{"bugs":[{"bugid":830041,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/kallisto-0.46.2 - \/...\/Bootstrap.h: error: uint has not been declared"},{"bugid":907972,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/kallisto-0.46.2-r1 fails to compile (MUSL-SYSTEM): common.h:132:24: error: std::string pretty_num redeclared as different kind of entity"},{"bugid":951809,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/kallisto-0.46.2-r1 - [gcc-15] [cmake-4] -- Configuring incomplete, errors occurred!"}],"categories":[{"categoryid":429,"name":"dev-cpp","summary":"The dev-cpp category contains libraries and utilities relevant to the c++ programming language."},{"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":"a198e862478387fe37b4d232d51a3edb558cd3e0","committime":"2025-12-19T10:01:01","packageid":68458,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"grobian@gentoo.org","authorname":"Fabian Groffen","body":"Bug: https:\/\/bugs.gentoo.org\/473598\nBug: https:\/\/bugs.gentoo.org\/720224\nSigned-off-by: Fabian Groffen ","commitid":"2d25fad95cbaa525c8945d8e582c749d49524f49","committime":"2025-12-19T09:25:43","packageid":68458,"repoid":1,"summary":"*\/*: drop *-linux keywords"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"5a1adb610b1d91ab6683cbe671e266f424224c16","committime":"2025-11-04T08:35:48","packageid":68458,"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":68458,"repoid":1,"summary":"sci-*\/*: update for virtual\/zlib"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"42a6e504e2e1653311d0335c59d14b42242af17b","committime":"2024-04-07T06:33:52","packageid":68458,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"eschwartz93@gmail.com","authorname":"Eli Schwartz","body":"Signed-off-by: Eli Schwartz \nSigned-off-by: Sam James ","commitid":"aee8ccbdd75ea534b83353705892e8471012f326","committime":"2024-04-05T00:40:33","packageid":68458,"repoid":1,"summary":"sci-biology\/kallisto: update EAPI 7 -> 8"},{"authoremail":"eschwartz93@gmail.com","authorname":"Eli Schwartz","body":"Which is the current default distributed version. Nicer than requiring\npeople to downgrade to an old version.\n\nCloses: https:\/\/bugs.gentoo.org\/877887\nSigned-off-by: Eli Schwartz \nSigned-off-by: Sam James ","commitid":"14bc51e9759c448132391901ff1eb528fe0f5a0c","committime":"2024-04-05T00:37:31","packageid":68458,"repoid":1,"summary":"sci-biology\/kallisto: port to catch2 version 3"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"a1ecca558356110750acdc8b655e8b79ef995c58","committime":"2021-05-08T14:35:03","packageid":68458,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"* Upstream is barely active and doesn't merge PRs\n\nPackage-Manager: Portage-3.0.18, Repoman-3.0.3\nSigned-off-by: David Seifert ","commitid":"56be5d1bb2ed27e39ac7284038fcd6777351a982","committime":"2021-05-08T14:15:00","packageid":68458,"repoid":1,"summary":"sci-biology\/kallisto: Remove live ebuild"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/696504\nCloses: https:\/\/bugs.gentoo.org\/708658\nCloses: https:\/\/bugs.gentoo.org\/788427\nPackage-Manager: Portage-3.0.18, Repoman-3.0.3\nSigned-off-by: David Seifert ","commitid":"06fc538689feab7fb91e62f619cfdc213074e8e3","committime":"2021-05-08T14:14:57","packageid":68458,"repoid":1,"summary":"sci-biology\/kallisto: Remove old 0.43.1"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Bug: https:\/\/bugs.gentoo.org\/696504\nBug: https:\/\/bugs.gentoo.org\/708658\nBug: https:\/\/bugs.gentoo.org\/788427\nPackage-Manager: Portage-3.0.18, Repoman-3.0.3\nSigned-off-by: David Seifert ","commitid":"5c94901047b60e7e21d38dea38be43e2d5f7a816","committime":"2021-05-08T14:14:54","packageid":68458,"repoid":1,"summary":"sci-biology\/kallisto: Bump to 0.46.2"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"eb8f2a1a8dfb251fc9fcc08419d610af3d87f162","committime":"2017-11-16T13:31:12","packageid":68458,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/github.com\/gentoo\/sci\/pull\/814\nPackage-Manager: Portage-2.3.14, Repoman-2.3.6","commitid":"3dcd860e419d637e622ff61ee6f0acec2916e7d7","committime":"2017-11-16T13:15:49","packageid":68458,"repoid":1,"summary":"sci-biology\/kallisto: Initial addition"}],"dependencies":[{"block":false,"categoryid":318,"description":"General purpose library and file format for storing scientific data","ebuildids":[821731,821731],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"xarthisius@gentoo.org","maintainername":"Kacper Kowalik","name":"hdf5","packageid":42259,"summary":"HDF5 is a file format and library for storing scientific data. HDF5 was designed and implemented to address the deficiencies of HDF4.x. It has a more powerful and flexible data model, supports files larger than 2 GB, and supports parallel I\/O."},{"block":false,"categoryid":318,"description":"C library for high-throughput sequencing data formats","ebuildids":[821731],"firstseen":"2014-09-21T13:51:26.076524","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"htslib","packageid":62539},{"block":false,"categoryid":429,"description":"Modern C++ header-only framework for unit-tests","ebuildids":[821731],"firstseen":"2016-05-24T13:40:34.417370","maintainer":"mgorny@gentoo.org","maintainername":"Michał Górny","name":"catch","packageid":65465},{"block":false,"categoryid":396,"description":"Virtual for libz.so providers","ebuildids":[821731],"firstseen":"2025-11-04T07:31:41.418357","name":"zlib","packageid":78605}],"depending":[],"ebuilds":[{"archs":["~amd64","~x86"],"ebuildid":821731,"firstseen":"2024-04-07T07:48:21.737652","license":"BSD","moddate":"2026-03-28T18:04:21","packageid":68458,"repoid":1,"slot":"0","uses":["hdf5","test"],"version":"0.46.2-r1"}],"masks":[],"package":{"categoryid":353,"description":"Near-optimal RNA-Seq quantification","firstseen":"2017-11-16T13:46:45.075214","name":"kallisto","packageid":68458},"rdependencies":[{"block":false,"categoryid":318,"description":"General purpose library and file format for storing scientific data","ebuildids":[821731],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"xarthisius@gentoo.org","maintainername":"Kacper Kowalik","name":"hdf5","packageid":42259,"summary":"HDF5 is a file format and library for storing scientific data. HDF5 was designed and implemented to address the deficiencies of HDF4.x. It has a more powerful and flexible data model, supports files larger than 2 GB, and supports parallel I\/O."},{"block":false,"categoryid":318,"description":"C library for high-throughput sequencing data formats","ebuildids":[821731],"firstseen":"2014-09-21T13:51:26.076524","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"htslib","packageid":62539},{"block":false,"categoryid":396,"description":"Virtual for libz.so providers","ebuildids":[821731],"firstseen":"2025-11-04T07:31:41.418357","name":"zlib","packageid":78605}],"repos":[{"branch":"master","lastcommit":"b112e2b2384c2048502a919dd687fffa675792e8","name":"gentoo","path":"\/usr\/portage","repoid":1,"upstream":"origin"}],"tracked":false,"urls":["http:\/\/pachterlab.github.io\/kallisto\/"],"uses":[{"description":"Add support for the Hierarchical Data Format v5","isdefault":false,"use":"hdf5"},{"description":"Enable dependencies and\/or preparations necessary to run tests (usually controlled by FEATURES=test but can be toggled independently)","isdefault":false,"use":"test"}]}