{"bugs":[{"bugid":927355,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/muscle-5.1.0 - x86_64-pc-linux-gnu-g++: fatal error: cannot read spec file libgomp.spec: No such file or directory"},{"bugid":938273,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/muscle-5.1.0 - Fatal error: cant create Linux\/efabestcols.o: No such file or directory"}],"categories":[{"categoryid":353,"name":"sci-biology","summary":"The sci-biology category contains software that can be used in biological and related scientific environments."},{"categoryid":416,"name":"sci-chemistry","summary":"The sci-chemistry category contains software that can be used in chemistral scientific environments."},{"categoryid":318,"name":"sci-libs","summary":"The sci-libs category contains various science-related libraries."}],"changelog":[{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"75b4d569f0bce841ce1b97e6cdbdc1c494b90746","committime":"2026-02-22T16:00:55","packageid":53549,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"asturm@gentoo.org","authorname":"Andreas Sturmlechner","body":"Signed-off-by: Andreas Sturmlechner ","commitid":"eb36afed0ebdb0323da077573076f795b2038741","committime":"2026-02-22T14:05:45","packageid":53549,"repoid":1,"summary":"sci-biology\/muscle: drop 3.8.31"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"14e799c05d11bdcaf26de2a1e08d98d43556be7b","committime":"2024-12-05T18:48:15","packageid":53549,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"Signed-off-by: Sam James ","commitid":"a0ebc28e7998b9489e856d93331902f90dbc9292","committime":"2024-12-05T18:30:08","packageid":53549,"repoid":1,"summary":"sci-biology\/muscle: Stabilize 5.1.0 amd64, #945576"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"5eb9f90f33f8cc0455999d72008a02427e1ec423","committime":"2024-03-20T06:33:52","packageid":53549,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"Signed-off-by: Sam James ","commitid":"6c084e5a487050124f20519ee97c5bd36fdfbdbe","committime":"2024-03-20T06:20:22","packageid":53549,"repoid":1,"summary":"sci-biology\/muscle: fix variable order"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"Signed-off-by: Sam James ","commitid":"8ab389ebe46e90ae367318d678ddba2258451b66","committime":"2024-03-20T06:20:02","packageid":53549,"repoid":1,"summary":"sci-biology\/muscle: drop unused flag-o-matic from 5.1.0"},{"authoremail":"eschwartz93@gmail.com","authorname":"Eli Schwartz","body":"Major new release, major new build system that is majorly broken. <3\nscientific code.\n\nThis package has not been updated since before the import of gentoo into\ngit, so I shall simply assume this major version is safe. From the\nhomepage, it is a \"major rewrite\", \"based on new algorithms\", which is\n\"much more accurate, is often faster, and scales to much larger datasets\".\n\nI think that's another way of saying \"same old program but with fixes\".\n\nSigned-off-by: Eli Schwartz \nSigned-off-by: Sam James ","commitid":"676077c732029914876df94a29591ae5ed6b4ba2","committime":"2024-03-20T03:59:32","packageid":53549,"repoid":1,"summary":"sci-biology\/muscle: add 5.1.0"},{"authoremail":"eschwartz93@gmail.com","authorname":"Eli Schwartz","body":"Closes: https:\/\/bugs.gentoo.org\/862276\nSigned-off-by: Eli Schwartz \nSigned-off-by: Sam James ","commitid":"c33c578e0eaeda556d7b5467fce0e97726c0d8f5","committime":"2024-03-20T03:58:33","packageid":53549,"repoid":1,"summary":"sci-biology\/muscle: mark as LTO-unsafe, strict-aliasing unsafe"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"f2979793991144637956e4225ce4d0235900c1a2","committime":"2023-06-09T15:16:56","packageid":53549,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"arthurzam@gentoo.org","authorname":"Arthur Zamarin","body":"Signed-off-by: Arthur Zamarin ","commitid":"9d8c251c36e5d6a8364a9fa8082cbfdbc2a8f067","committime":"2023-06-03T14:46:10","packageid":53549,"repoid":1,"summary":"sci-biology\/muscle: destabilize for ~x86"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"6a73593a58d469c462b5ed8b89a44291f1a463b3","committime":"2022-08-23T12:16:54","packageid":53549,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mmk@levelnine.at","authorname":"Michael Mair-Keimberger","body":"Signed-off-by: Michael Mair-Keimberger \nPortage 3.0.34 \/ pkgdev 0.2.1 \/ pkgcheck 0.10.11\nSigned-off-by: Andrew Ammerlaan ","commitid":"28edb0964e4440787196c2128b143903a501ddc7","committime":"2022-08-02T17:13:37","packageid":53549,"repoid":1,"summary":"sci-biology\/muscle: use HTTPS"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"39da18b49f0f1c5486a1cddc64d32bac28abc59b","committime":"2021-11-19T00:07:44","packageid":53549,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"gyakovlev@gentoo.org","authorname":"Georgy Yakovlev","body":"Bug: https:\/\/bugs.gentoo.org\/823768\nSigned-off-by: Georgy Yakovlev ","commitid":"031cf9ad4d10c5620a9874c5dc05b9b80ab627ba","committime":"2021-11-18T23:44:51","packageid":53549,"repoid":1,"summary":"sci-biology\/muscle: de-stabilize for ~ppc, bug #823768"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"e5353d231ce3b7ce6238f952b5a39ccc17b5e82a","committime":"2020-10-27T22:05:17","packageid":53549,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-3.0.8, Repoman-3.0.2\nSigned-off-by: David Seifert ","commitid":"45c64c3c183dc177c982882b9177abeb0df467dd","committime":"2020-10-27T21:40:04","packageid":53549,"repoid":1,"summary":"sci-biology\/muscle: Port to EAPI 7"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"25093d6359f778b8d1052f66ba9e26fc29ded21a","committime":"2017-02-28T20:35:29","packageid":53549,"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":53549,"repoid":1,"summary":"Drop $Id$ per council decision in bug #611234."},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"945f0d2a26da4f944fd06ad6a874f69d37ce1e06","committime":"2015-08-09T09:26:46","packageid":53549,"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":53549,"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":53549,"repoid":1,"summary":"2015-06-19 16:35:30 UTC"}],"dependencies":[],"depending":[{"block":false,"categoryid":353,"description":"Analysis of repetitive DNA found in genome sequences","ebuildids":[755474],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"piler","packageid":43252},{"block":true,"categoryid":318,"description":"Library for sci-biology\/mauve","ebuildids":[820278],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"libmuscle","packageid":44815},{"block":false,"categoryid":353,"description":"A graphical multiple sequence alignment editor","ebuildids":[849074,849074],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"seaview","packageid":54725,"summary":"SeaView is a graphical multiple sequence alignment editor developped by Manolo Gouy. SeaView is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW programs to locally improve the alignment."},{"block":false,"categoryid":416,"description":"Maximum likelihood superpositioning and analysis of macromolecular structures","ebuildids":[713620,713620],"firstseen":"2012-03-21T20:52:40.034466","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"theseus","packageid":59040}],"ebuilds":[{"archs":["amd64","~ppc","~x86"],"ebuildid":819865,"firstseen":"2024-03-20T06:42:06.012985","license":"public-domain","moddate":"2026-03-22T20:20:57","packageid":53549,"repoid":1,"slot":"0","uses":[],"version":"5.1.0"}],"masks":[],"package":{"categoryid":353,"description":"Multiple sequence comparison by log-expectation","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"muscle","packageid":53549},"rdependencies":[{"block":true,"categoryid":318,"description":"Library for sci-biology\/mauve","ebuildids":[819865],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"libmuscle","packageid":44815}],"repos":[{"branch":"master","lastcommit":"82366aa45a35f6900f43023917c2c86ccdbb00a3","name":"gentoo","path":"\/usr\/portage","repoid":1,"upstream":"origin"}],"tracked":false,"urls":["https:\/\/www.drive5.com\/muscle\/"],"uses":[]}