{"bugs":[{"bugid":882355,"firstseen":"2022-11-21T09:03:15.073094","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/hmmer-3.1_beta2-r1 leaves trace of segfault in dmesg"}],"categories":[{"categoryid":353,"name":"sci-biology","summary":"The sci-biology category contains software that can be used in biological and related scientific environments."},{"categoryid":318,"name":"sci-libs","summary":"The sci-libs category contains various science-related libraries."},{"categoryid":396,"name":"virtual","summary":"The virtual category contains packages which satisfy virtual dependencies."}],"changelog":[{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"d881a81eda965af2135abceb2df6456362611318","committime":"2024-05-09T01:18:33","packageid":43083,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"jy6x2b32pie9@yahoo.com","authorname":"NHOrus","body":"There are no autotools source files, so we can't just autoreconf the problem out of existence\n\n[sam: Revbump.]\n\nCloses: https:\/\/bugs.gentoo.org\/900551\nSigned-off-by: NHOrus \nCloses: https:\/\/github.com\/gentoo\/gentoo\/pull\/36599\nSigned-off-by: Sam James ","commitid":"4919e107f95d762348df57ca9a8e75307d9222bc","committime":"2024-05-08T09:30:27","packageid":43083,"repoid":1,"summary":"sci-biology\/hmmer: Add missing include into configure"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"4908c692a2bd0846de869fcb1767455d3fc33e58","committime":"2022-11-20T21:31:45","packageid":43083,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/882279\nSigned-off-by: David Seifert ","commitid":"41183c48ca86eaaee196abfb18b935f12836f75a","committime":"2022-11-20T21:23:10","packageid":43083,"repoid":1,"summary":"sci-biology\/hmmer: expose XSI pthread_setconcurrency() prototypes"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"af6f0e8ef0bcb907ba1d0760fbc87f04990100a3","committime":"2022-07-07T20:01:37","packageid":43083,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert ","commitid":"d31ff028511de2e2cc29e125cae3a6862aa6e2ec","committime":"2022-07-07T19:56:56","packageid":43083,"repoid":1,"summary":"sci-biology\/hmmer: update EAPI 6 -> 8 (3.1_beta2)"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/725306\nSigned-off-by: David Seifert ","commitid":"9215238aeb785b45c5c95d9008dcfc76a1ca9507","committime":"2022-07-07T19:56:55","packageid":43083,"repoid":1,"summary":"sci-biology\/hmmer: update EAPI 6 -> 8 (2.3.2)"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"fef742528aacdd4ffa4e59ea0354106ca161650e","committime":"2019-12-10T23:48:11","packageid":43083,"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":43083,"repoid":1,"summary":"*\/*: [QA] Fix trivial cases of MissingTestRestrict"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"ddb332065058e977a8787e8c3380e9cade8ad8c0","committime":"2017-09-26T05:23:30","packageid":43083,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"kentnl@gentoo.org","authorname":"Kent Fredric","body":"Closes: https:\/\/bugs.gentoo.org\/421799\nPackage-Manager: Portage-2.3.8, Repoman-2.3.3","commitid":"fe3bbbb5d658bf8673eba70e65f1b6b6de9d7c88","committime":"2017-09-25T13:24:20","packageid":43083,"repoid":1,"summary":"sci-biology\/hmmer: Cleanup broken versions re bug #421799"},{"authoremail":"kentnl@gentoo.org","authorname":"Kent Fredric","body":"Sci Team don't want unnecessary stable pacakges, and this is not\nnecessary.\n\nThe stated stable versions are broken on all available perls anyway.\n\nPackage-Manager: Portage-2.3.8, Repoman-2.3.3","commitid":"522907f07209b4b34bd3e8c569edbb31058c7917","committime":"2017-09-25T13:22:54","packageid":43083,"repoid":1,"summary":"sci-biology\/hmmer: de-stabilize"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"25093d6359f778b8d1052f66ba9e26fc29ded21a","committime":"2017-02-28T20:35:29","packageid":43083,"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":43083,"repoid":1,"summary":"Drop $Id$ per council decision in bug #611234."},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"e276789fbac1f63ee217f1146713347048bdbfe3","committime":"2017-02-06T21:38:43","packageid":43083,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-2.3.3, Repoman-2.3.1\nCloses: https:\/\/github.com\/gentoo\/gentoo\/pull\/3856","commitid":"cbfe0e33651a8811229d663a9469cc97957b994e","committime":"2017-02-06T20:48:01","packageid":43083,"repoid":1,"summary":"sci-biology\/hmmer: Remove old"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-2.3.3, Repoman-2.3.1\nCloses: https:\/\/github.com\/gentoo\/gentoo\/pull\/3856","commitid":"99b5ad341522b2e3b1a5c99d3fa7029d521f2351","committime":"2017-02-06T20:48:01","packageid":43083,"repoid":1,"summary":"sci-biology\/hmmer: Only keep amd64 and x86 in KEYWORDS"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"fe8b2cea47447810dcc0c37bdb94f3c15c104f59","committime":"2016-10-09T15:25:28","packageid":43083,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Gentoo-bug: 328911, 586960\n* EAPI=6\n* Introduce SLOT=2 and rename binaries and\n static libraries\n\nPackage-Manager: portage-2.3.1","commitid":"895b3abfbdacf52dbd7a0e817eb7ebf101ce55a7","committime":"2016-10-09T14:52:52","packageid":43083,"repoid":1,"summary":"sci-biology\/hmmer: Properly SLOT=2 hmmer-2.3.2"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"* EAPI=6\n* Make perl shebangs portable\n* Install headers into 'hmmer3' subdir\n\nPackage-Manager: portage-2.3.1","commitid":"c0a145c569b658ac97b0addecdee386768d4bb16","committime":"2016-10-09T12:44:16","packageid":43083,"repoid":1,"summary":"sci-biology\/hmmer: Version bump to 3.1_beta2"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"907925b64feea4182a3ed5decfdad3deef5f9ee2","committime":"2016-04-19T21:02:16","packageid":43083,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"axs@gentoo.org","authorname":"Ian Stakenvicius","body":"* Bumped EAPI\n* Merged KEYWORDS between 2.3.2-r1 and 2.3.2-r2\n* dropped IUSE=\"pvm\" as package was dropped 5 years ago\n* fixed metadata.xml to match\n\nPackage-Manager: portage-2.2.26","commitid":"cd5113534b40b92c4b055c9a12c52e105e22828a","committime":"2016-04-19T20:34:54","packageid":43083,"repoid":1,"summary":"sci-biology\/hmmer: cheamup of 2.3.2 version"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"945f0d2a26da4f944fd06ad6a874f69d37ce1e06","committime":"2015-08-09T09:26:46","packageid":43083,"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":43083,"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":43083,"repoid":1,"summary":"2015-06-19 16:35:30 UTC"}],"dependencies":[{"block":false,"categoryid":396,"description":"Virtual for Message Passing Interface (MPI) v2.0 implementation","ebuildids":[755464],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"cluster@gentoo.org","maintainername":"Gentoo Cluster Project","name":"mpi","packageid":42101},{"block":false,"categoryid":318,"description":"The GNU Scientific Library","ebuildids":[755464],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci@gentoo.org","maintainername":"Gentoo Science Project","name":"gsl","packageid":46545,"summary":"The GNU Scientific Library (GSL) is a collection of routines for numerical analysis. The routines are written from scratch by the GSL team in C, and present a modern API for C programmers, while allowing wrappers to be written for very high level languages. GSL includes data types and routines for complex numbers, vectors, matrices, basic linear algebra subroutines (BLAS), eigensystems, simulated annealing, minimization, root finding, pseudo-random numbers, least-squares fitting, fast Fourier transforms (FFT), differential equations, quadrature, Monte Carlo integration, special functions, physical constants, and much more."}],"depending":[{"block":false,"categoryid":353,"description":"Prototype ncRNA genefinder","ebuildids":[620254,620254,819990,819990],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"qrna","packageid":51704},{"block":false,"categoryid":353,"description":"EMBOSS integrated version of HMMER wrapper - sequence analysis with profile HMMs","ebuildids":[740086],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"embassy-hmmer","packageid":54710},{"block":false,"categoryid":353,"description":"Intelligent algorithms for DNA searches","ebuildids":[722370,722370],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"wise","packageid":55024}],"ebuilds":[{"archs":["~amd64","~amd64-linux","~ppc-macos","~x86","~x86-linux"],"ebuildid":755464,"firstseen":"2022-07-07T21:10:47.213865","license":"GPL-3","moddate":"2024-12-17T22:35:47","packageid":43083,"repoid":1,"slot":"0","uses":["cpu_flags_ppc_altivec","cpu_flags_x86_sse","gsl","mpi","test"],"version":"3.1_beta2-r1"},{"archs":["~amd64","~x86"],"ebuildid":825437,"firstseen":"2024-05-09T02:20:24.943909","license":"GPL-2","moddate":"2024-12-17T22:35:47","packageid":43083,"repoid":1,"slot":"2","uses":["cpu_flags_ppc_altivec","test"],"version":"2.3.2-r6"}],"masks":[],"package":{"categoryid":353,"description":"Sequence analysis using profile hidden Markov models","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"hmmer","packageid":43083},"rdependencies":[{"block":false,"categoryid":396,"description":"Virtual for Message Passing Interface (MPI) v2.0 implementation","ebuildids":[755464],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"cluster@gentoo.org","maintainername":"Gentoo Cluster Project","name":"mpi","packageid":42101},{"block":false,"categoryid":318,"description":"The GNU Scientific Library","ebuildids":[755464],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci@gentoo.org","maintainername":"Gentoo Science Project","name":"gsl","packageid":46545,"summary":"The GNU Scientific Library (GSL) is a collection of routines for numerical analysis. The routines are written from scratch by the GSL team in C, and present a modern API for C programmers, while allowing wrappers to be written for very high level languages. GSL includes data types and routines for complex numbers, vectors, matrices, basic linear algebra subroutines (BLAS), eigensystems, simulated annealing, minimization, root finding, pseudo-random numbers, least-squares fitting, fast Fourier transforms (FFT), differential equations, quadrature, Monte Carlo integration, special functions, physical constants, and much more."}],"repos":[{"branch":"master","lastcommit":"d6202e218f5f01a40303aab1070d88d9c9f13272","name":"gentoo","path":"\/usr\/portage","repoid":1,"upstream":"origin"}],"tracked":false,"urls":["http:\/\/hmmer.org\/"],"uses":[{"description":"Use the GNU scientific library for calculations","isdefault":false,"use":"gsl"},{"description":"Add MPI (Message Passing Interface) layer to the apps that support it","isdefault":false,"use":"mpi"},{"description":"Enable dependencies and\/or preparations necessary to run tests (usually controlled by FEATURES=test but can be toggled independently)","isdefault":false,"use":"test"},{"description":"Use the AltiVec\/VMX instruction set","group":"cpu_flags_ppc","isdefault":false,"use":"altivec"},{"description":"Use the SSE instruction set","group":"cpu_flags_x86","isdefault":false,"use":"sse"}]}