{"bugs":[{"bugid":868363,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/augustus-3.4.0-r3 calls g++ directly"},{"bugid":873025,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/augustus-3.4.0-r2 fails tests (MUSL)"},{"bugid":940693,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/augustus-2.5.5 - [ncurses-6.5] [libtool] [gcc-15] list.c: error: implicit declaration of function FatalError [-Wimplicit-function-declaration]"},{"bugid":958507,"firstseen":"2025-07-11T02:48:40.189262","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/augustus-3.5.0 - [cmake-4] Fatal error: cant create build\/Genomic_Data.o: No such file or directory"}],"categories":[{"categoryid":452,"name":"dev-db","summary":"The dev-db category contains libraries and utilities for database related programming."},{"categoryid":393,"name":"dev-libs","summary":"The dev-libs category contains various miscellaneous programming libraries."},{"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":317,"name":"sci-mathematics","summary":"The sci-mathematics category contains mathematical software."},{"categoryid":396,"name":"virtual","summary":"The virtual category contains packages which satisfy virtual dependencies."}],"changelog":[{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"00b4cc6bb3b864fbeaa6dca1da399c3716afed16","committime":"2025-11-04T09:50:46","packageid":54585,"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":54585,"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":54585,"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":54585,"repoid":1,"summary":"sci-*\/*: update for virtual\/zlib"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"bf249d7184286a8e3d740ed0d5eb6478e1c2a2e9","committime":"2025-05-20T19:24:04","packageid":54585,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"asturm@gentoo.org","authorname":"Andreas Sturmlechner","body":"Signed-off-by: Andreas Sturmlechner ","commitid":"2c862807546f666b21c5ab2c01ba3a1402f5c38a","committime":"2025-05-19T20:38:27","packageid":54585,"repoid":1,"summary":"sci-biology\/augustus: drop 2.5.5"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"2787fcfad93d0bd14da9380e0f852c46cefde2b3","committime":"2025-04-14T16:05:14","packageid":54585,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"Signed-off-by: Sam James ","commitid":"62bb07cf8ef1d17c2ab1228094b5aa4694bb602d","committime":"2025-04-14T15:57:55","packageid":54585,"repoid":1,"summary":"sci-biology\/augustus: Stabilize 3.4.0-r3 amd64, #920140"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"59b3298e63b2ba0beeb78e2f6e047eda1593b368","committime":"2025-02-13T09:24:23","packageid":54585,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"parona@protonmail.com","authorname":"Alfred Wingate","body":"Closes: https:\/\/bugs.gentoo.org\/949617\nSigned-off-by: Alfred Wingate \nCloses: https:\/\/github.com\/gentoo\/gentoo\/pull\/40531\nSigned-off-by: Sam James ","commitid":"eb668702f3bd1a2f3b9ff0e7ad4f19edca41fb76","committime":"2025-02-11T13:05:38","packageid":54585,"repoid":1,"summary":"sci-biology\/augustus: fix gcc15 build"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"60d61ddbb782f5616b0a2fb35b118da4c6619165","committime":"2025-02-11T01:48:34","packageid":54585,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"... to match execution order.\n\nSigned-off-by: Sam James ","commitid":"b9a680c3170455acf212a7f50c2249c061968cba","committime":"2025-02-11T01:37:12","packageid":54585,"repoid":1,"summary":"sci-biology\/augustus: fix phase definition order"},{"authoremail":"parona@protonmail.com","authorname":"Alfred Wingate","body":"Closes: https:\/\/bugs.gentoo.org\/895204\nSigned-off-by: Alfred Wingate \nSigned-off-by: Sam James ","commitid":"46398746b50dc4be683f7777230477bef9780ee7","committime":"2025-02-10T19:15:07","packageid":54585,"repoid":1,"summary":"sci-biology\/augustus: include cstdint for gcc-13"},{"authoremail":"parona@protonmail.com","authorname":"Alfred Wingate","body":"* Add missing dependency on python with tests.\n* Wire up unittests.