{"bugs":[{"bugid":890417,"firstseen":"2023-01-11T06:49:31.490297","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/fasta-36.3.8i fails to compile (DASH-SYSTEM): comp_lib9.c:(.text+0xad6): undefined reference to adler32"},{"bugid":938324,"firstseen":"2024-08-22T18:54:44.995916","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/fasta-36.3.8i - mm_file.h: error: implicit declaration of function ftello"}],"categories":[{"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":"88b39a553d38b18aec502bbbf3b540cbb137d525","committime":"2024-08-22T04:34:06","packageid":46474,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"eschwartz@gentoo.org","authorname":"Eli Schwartz","body":"A 2022 release, how modern. :D Ignore the part where the tag name\ncontains the date \"2020\".\n\nIt obsoletes the patch as well, which seems good. However it does NOT\nfix the LTO issue.\n\nSigned-off-by: Eli Schwartz ","commitid":"17f6c86d219f1f04c0cb2852ce1cd810169985a2","committime":"2024-08-22T04:14:40","packageid":46474,"repoid":1,"summary":"sci-biology\/fasta: add 36.3.8i"},{"authoremail":"eschwartz@gentoo.org","authorname":"Eli Schwartz","body":"Closes: https:\/\/bugs.gentoo.org\/862267\nSigned-off-by: Eli Schwartz ","commitid":"d9f0a90cdc4b14c9684749be04f3fd78e1c853d5","committime":"2024-08-22T04:12:09","packageid":46474,"repoid":1,"summary":"sci-biology\/fasta: mark as LTO-unsafe"},{"authoremail":"eschwartz@gentoo.org","authorname":"Eli Schwartz","body":"This has been present since the initial import into cvs:\nhttps:\/\/gitweb.gentoo.org\/archive\/repo\/gentoo-2.git\/commit\/?id=fe5d632c39746b7b396434277896dd0e58e15567\n\nIt does not seem to have made any sense at the time -- the compile phase\nrequired running `emake -f ..\/make\/Makefile***` because upstream was one\nof those projects that apparently liked having code separate from ways\nto build the code (???) and no src_test was defined at all. So having a\ntest dependency made no real sense as tests were never run!!!\n\nThere is an actual test phase today. It manually runs an sh script, and\ntcsh still isn't involved anywhere. There are two entirely separate tcsh\nscripts in the upstream codebase, though.\n\nRegardless, having this test dependency is nonsensical. So is having\nIUSE=test and a matching RESTRICT. None of this gets us *anything*.\nTherefore, drop it.\n\nSigned-off-by: Eli Schwartz ","commitid":"e13c18b293f82931681b74b1973af90217526354","committime":"2024-08-22T03:36:08","packageid":46474,"repoid":1,"summary":"sci-biology\/fasta: remove tcsh as a test dependency, drop IUSE"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"82b37a27e889ff1af7cfc1e3a8c2f06ef8622566","committime":"2022-03-20T19:04:16","packageid":46474,"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":"0e456e888bc1895caf56c1ba4a44980117b6b5c8","committime":"2022-03-20T18:49:28","packageid":46474,"repoid":1,"summary":"sci-biology\/fasta: [QA] fix tc-get* quoting"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"b4980e76bedebfccb2fd200de41de7ab549d4f51","committime":"2022-03-19T19:49:10","packageid":46474,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/835634\nSigned-off-by: David Seifert ","commitid":"b49951fbe7556d78601553909d034080a98e9e5f","committime":"2022-03-19T19:33:05","packageid":46474,"repoid":1,"summary":"sci-biology\/fasta: fix broken README symlink"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"6471433e11fd75f7ee15d047490dd3e9ebe69fa0","committime":"2022-03-19T17:19:10","packageid":46474,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/648618\nCloses: https:\/\/bugs.gentoo.org\/828700\nSigned-off-by: David Seifert ","commitid":"5d5c2e0b0e7e7bf0a1a79187db493ba0095d414d","committime":"2022-03-19T17:07:58","packageid":46474,"repoid":1,"summary":"sci-biology\/fasta: drop 36.3.5e"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Bug: https:\/\/bugs.gentoo.org\/648618\nBug: https:\/\/bugs.gentoo.org\/828700\nSigned-off-by: David Seifert ","commitid":"84e1af9d2932d855c6f05b3bda91a4dfedd2b0a4","committime":"2022-03-19T17:07:57","packageid":46474,"repoid":1,"summary":"sci-biology\/fasta: add 36.3.8h"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"1dff16feef2bb9d2ccf6e0e5f2a4f87e02f7a94d","committime":"2021-04-18T06:22:06","packageid":46474,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"Package-Manager: Portage-3.0.14-prefix, Repoman-3.0.2\nSigned-off-by: Sam James ","commitid":"3d8792a28d1ca550e0e2dc14d43ff81dfd86ed56","committime":"2021-04-16T13:56:38","packageid":46474,"repoid":1,"summary":"sci-biology\/fasta: eutils->epatch"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"e09fb731e1e423680e7686c41224fdce5e996fa7","committime":"2021-01-06T15:35:03","packageid":46474,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"grobian@gentoo.org","authorname":"Fabian Groffen","body":"Package-Manager: Portage-3.0.12, Repoman-3.0.2\nSigned-off-by: Fabian Groffen ","commitid":"14b94e0f1f220e1dbd6be0e01ae67b70a68c61d7","committime":"2021-01-06T15:08:50","packageid":46474,"repoid":1,"summary":"sci-biology\/fasta: drop x86-macos"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"824dac76531dbf1a15c3b6ae4edadba511fe07b1","committime":"2019-12-11T12:45:54","packageid":46474,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"* Since all ebuilds in the tree are EAPI>=4,\n `|| die` on builtin commands is redundant\n and dead code.\n\nCloses: https:\/\/github.com\/gentoo\/gentoo\/pull\/13940\nReviewed-by: Ulrich Müller \nReviewed-by: Michał Górny \nReviewed-by: Andreas K. Hüttel \nSigned-off-by: David Seifert ","commitid":"398a42634f34afa1979d88ae1d8b38194e911c2d","committime":"2019-12-11T12:32:00","packageid":46474,"repoid":1,"summary":"*\/*: [QA] Remove redundant `|| die` guards"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"fef742528aacdd4ffa4e59ea0354106ca161650e","committime":"2019-12-10T23:48:11","packageid":46474,"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":46474,"repoid":1,"summary":"*\/*: [QA] Fix trivial cases of MissingTestRestrict"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"2fbdfbc003d28cd80696303439a07a13ff2dc035","committime":"2018-05-21T17:29:55","packageid":46474,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"m.mairkeimberger@gmail.com","authorname":"Michael Mair-Keimberger","body":"Closes: https:\/\/github.com\/gentoo\/gentoo\/pull\/8513","commitid":"7d108794dce54cb34c09df68ef26a962c08ad956","committime":"2018-05-21T10:11:07","packageid":46474,"repoid":1,"summary":"sci-biology\/fasta: use HTTPs"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"574504a7468cf2df80def3032e5d31ac05afc69f","committime":"2018-01-01T13:05:34","packageid":46474,"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":"a41c01197596738c1f3af00bda7e3cbf52bc9f1c","committime":"2018-01-01T12:42:45","packageid":46474,"repoid":1,"summary":"sci-biology\/fasta: Remove old"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"25093d6359f778b8d1052f66ba9e26fc29ded21a","committime":"2017-02-28T20:35:29","packageid":46474,"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":46474,"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":46474,"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":46474,"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":46474,"repoid":1,"summary":"2015-06-19 16:35:30 UTC"}],"dependencies":[],"depending":[],"ebuilds":[{"archs":["~amd64","~amd64-linux","~ppc","~x64-macos","~x86","~x86-linux"],"ebuildid":835759,"firstseen":"2024-08-22T05:35:38.087138","license":"fasta","moddate":"2024-12-17T22:35:47","packageid":46474,"repoid":1,"slot":"0","uses":["cpu_flags_x86_sse2","debug"],"version":"36.3.8i"},{"archs":["~amd64","~amd64-linux","~ppc","~x64-macos","~x86","~x86-linux"],"ebuildid":743648,"firstseen":"2022-03-19T19:55:30.928222","license":"fasta","moddate":"2024-12-17T22:35:47","packageid":46474,"repoid":1,"slot":"0","uses":["cpu_flags_x86_sse2","debug"],"version":"36.3.8h-r1"}],"masks":[],"package":{"categoryid":353,"description":"FASTA is a DNA and Protein sequence alignment software package","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"fasta","packageid":46474},"rdependencies":[],"repos":[{"branch":"master","lastcommit":"893995b572054b456eb772704a4fcb47bc61545f","name":"gentoo","path":"\/usr\/portage","repoid":1,"upstream":"origin"}],"tracked":false,"urls":["https:\/\/fasta.bioch.virginia.edu\/fasta_www2\/fasta_down.shtml"],"uses":[{"description":"Enable extra debug codepaths, like asserts and extra output. If you want to get meaningful backtraces see https:\/\/wiki.gentoo.org\/wiki\/Project:Quality_Assurance\/Backtraces","isdefault":false,"use":"debug"},{"description":"Use the SSE2 instruction set","group":"cpu_flags_x86","isdefault":false,"use":"sse2"}]}