1"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"5a1adb610b1d91ab6683cbe671e266f424224c16","committime":"2025-11-04T08:35:48","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Update done using:\n\n```\ngit grep -l sys-libs\/zlib dev-* | xargs sed -i -e s@sys-libs\/zlib@virtual\/zlib@g\ngit diff --name-only | xargs copybump\ngit diff --name-only | xargs grep -l PYTHON_COMPAT | xargs gpy-impl -@dead\npkgcheck scan --commits -c SourcingCheck,VisibilityCheck --exit error\n```\n\nSigned-off-by: Michał Górny ","commitid":"f1351833569f8b22abc3dc9e74abeed7e8641096","committime":"2025-11-04T08:17:06","packageid":51612,"repoid":1,"summary":"sci-*\/*: update for virtual\/zlib"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"000e03edeaa4a684b36e40e996208ade274ec647","committime":"2025-05-01T11:56:56","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Signed-off-by: Michał Górny \nPart-of: https:\/\/github.com\/gentoo\/gentoo\/pull\/41697\nSigned-off-by: Michał Górny ","commitid":"dc223750a96c8b733efbb85d5da6366f22f61a6d","committime":"2025-04-22T11:45:47","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: Remove old"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"40d6496cc807662ae2b572affd447adf187d260f","committime":"2024-07-30T21:18:58","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"pacho@gentoo.org","authorname":"Pacho Ramos","body":"Closes: https:\/\/bugs.gentoo.org\/929753\nSigned-off-by: Pacho Ramos ","commitid":"9de8c676fe59c8570f2982846b440973beb8cafd","committime":"2024-07-30T19:40:05","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: enable py3.12"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"e817756739654c06c8a96e8fb68a3da1ba3af055","committime":"2024-04-30T18:48:55","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"watermanpaint@posteo.net","authorname":"Lucio Sauer","body":"bump copyright of touched ebuilds to 2024\n\nSigned-off-by: Lucio Sauer \nSigned-off-by: Michał Górny ","commitid":"794061a3298b5716db015defa7b3e2c583b73980","committime":"2024-04-12T10:47:52","packageid":51612,"repoid":1,"summary":"*\/*: inline mirror:\/\/sourceforge"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"93c22b54496b0b109281f96e9d4fbe1ada796502","committime":"2023-02-24T07:46:54","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"andrewammerlaan@gentoo.org","authorname":"Andrew Ammerlaan","body":"Signed-off-by: Andrew Ammerlaan ","commitid":"ad0f0da9f1b0df76d06b2bd4c52ce233ce4c8001","committime":"2023-02-24T07:29:55","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: add 2.5.1"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"8d0ebee607de5c63d747980fbeb0806c193a29c9","committime":"2023-01-14T13:02:17","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert ","commitid":"ed468028e725c9580a7b2ee02d6b7b9375f7a0b2","committime":"2023-01-14T12:51:19","packageid":51612,"repoid":1,"summary":"*\/*: remove py3.8 from PYTHON_COMPAT"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"86b69bec43600bff82b78cf89d5c369ccf3813a7","committime":"2021-08-01T17:36:44","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert ","commitid":"e99b33b0d98ad381a2a4ceaab86f86dd5e2d2d00","committime":"2021-08-01T17:02:01","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: fix QA issues"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"49fdab10f64515f92f5cbea0fe6239a21828f288","committime":"2021-08-01T16:52:17","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/722870\nSigned-off-by: David Seifert ","commitid":"b3c6b97c03059d44b801c71c3ccf7a6165593149","committime":"2021-08-01T16:40:42","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: drop 2.2.9"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Bug: https:\/\/bugs.gentoo.org\/722870\nSigned-off-by: David Seifert ","commitid":"20633430c439732edc1dd09d5b76acefcaa54c9d","committime":"2021-08-01T16:40:40","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: add 2.4.4"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"3d3e4684f177c123765283df6ea708c75d6d8937","committime":"2020-09-09T11:05:24","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Signed-off-by: Michał Górny ","commitid":"72b619bb3a27ec63f571afbf73ec75893fcc2d99","committime":"2020-09-09T10:26:34","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: Remove old"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"2e2a4d9cd52c0e555d5f4e5436df545fbc52512b","committime":"2017-12-25T16:25:47","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/630140\nPackage-Manager: Portage-2.3.19, Repoman-2.3.6\nCloses: https:\/\/github.com\/gentoo\/gentoo\/pull\/6626","commitid":"6d8d74d327137358ffb5e4dad142b9c8b280f71c","committime":"2017-12-25T09:57:08","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: Remove old"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"25093d6359f778b8d1052f66ba9e26fc29ded21a","committime":"2017-02-28T20:35:29","packageid":51612,"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":51612,"repoid":1,"summary":"Drop $Id$ per council decision in bug #611234."