{"bugs":[{"bugid":941490,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/vcftools-0.1.16 - [libtool] [llvm] variant_file_filters.cpp: error: use of undeclared identifier random_shuffle"}],"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":"84205fec17c970e3b31aaf0c2db7f453dcf33a90","committime":"2026-03-07T19:16:09","packageid":58004,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"floppym@gentoo.org","authorname":"Mike Gilbert","body":"This prevents special characters like '*' from being interpreted as a\npattern match.\n\nSigned-off-by: Mike Gilbert \nMerges: https:\/\/codeberg.org\/gentoo\/gentoo\/pulls\/232","commitid":"eccf647e5ed9dc7d3337f893cc46f0183528ff1f","committime":"2026-03-06T18:47:38","packageid":58004,"repoid":1,"summary":"Quote EPREFIX when used in a parameter expansion"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"00b4cc6bb3b864fbeaa6dca1da399c3716afed16","committime":"2025-11-04T09:50:46","packageid":58004,"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":58004,"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":58004,"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":58004,"repoid":1,"summary":"sci-*\/*: update for virtual\/zlib"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"19125f361eb5bb17b594ca08f304d6da73a0b521","committime":"2022-07-02T22:46:39","packageid":58004,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"Signed-off-by: Sam James ","commitid":"4e3464f740a62b786296d21274e6197b8f3a4bd0","committime":"2022-07-02T22:33:11","packageid":58004,"repoid":1,"summary":"sci-biology\/vcftools: drop 0.1.14"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"4537f12d270be55f3d78e2f55e382d72aac33c0c","committime":"2022-02-19T14:21:51","packageid":58004,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"andrewammerlaan@gentoo.org","authorname":"Andrew Ammerlaan","body":"Closes: https:\/\/bugs.gentoo.org\/833503\nPackage-Manager: Portage-3.0.30, Repoman-3.0.3\nSigned-off-by: Andrew Ammerlaan ","commitid":"dc7beed7f021c6afe109a71cd67a3cf014538a57","committime":"2022-02-19T14:05:07","packageid":58004,"repoid":1,"summary":"sci-biology\/vcftools: add version 0.1.16"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"c244a5f932cd4df61def2b8b1db2d60f05f91c39","committime":"2019-07-15T15:46:59","packageid":58004,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Signed-off-by: Michał Górny ","commitid":"bebdc7885620311c4c78ecc26c837090971c94dc","committime":"2019-07-15T15:25:58","packageid":58004,"repoid":1,"summary":"sci-biology\/vcftools: Sort KEYWORDS"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"25093d6359f778b8d1052f66ba9e26fc29ded21a","committime":"2017-02-28T20:35:29","packageid":58004,"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":58004,"repoid":1,"summary":"Drop $Id$ per council decision in bug #611234."},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"177a1674049c8bc37f13ce25abdd34bfe22dc2f0","committime":"2016-09-25T10:25:02","packageid":58004,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: portage-2.3.1","commitid":"1618e0bc8341fcb31c9a1b79c21a2a084cf282fd","committime":"2016-09-25T10:11:30","packageid":58004,"repoid":1,"summary":"sci-biology\/vcftools: Add missing RDEPEND on sys-libs\/zlib"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"f61ea6029253282807392d89895b737b91720fb1","committime":"2016-09-25T09:45:04","packageid":58004,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: portage-2.3.1\nCloses: https:\/\/github.com\/gentoo\/gentoo\/pull\/2407\n\nSigned-off-by: David Seifert ","commitid":"e81e21772377c90519cdd2e095b305e1039ecead","committime":"2016-09-25T09:26:02","packageid":58004,"repoid":1,"summary":"sci-biology\/vcftools: Remove old ebuild"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Gentoo-bug: 594924\n* EAPI=6\n* Properly RDEPEND on dev-lang\/perl\n\nPackage-Manager: portage-2.3.1\nCloses: https:\/\/github.com\/gentoo\/gentoo\/pull\/2407\n\nSigned-off-by: David Seifert ","commitid":"bdf7251db30941f3912dd646d37fb125fbabf018","committime":"2016-09-25T09:24:17","packageid":58004,"repoid":1,"summary":"sci-biology\/vcftools: Version bump to 0.1.14"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"945f0d2a26da4f944fd06ad6a874f69d37ce1e06","committime":"2015-08-09T09:26:46","packageid":58004,"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":58004,"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":58004,"repoid":1,"summary":"2015-06-19 16:35:30 UTC"}],"dependencies":[{"block":false,"categoryid":450,"description":"Larry Wall's Practical Extraction and Report Language","ebuildids":[740768],"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 Linear Algebra Package FORTRAN 77 (LAPACK) implementation","ebuildids":[740768],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci@gentoo.org","maintainername":"Gentoo Science Project","name":"lapack","packageid":55481},{"block":false,"categoryid":396,"description":"Virtual for libz.so providers","ebuildids":[740768],"firstseen":"2025-11-04T07:31:41.418357","name":"zlib","packageid":78605}],"depending":[],"ebuilds":[{"archs":["~amd64","~x86"],"ebuildid":740768,"firstseen":"2022-02-19T14:24:04.267337","license":"LGPL-3","moddate":"2026-03-22T20:20:57","packageid":58004,"repoid":1,"slot":"0","uses":["lapack"],"version":"0.1.16"}],"masks":[],"package":{"categoryid":353,"description":"Tools for working with VCF (Variant Call Format) files","firstseen":"2011-10-03T14:35:06.100551","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"vcftools","packageid":58004},"rdependencies":[{"block":false,"categoryid":450,"description":"Larry Wall's Practical Extraction and Report Language","ebuildids":[740768],"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 Linear Algebra Package FORTRAN 77 (LAPACK) implementation","ebuildids":[740768],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci@gentoo.org","maintainername":"Gentoo Science Project","name":"lapack","packageid":55481},{"block":false,"categoryid":396,"description":"Virtual for libz.so providers","ebuildids":[740768],"firstseen":"2025-11-04T07:31:41.418357","name":"zlib","packageid":78605}],"repos":[{"branch":"master","lastcommit":"d5ea4ae79d5a357ba2876224bf1167c46a1f4651","name":"gentoo","path":"\/usr\/portage","repoid":1,"upstream":"origin"}],"tracked":false,"urls":["http:\/\/vcftools.sourceforge.net\/"],"uses":[{"description":"Add support for the virtual\/lapack numerical library","isdefault":false,"use":"lapack"}]}