{"bugs":[{"bugid":247394,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"app-crypt\/pkcrack media-sound\/csound sci-chemistry\/pdb-extract sci-biology\/glimmer - file collision in \/usr\/bin\/extract"}],"categories":[{"categoryid":386,"name":"app-shells","summary":"The app-shells category contains shells and their extensions."},{"categoryid":353,"name":"sci-biology","summary":"The sci-biology category contains software that can be used in biological and related scientific environments."}],"changelog":[{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"82b37a27e889ff1af7cfc1e3a8c2f06ef8622566","committime":"2022-03-20T19:04:16","packageid":52050,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"This can cause build problems for e.g. 32-bit (gcc -m32 ...)\n\nSigned-off-by: Sam James ","commitid":"94cbce6f250b841d2f94e62b1b44a37a50958090","committime":"2022-03-20T18:49:31","packageid":52050,"repoid":1,"summary":"sci-biology\/glimmer: [QA] fix tc-get* quoting"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"484f7c925785a3c30076d8c7150e610fa0bfc48e","committime":"2021-04-05T13:49:53","packageid":52050,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/731892\nPackage-Manager: Portage-3.0.18, Repoman-3.0.3\nSigned-off-by: David Seifert ","commitid":"08a072e6e7aeb962594f489db2000ea89c2599bb","committime":"2021-04-05T13:30:36","packageid":52050,"repoid":1,"summary":"sci-biology\/glimmer: Port to EAPI 7"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-3.0.18, Repoman-3.0.3\nSigned-off-by: David Seifert ","commitid":"d3ede632793d65970f45479128628a23355d175d","committime":"2021-04-05T13:30:33","packageid":52050,"repoid":1,"summary":"sci-biology\/glimmer: Remove old 3.02"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"2fbdfbc003d28cd80696303439a07a13ff2dc035","committime":"2018-05-21T17:29:55","packageid":52050,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"m.mairkeimberger@gmail.com","authorname":"Michael Mair-Keimberger","commitid":"e8739e59b6b6a408b72794f8e8c1428b002eaa2c","committime":"2018-05-21T10:18:38","packageid":52050,"repoid":1,"summary":"sci-biology\/glimmer: use HTTPs"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"25093d6359f778b8d1052f66ba9e26fc29ded21a","committime":"2017-02-28T20:35:29","packageid":52050,"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":52050,"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":52050,"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":52050,"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":52050,"repoid":1,"summary":"2015-06-19 16:35:30 UTC"}],"dependencies":[],"depending":[],"ebuilds":[{"archs":["~amd64","~x86"],"ebuildid":543991,"firstseen":"2015-05-26T13:36:28.026672","license":"Artistic","moddate":"2026-03-22T20:20:57","packageid":52050,"repoid":1,"slot":"0","uses":[],"version":"3.02b"}],"masks":[],"package":{"categoryid":353,"description":"An HMM-based microbial gene finding system from TIGR","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"glimmer","packageid":52050},"rdependencies":[{"block":false,"categoryid":386,"description":"Enhanced version of the Berkeley C shell (csh)","ebuildids":[543991],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"grobian@gentoo.org","maintainername":"Fabian Groffen","name":"tcsh","packageid":49213,"summary":"Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax."},{"block":false,"categoryid":353,"description":"Estimated Locations of Pattern Hits - Motif finder program","ebuildids":[543991],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"elph","packageid":55065,"summary":"ELPH is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences. The program takes as input a set containing anywhere from a few dozen to thousands of sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif."}],"repos":[{"branch":"master","lastcommit":"f87ce2b74421571078063820dc1065e7089c9fa7","name":"gentoo","path":"\/usr\/portage","repoid":1,"upstream":"origin"}],"tracked":false,"urls":["https:\/\/ccb.jhu.edu\/software\/glimmer\/index.shtml"],"uses":[]}