},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"d0a99b11f657e9ccb20ca7c889545d8315c2ccdf","committime":"2016-09-18T22:43:07","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Gentoo-bug: 593966\n\nPackage-Manager: portage-2.3.0","commitid":"a4da0209640e967dbbc8cd85820ff8858e34f872","committime":"2016-09-18T22:39:18","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: Allow for compiling with GCC 6"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"9bf9192cd16e3de4f27ec279a1b31e47d277e9ee","committime":"2016-06-04T21:33:52","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: portage-2.3.0_rc1","commitid":"adf47f7e0b7623ad7740c8226b95a69f978072ba","committime":"2016-06-04T21:17:19","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: version bump"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"b98e0404c030bc8e760f9a051cbba4da744da79c","committime":"2016-04-10T10:02:10","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"* EAPI=6\n\nPackage-Manager: portage-2.2.28","commitid":"c9b8497a77f3a72c025ca02d8fd8bdb024e34189","committime":"2016-04-10T09:47:56","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: Version bump to 2.2.8"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"e67ae1c313e3cda88357396590b166101c8801cb","committime":"2016-04-09T19:02:25","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"* EAPI=6\n\nPackage-Manager: portage-2.2.28","commitid":"1e3f5d88f730c5d04b64095114d2e48c1ec4ba58","committime":"2016-04-09T18:26:28","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: unbundle SeqAn, import Debian patches"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"b169de997104f96f584770fdc17e2d9d375bf730","committime":"2015-12-26T18:21:44","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"jlec@gentoo.org","authorname":"Justin Lecher","body":"Package-Manager: portage-2.2.26\nSigned-off-by: Justin Lecher ","commitid":"f2f3752753b3b078ecf3c8e3b38859e932b7784c","committime":"2015-12-26T18:05:43","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: Chop DESCRIPTION to 80 chars"},{"authoremail":"jlec@gentoo.org","authorname":"Justin Lecher","body":"obsoletes:\nGentoo-Bug: https:\/\/bugs.gentoo.org\/show_bug.cgi?id=564320\n\nPackage-Manager: portage-2.2.26\nSigned-off-by: Justin Lecher ","commitid":"369678cffc9f7ecae414f3800f01a2c2251e8669","committime":"2015-12-26T18:02:47","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: Drop old"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"82d8c47bcb407915b0b52544d4e64b6c28fdb576","committime":"2015-12-25T16:24:57","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"ago@gentoo.org","authorname":"Agostino Sarubbo","body":"Package-Manager: portage-2.2.24\nRepoMan-Options: --include-arches=\"x86\"\nSigned-off-by: Agostino Sarubbo ","commitid":"e143c824a96f9dc58f875e769edc5197f8d4fb65","committime":"2015-12-25T16:20:04","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: x86 stable wrt bug #569706"},{"authoremail":"ago@gentoo.org","authorname":"Agostino Sarubbo","body":"Package-Manager: portage-2.2.24\nRepoMan-Options: --include-arches=\"x86\"\nSigned-off-by: Agostino Sarubbo ","commitid":"4689bed149c155c70325079e27a7377a388df474","committime":"2015-12-25T16:14:12","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: x86 stable wrt bug #569708"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"00b925a8e6c45b3674cb5693e56e588672f52a30","committime":"2015-12-25T16:02:08","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"ago@gentoo.org","authorname":"Agostino Sarubbo","body":"Package-Manager: portage-2.2.24\nRepoMan-Options: --include-arches=\"amd64\"\nSigned-off-by: Agostino Sarubbo ","commitid":"62f64bf8cd5d10ea03ec75418e188334aa97ffd5","committime":"2015-12-25T15:42:02","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: amd64 stable wrt bug #569706"},{"authoremail":"ago@gentoo.org","authorname":"Agostino Sarubbo","body":"Package-Manager: portage-2.2.24\nRepoMan-Options: --include-arches=\"amd64\"\nSigned-off-by: Agostino Sarubbo ","commitid":"61b5a70cfc5a969ba20675c55b70ee02a7c6e854","committime":"2015-12-25T15:41:56","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: amd64 stable wrt bug #569708"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"56dc902429720590564e965e1338610f04e8d840","committime":"2015-10-14T13:02:07","packageid":51612,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"jlec@gentoo.org","authorname":"Justin Lecher","body":"Package-Manager: portage-2.2.23\nSigned-off-by: Justin Lecher ","commitid":"92c7d34329f99fec50cecea8d62647653504ab2f","committime":"2015-10-14T12:45:36","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: Respect CXX"},{"authoremail":"ted.tanberry@gmail.com","authorname":"Ted Tanberry","body":"bowtie-0.12.8 is the only stable variant and removing it\nbreaks the stable depgraph.","commitid":"50fe91c03b9c8431a871463ee75ae68bdfc8a171","committime":"2015-10-11T08:04:43","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: bring back stable