{"bugs":[{"bugid":881783,"firstseen":"2022-11-18T10:06:51.912644","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/bedtools-2.30.0 - src\/...\/version.cpp: fatal error: version_git.h: No such file or directory"},{"bugid":896172,"firstseen":"2023-02-24T09:03:54.523547","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/bedtools-2.30.0 fails tests (HARDENED-SYSTEM)"},{"bugid":907971,"firstseen":"2023-06-07T08:51:31.118774","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/bedtools-2.30.0 fails to compile (MUSL-SYSTEM): BamAux.h:10:17: error: int32_t does not name a type"},{"bugid":929751,"firstseen":"2024-04-13T10:54:20.227576","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/bedtools: needs upgrade to Python 3.12 (PythonCompatUpdate)"}],"categories":[{"categoryid":449,"name":"app-arch","summary":"The app-arch category contains tools for archiving, compressing and uncompressing files or groups of files."},{"categoryid":353,"name":"sci-biology","summary":"The sci-biology category contains software that can be used in biological and related scientific environments."},{"categoryid":381,"name":"sys-libs","summary":"The sys-libs category contains various system-level libraries."}],"changelog":[{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"b869ee27a2c20af84352b270d45fe78d4243ad54","committime":"2024-04-25T09:49:16","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Bug: https:\/\/bugs.gentoo.org\/881783\nBug: https:\/\/bugs.gentoo.org\/907971\nBug: https:\/\/bugs.gentoo.org\/929751\nSigned-off-by: David Seifert ","commitid":"6659d55f12a3e8b75dbf9545cac23f37ca00bd58","committime":"2024-04-25T09:37:47","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: add 2.31.1"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"2999d637d073600787176e7957c8d5eb8e317a7f","committime":"2023-04-18T10:32:22","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/895860\nSigned-off-by: David Seifert ","commitid":"0f6ed95b2b57ae7f9978b1a3b1620c3dcb06256e","committime":"2023-04-18T10:04:37","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: fix gcc 13 build"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"8d0ebee607de5c63d747980fbeb0806c193a29c9","committime":"2023-01-14T13:02:17","packageid":58019,"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":58019,"repoid":1,"summary":"*\/*: remove py3.8 from PYTHON_COMPAT"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"1d43d7071f9633764d6fe2007d6f7a7ddabca7d4","committime":"2022-07-08T09:16:23","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/846215\nSigned-off-by: David Seifert ","commitid":"c9aeab08ce9b02bf1d0ebb88bc599bcceb08c07b","committime":"2022-07-08T09:09:23","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: update EAPI 7 -> 8"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"889293f491da0405efbecdaea7bb623755193a64","committime":"2022-03-19T11:49:11","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert ","commitid":"668ca73d47c048362cec2674c3bced215423a533","committime":"2022-03-19T11:38:06","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: drop 2.29.2"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"3781b22d380896174e6bc99bf0fda52843e404ce","committime":"2021-02-23T17:07:14","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"ezzieyguywuf@gmail.com","authorname":"Wolfgang E. Sanyer","body":"* The samtools patch is no longer needed, as upstream has fixed this.\n Test suite passes without it now.\n\nCloses: https:\/\/github.com\/gentoo\/gentoo\/pull\/19616\nCloses: https:\/\/bugs.gentoo.org\/696188\nSigned-off-by: Wolfgang E. Sanyer \nSigned-off-by: David Seifert ","commitid":"3f7de88151115f14fdb6036dcffa110a0104d55b","committime":"2021-02-23T16:49:45","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: bump to 2.30.0"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"2c6c2efe4c1a02689bcd5e6e58a54035dec44025","committime":"2021-01-31T02:18:05","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Signed-off-by: Michał Górny ","commitid":"d8cbaa62dbf4abc31cc74d2cc12e3d0c7ac9b70a","committime":"2021-01-30T23:36:06","packageid":58019,"repoid":1,"summary":"*\/*: Remove obsolete values from PYTHON_COMPAT"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"aa4e925ec3416ab383ff859582de739ec7e7643b","committime":"2020-08-16T21:40:28","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-3.0.2, Repoman-2.3.23\nSigned-off-by: David Seifert ","commitid":"cf0b0d69d8ac7e8df14964cf9ab8b20eb224ff33","committime":"2020-08-16T21:25:14","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: Add missing ${PYTHON_DEPS} to BDEPEND"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"fef889a5fea2b5f7ed81af318c3ff595f47c70b1","committime":"2020-08-16T21:09:43","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/718468\nPackage-Manager: Portage-3.0.2, Repoman-2.3.23\nSigned-off-by: David Seifert ","commitid":"e242a698ff6c378fa19286f02c735606e6a66fd6","committime":"2020-08-16T20:49:52","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: Remove old"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Bug: https:\/\/bugs.gentoo.org\/718468\nPackage-Manager: Portage-3.0.2, Repoman-2.3.23\nSigned-off-by: David Seifert ","commitid":"3a1f5a9faf6dfeb828e148cd397290d670c93744","committime":"2020-08-16T20:49:49","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: Version bump to 2.29.2"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"f1d16810fd086b1d6fde6c6f92a8f6fb1704941c","committime":"2020-02-10T14:10:12","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Signed-off-by: Michał Górny ","commitid":"cf72c05d0fba9c3ed1c9dbe63e2e1bcac1dd92ae","committime":"2020-02-10T13:05:45","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: Remove py2 where possible"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"4747d40122d485033fe9f863f4b4330bf0651903","committime":"2020-01-05T11:14:55","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Closes: https:\/\/github.com\/gentoo\/gentoo\/pull\/14246\nSigned-off-by: Michał Górny ","commitid":"cd3f25deb13cf4d6c9d721d515dbf772a988426f","committime":"2020-01-05T09:36:11","packageid":58019,"repoid":1,"summary":"*\/*: Clean PYTHON_COMPAT of obsolete impls"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"fef742528aacdd4ffa4e59ea0354106ca161650e","committime":"2019-12-10T23:48:11","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"The result was achieved via the following pipeline:\n\n pkgcheck scan -c RestrictTestCheck -R FormatReporter \\\n --format '{category}\/{package}\/{package}-{version}.ebuild' |\n xargs -n32 grep -L RESTRICT |\n xargs -n32 sed -i -e '\/^IUSE=.*test\/aRESTRICT=\"!test? ( test )\"'\n\nThe resulting metadata was compared before and after the change.\nFew Go ebuilds had to be fixed manually due to implicit RESTRICT=strip\nadded by the eclass. Two ebuilds have to be fixed because of multiline\nIUSE.\n\nSuggested-by: Robin H. Johnson \nCloses: https:\/\/github.com\/gentoo\/gentoo\/pull\/13942\nSigned-off-by: Michał Górny ","commitid":"064af661d0c9a31cecdf348632bc5603333a9149","committime":"2019-12-10T22:02:54","packageid":58019,"repoid":1,"summary":"*\/*: [QA] Fix trivial cases of MissingTestRestrict"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"c244a5f932cd4df61def2b8b1db2d60f05f91c39","committime":"2019-07-15T15:46:59","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Signed-off-by: Michał Górny ","commitid":"633473c659456bc25ce696de7e0282683909986e","committime":"2019-07-15T15:25:54","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: Sort KEYWORDS"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"b77b675b9d13c3d2dff7b40234257979f2f5cd0d","committime":"2019-04-16T13:04:21","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Closes: https:\/\/github.com\/gentoo\/gentoo\/pull\/11706\nSigned-off-by: Michał Górny ","commitid":"ef28997cd547dad210da754281a3931abf21c71e","committime":"2019-04-16T11:17:14","packageid":58019,"repoid":1,"summary":"*\/*: Drop python3_4 from PYTHON_COMPAT"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"839f4af117ab31f21009173d3cac2ea5317efcf2","committime":"2017-12-10T10:43:44","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"pacho@gentoo.org","authorname":"Pacho Ramos","body":"Package-Manager: Portage-2.3.16, Repoman-2.3.6","commitid":"13ce867dc1600eccdb3fed302ce78265843d1980","committime":"2017-12-10T10:21:44","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: Add support for newer python"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"27938a2175ae18e670f4aee7ed284e2dcdf96a8c","committime":"2017-12-10T00:13:35","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Closes: https:\/\/bugs.gentoo.org\/620612","commitid":"96adca668f64cdeb561fab922e1489e8f5aa01de","committime":"2017-12-09T23:15:36","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: [QA] Move patch to a distfile"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"25093d6359f778b8d1052f66ba9e26fc29ded21a","committime":"2017-02-28T20:35:29","packageid":58019,"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":58019,"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":58019,"repoid":1,"summary":"media-libs\/portaudio: Version bump"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"0410c6968fe16a9aecafef42315a7218709e7ec1","committime":"2016-11-27T12:47:46","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"pacho@gentoo.org","authorname":"Pacho Ramos","body":"Package-Manager: portage-2.3.2","commitid":"20fe6fef605ee8b42405629bcef94fe24f158c21","committime":"2016-11-27T12:37:49","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: This needs slot 0 of samtools (#597982)"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"c80cd6a37c7abfb05f3bc14e6e00090f330ec4fd","committime":"2016-09-24T23:25:01","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: portage-2.3.1","commitid":"566e3ceb401d95f67a2c31933b547ecd4646d48f","committime":"2016-09-24T23:12:20","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: Add missing RDEPEND on sys-libs\/zlib"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"a36e98042659eb7a99d59ab76984af563e3dcf1d","committime":"2016-09-24T23:05:00","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: portage-2.3.1","commitid":"8f2c0bf2f444a049e647bc49788ff9ae9f57b9e9","committime":"2016-09-24T22:48:54","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: Remove old ebuilds"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Gentoo-bug: 594994\n* EAPI=6\n* Make buildsystem output verbose\n* Inherit 'python-any-r1', due to python script\n* Add dependencies for test suite\n* Properly set CXX and CXXFLAGS\n\nPackage-Manager: portage-2.3.1","commitid":"c8c95dc5616fe51e1fffe9f875556a5ff14be39e","committime":"2016-09-24T22:47:39","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: Version bump to 2.26.0"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"0d26bb7ab12eb16cdd2a3ba164fb82e1dfc71fb5","committime":"2015-09-01T20:37:14","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"klausman@gentoo.org","authorname":"Tobias Klausmann","body":"Package-Manager: portage-2.2.20.1","commitid":"6b6bd3af0034a2360cf0085a13e4d3d560639fc8","committime":"2015-09-01T19:57:29","packageid":58019,"repoid":1,"summary":"sci-biology\/bedtools: Fixing HOMEPAGE move due to code.google.com shutdown"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"807d7c8ef7ce9a17a831c4b042b497afa97d470d","committime":"2015-08-24T14:06:35","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"jlec@gentoo.org","authorname":"Justin Lecher","body":"Signed-off-by: Justin Lecher ","commitid":"dea7c3060641b628cd6a2e2d97db18903c86862e","committime":"2015-08-24T13:41:27","packageid":58019,"repoid":1,"summary":"Convert URIs for googlecode.com to https"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"b8cce015b8b1869513a3bbb621225f2b688c56c8","committime":"2015-08-24T11:46:39","packageid":58019,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"jlec@gentoo.org","authorname":"Justin Lecher","body":"Signed-off-by: Justin Lecher ","commitid":"769c75f84ac0d1be61ecaeaff0fcc8c509063ec5","committime":"2015-08-24T11:35:05","packageid":58019,"repoid":1,"summary":"Enable https for all google URIs"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"945f0d2a26da4f944fd06ad6a874f69d37ce1e06","committime":"2015-08-09T09:26:46","packageid":58019,"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":58019,"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":58019,"repoid":1,"summary":"2015-06-19 16:35:30 UTC"}],"dependencies":[{"block":false,"categoryid":449,"description":"A high-quality data compressor used extensively by Gentoo Linux","ebuildids":[704146,824256],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"base-system@gentoo.org","maintainername":"Gentoo Base System","name":"bzip2","packageid":47649},{"block":false,"categoryid":449,"description":"Utils for managing LZMA compressed files","ebuildids":[704146,824256],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"base-system@gentoo.org","maintainername":"Gentoo Base System","name":"xz-utils","packageid":53735},{"block":false,"categoryid":381,"description":"Standard (de)compression library","ebuildids":[704146,824256],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"base-system@gentoo.org","maintainername":"Gentoo Base System","name":"zlib","packageid":55408}],"depending":[],"ebuilds":[{"archs":["~amd64","~x86"],"ebuildid":824256,"firstseen":"2024-04-25T11:00:38.966689","license":"GPL-2","moddate":"2024-12-17T22:35:47","packageid":58019,"repoid":1,"slot":"0","uses":["test"],"version":"2.31.1"},{"archs":["~amd64","~x86"],"ebuildid":704146,"firstseen":"2021-02-23T17:14:12.423819","license":"GPL-2","moddate":"2024-12-17T22:35:47","packageid":58019,"repoid":1,"slot":"0","uses":["test"],"version":"2.30.0"}],"masks":[],"package":{"categoryid":353,"description":"Tools for manipulation and analysis of BED, GFF\/GTF, VCF, SAM\/BAM file formats","firstseen":"2011-10-09T14:35:47.674450","maintainer":"mmokrejs@gmail.com","maintainername":"Martin Mokrejs","name":"bedtools","packageid":58019},"rdependencies":[{"block":false,"categoryid":449,"description":"A high-quality data compressor used extensively by Gentoo Linux","ebuildids":[704146,824256],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"base-system@gentoo.org","maintainername":"Gentoo Base System","name":"bzip2","packageid":47649},{"block":false,"categoryid":449,"description":"Utils for managing LZMA compressed files","ebuildids":[704146,824256],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"base-system@gentoo.org","maintainername":"Gentoo Base System","name":"xz-utils","packageid":53735},{"block":false,"categoryid":381,"description":"Standard (de)compression library","ebuildids":[704146,824256],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"base-system@gentoo.org","maintainername":"Gentoo Base System","name":"zlib","packageid":55408}],"repos":[{"branch":"master","lastcommit":"3dcdcb066317ac8a6b4956ad18dcb5fafc6a3ed5","name":"gentoo","path":"\/usr\/portage","repoid":1,"upstream":"origin"}],"tracked":false,"urls":["https:\/\/bedtools.readthedocs.io\/"],"uses":[{"description":"Enable dependencies and\/or preparations necessary to run tests (usually controlled by FEATURES=test but can be toggled independently)","isdefault":false,"use":"test"}]}