{"bugs":[{"bugid":725312,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/t-coffee-11.00-r2 does not respect LDFLAGS"},{"bugid":731862,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/t-coffee-11.00-r3 fails to compile: dp_lib\/evaluate_dirichlet.c:543:8: error: 'lgamma_r' is missing exception"},{"bugid":842387,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/t-coffee-11.00-r3 - io_lib\/io_func.c: error: cannot convert std::nullptr_t to int in return"},{"bugid":896062,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/t-coffee-11.00-r3 - io_lib\/tree_util.c: error: invalid operands of types long unsigned int and std::nullptr_t to binar"},{"bugid":921101,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/t-coffee-11.00-r3 - [clang] util_lib\/util_make_tree.c: error: ISO C++17 does not allow register"}],"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."}],"changelog":[{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"a198e862478387fe37b4d232d51a3edb558cd3e0","committime":"2025-12-19T10:01:01","packageid":49483,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"grobian@gentoo.org","authorname":"Fabian Groffen","body":"Bug: https:\/\/bugs.gentoo.org\/473598\nBug: https:\/\/bugs.gentoo.org\/720224\nSigned-off-by: Fabian Groffen ","commitid":"2d25fad95cbaa525c8945d8e582c749d49524f49","committime":"2025-12-19T09:25:43","packageid":49483,"repoid":1,"summary":"*\/*: drop *-linux keywords"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"ac2b0c033fef6efe97a32c94fdcbe4252ea5fc66","committime":"2024-03-21T00:04:49","packageid":49483,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"eschwartz93@gmail.com","authorname":"Eli Schwartz","body":"Closes: https:\/\/bugs.gentoo.org\/862327\nSigned-off-by: Eli Schwartz \nSigned-off-by: Sam James ","commitid":"86e4c6c3cfd2420dab5aae7c13f05e78e686d073","committime":"2024-03-20T20:10:01","packageid":49483,"repoid":1,"summary":"sci-biology\/t-coffee: mark as LTO-unsafe, strict-aliasing unsafe"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"af6f0e8ef0bcb907ba1d0760fbc87f04990100a3","committime":"2022-07-07T20:01:37","packageid":49483,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert ","commitid":"13297a735a8c0e36ab552d244f4935d21400d310","committime":"2022-07-07T19:57:12","packageid":49483,"repoid":1,"summary":"sci-biology\/t-coffee: update EAPI 6 -> 8"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"2e2a4d9cd52c0e555d5f4e5436df545fbc52512b","committime":"2017-12-25T16:25:47","packageid":49483,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-2.3.19, Repoman-2.3.6","commitid":"f1a2182baa171c729f5c2134144664780e041f37","committime":"2017-12-25T10:02:15","packageid":49483,"repoid":1,"summary":"sci-biology\/t-coffee: Remove old"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"fc4a83a904013d2098816734e3f5b6052e2c0dbb","committime":"2017-12-24T20:04:24","packageid":49483,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/639832\nPackage-Manager: Portage-2.3.19, Repoman-2.3.6","commitid":"6f595002c210652e224701d2483de54e8b195c56","committime":"2017-12-24T19:36:03","packageid":49483,"repoid":1,"summary":"sci-biology\/t-coffee: Fix building with GCC 7"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"25093d6359f778b8d1052f66ba9e26fc29ded21a","committime":"2017-02-28T20:35:29","packageid":49483,"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":49483,"repoid":1,"summary":"Drop $Id$ per council decision in bug #611234."},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"2a988d6ed9aa6769d5a0612e107231d192588fc4","committime":"2015-12-25T12:58:24","packageid":49483,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"jlec@gentoo.org","authorname":"Justin Lecher","body":"Gentoo-Bug: https:\/\/bugs.gentoo.org\/show_bug.cgi?id=569650\n\nPackage-Manager: portage-2.2.26\nSigned-off-by: Justin Lecher ","commitid":"15848c4175bd2c42967e5f09128a600f376febd3","committime":"2015-12-25T10:38:04","packageid":49483,"repoid":1,"summary":"sci-biology\/t-coffee: Import fix for CVE-2015-8621"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"945f0d2a26da4f944fd06ad6a874f69d37ce1e06","committime":"2015-08-09T09:26:46","packageid":49483,"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":49483,"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":49483,"repoid":1,"summary":"2015-06-19 16:35:30 UTC"}],"dependencies":[],"depending":[{"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","~ppc64","~x86"],"ebuildid":755480,"firstseen":"2022-07-07T21:10:47.213865","license":"GPL-2","moddate":"2026-03-22T20:20:57","packageid":49483,"repoid":1,"slot":"0","uses":[],"version":"11.00-r3"}],"masks":[],"package":{"categoryid":353,"description":"A multiple sequence alignment package","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"t-coffee","packageid":49483,"summary":"T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures. T-Coffee allows the combination of a collection of multiple\/pairwise, global or local alignments into a single model. It also allows to estimate the level of consistency of each position within the new alignment with the rest of the alignments."},"rdependencies":[{"block":false,"categoryid":353,"description":"General purpose multiple alignment program for DNA and proteins","ebuildids":[755480],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"clustalw","packageid":52977},{"block":false,"categoryid":416,"description":"Quick & Accurate Structural Alignment","ebuildids":[755480],"firstseen":"2012-03-21T20:52:40.034466","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"tm-align","packageid":59041,"summary":"TM-align is a computer algorithm for protein structure alignment using dynamic programming and TM-score rotation matrix. An optimal alignment between two proteins, as well as the TM-score, will be reported for each comparison. The value of TM-score lies in (0,1]. In general, a comparison of TM-score smaller 0.2 indicates that there is no similarity between two structures; a TM-score greater 0.5 means the structures share the same fold. What is the difference between TM-score and TM-align? The TM-score program is to compare two models based on their given and known residue equivalency. It is usually NOT applied to compare two proteins of different sequences. The TM-align is a structural alignment program for comparing two proteins whose sequences can be different. The TM-align will first find the best equivalent residues of two proteins based on the structure similarity and then output a TM-score. The TM-score values in both programs have the same definition."}],"repos":[{"branch":"master","lastcommit":"52197549fd3431fa256b8edbafdcd3702dd0e134","name":"gentoo","path":"\/usr\/portage","repoid":1,"upstream":"origin"}],"tracked":false,"urls":["http:\/\/www.tcoffee.org\/Projects_home_page\/t_coffee_home_page.html"],"uses":[]}