bowtie-0.12.8"},{"authoremail":"ted.tanberry@gmail.com","authorname":"Ted Tanberry","commitid":"a5cdb5129aa0e80c0f8883863db3b6a9bf00d0fd","committime":"2015-10-11T07:52:57","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie-2.2.6: Enable 'tbb' USE flag by default"},{"authoremail":"ted.tanberry@gmail.com","authorname":"Ted Tanberry","commitid":"5660b0815cc329a4983ec40012e883aafe11acee","committime":"2015-10-11T07:51:55","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie-1.1.2: Enable 'tbb' USE flag by default"},{"authoremail":"ted.tanberry@gmail.com","authorname":"Ted Tanberry","body":"When SSE2 support is not explicitly enabled, the user is\ninformed by erroring out instead of portage recommending\nenabling cpu flags.","commitid":"1f3b594dde68ff07ecf429b10b2501660adc0f1d","committime":"2015-10-10T20:18:12","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: remove REQUIRED_USE"},{"authoremail":"ted.tanberry@gmail.com","authorname":"Ted Tanberry","body":"Retain -Wall in CXXFLAGS in bowtie-1.1.2","commitid":"3e53a5793eaa33b60d58c8df34dbf5b6d33b4a6e","committime":"2015-10-10T19:45:34","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: do not remove -Wall from CXXFLAGS"},{"authoremail":"ted.tanberry@gmail.com","authorname":"Ted Tanberry","commitid":"5ca4d1505a37f273d7eaee41f89b676381e6305e","committime":"2015-10-10T19:07:16","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: Add bowtie2 in SLOT=2"},{"authoremail":"ted.tanberry@gmail.com","authorname":"Ted Tanberry","body":"sci-biology\/bowtie is now SLOTed, in order to allow for a\nparallel installation with bowtie2. In addition, the latest\nbowtie now supports dev-cpp\/tbb with 'tbb' USE flag.","commitid":"ddbfba3594bda0b32f359e057555d477ffbced1e","committime":"2015-10-10T19:04:45","packageid":51612,"repoid":1,"summary":"sci-biology\/bowtie: version bump, SLOT major version"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"945f0d2a26da4f944fd06ad6a874f69d37ce1e06","committime":"2015-08-09T09:26:46","packageid":51612,"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":51612,"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":51612,"repoid":1,"summary":"2015-06-19 16:35:30 UTC"}],"dependencies":[{"block":false,"categoryid":450,"description":"An interpreted, interactive, object-oriented programming language","ebuildids":[778997,778997],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"python@gentoo.org","maintainername":"Python","name":"python","packageid":43095},{"block":false,"categoryid":450,"description":"Larry Wall's Practical Extraction and Report Language","ebuildids":[778997],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"perl@gentoo.org","maintainername":"Gentoo Perl Project","name":"perl","packageid":44582},{"block":false,"categoryid":396,"description":"Virtual for libz.so providers","ebuildids":[778997],"firstseen":"2025-11-04T07:31:41.418357","name":"zlib","packageid":78605}],"depending":[],"ebuilds":[{"archs":["~amd64","~x86"],"ebuildid":778997,"firstseen":"2023-02-24T08:03:45.101814","license":"GPL-3","moddate":"2026-03-28T18:04:21","packageid":51612,"repoid":1,"slot":"2","uses":["cpu_flags_x86_sse2","examples","python_single_target_python3_11","python_single_target_python3_12","test"],"version":"2.5.1"}],"masks":[],"package":{"categoryid":353,"description":"Popular short read aligner for Next-generation sequencing data","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"bowtie","packageid":51612},"rdependencies":[{"block":false,"categoryid":450,"description":"An interpreted, interactive, object-oriented programming language","ebuildids":[778997,778997],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"python@gentoo.org","maintainername":"Python","name":"python","packageid":43095},{"block":false,"categoryid":450,"description":"Larry Wall's Practical Extraction and Report Language","ebuildids":[778997],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"perl@gentoo.org","maintainername":"Gentoo Perl Project","name":"perl","packageid":44582},{"block":false,"categoryid":396,"description":"Virtual for libz.so providers","ebuildids":[778997],"firstseen":"2025-11-04T07:31:41.418357","name":"zlib","packageid":78605}],"repos":[{"branch":"master","lastcommit":"52197549fd3431fa256b8edbafdcd3702dd0e134","name":"gentoo","path":"\/usr\/portage","repoid":1,"upstream":"origin"}],"tracked":false,"urls":["https:\/\/bowtie-bio.sourceforge.net\/bowtie2\/"],"uses":[{"description":"Install examples, usually source code","isdefault":false,"use":"examples"},{"description":"Enable dependencies and\/or preparations necessary to run tests (usually controlled by FEATURES=test but can be toggled independently)","isdefault":false,"use":"test"},{"description":"Use the SSE2 instruction set","group":"cpu_flags_x86","isdefault":false,"use":"sse2"},{"description":"Build for Python 3.11 only","group":"python_single_target","isdefault":false,"use":"python3_11"},{"description":"Build for Python 3.12 only","group":"python_single_target","isdefault":false,"use":"python3_12"}]}