\n* Disable test comparing on musl. This follows upstream with non-amd64 and\n non-linux environments.\n\nBug: https:\/\/bugs.gentoo.org\/868363\nBug: https:\/\/bugs.gentoo.org\/873025\nSigned-off-by: Alfred Wingate \nCloses: https:\/\/github.com\/gentoo\/gentoo\/pull\/40521\nSigned-off-by: Sam James ","commitid":"7fdfd97f34314b9fb85bcbadb46efc07b94b67aa","committime":"2025-02-10T19:14:46","packageid":54585,"repoid":1,"summary":"sci-biology\/augustus: add 3.5.0"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"f2979793991144637956e4225ce4d0235900c1a2","committime":"2023-06-09T15:16:56","packageid":54585,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"arthurzam@gentoo.org","authorname":"Arthur Zamarin","body":"Signed-off-by: Arthur Zamarin ","commitid":"7cfe7ab29638264f1dcf98d78ad189516f5f1da1","committime":"2023-06-03T14:45:26","packageid":54585,"repoid":1,"summary":"sci-biology\/augustus: destabilize for ~x86"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"a97958ff65140b6346822bc23309facaf3c1ee5e","committime":"2023-02-04T17:31:53","packageid":54585,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"Bug: https:\/\/bugs.gentoo.org\/614866\nSigned-off-by: Sam James ","commitid":"25774a0a53557d280b9519cd6b85cf7da886e95f","committime":"2023-02-04T17:19:53","packageid":54585,"repoid":1,"summary":"sci-biology\/augustus: add lpsolve subslot dep"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"e697309540271067ac48ba6fd85e0fa730290863","committime":"2022-09-03T22:16:50","packageid":54585,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"Closes: https:\/\/bugs.gentoo.org\/832187\nSigned-off-by: Sam James ","commitid":"792d8f2c5fe18c131fc63df1dda88c4d791eb5bf","committime":"2022-09-03T22:09:15","packageid":54585,"repoid":1,"summary":"sci-biology\/augustus: respect CC, CXX"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"Closes: https:\/\/bugs.gentoo.org\/864773\nSigned-off-by: Sam James ","commitid":"405d411472329b890d43b44367b7874514c30379","committime":"2022-09-03T22:04:43","packageid":54585,"repoid":1,"summary":"sci-biology\/augustus: fix Boost dep"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"4d3a85ee194f8c9541e9d822d8d3dbb11491d198","committime":"2022-01-28T22:06:54","packageid":54585,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"andrewammerlaan@gentoo.org","authorname":"Andrew Ammerlaan","body":"Closes: https:\/\/bugs.gentoo.org\/832186\nPackage-Manager: Portage-3.0.30, Repoman-3.0.3\nSigned-off-by: Andrew Ammerlaan ","commitid":"c974dd2172656250d7e432b3619652ea68b1e723","committime":"2022-01-28T21:48:40","packageid":54585,"repoid":1,"summary":"sci-biology\/augustus: add forgotten runtime dependency"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"82c69a16c6d401bca14c57d06b163668bc52dabe","committime":"2022-01-27T21:21:22","packageid":54585,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"andrewammerlaan@gentoo.org","authorname":"Andrew Ammerlaan","body":"Closes: https:\/\/bugs.gentoo.org\/515996\nPackage-Manager: Portage-3.0.30, Repoman-3.0.3\nSigned-off-by: Andrew Ammerlaan ","commitid":"aea4f8147ac23b904f17d3890b398d5fb30c9eee","committime":"2022-01-27T19:08:10","packageid":54585,"repoid":1,"summary":"sci-biology\/augustus: add version 3.4.0"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"0da74f9e557ec388bdcfe974722f0f8c59012b4f","committime":"2019-12-11T00:25:48","packageid":54585,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-2.3.81, Repoman-2.3.20\nSigned-off-by: David Seifert ","commitid":"c5138c7f261799f62b944004c108f7a01b138be7","committime":"2019-12-10T23:48:28","packageid":54585,"repoid":1,"summary":"sci-biology\/augustus: Port to EAPI 7"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"25093d6359f778b8d1052f66ba9e26fc29ded21a","committime":"2017-02-28T20:35:29","packageid":54585,"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":54585,"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":54585,"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":54585,"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":54585,"repoid":1,"summary":"2015-06-19 16:35:30 UTC"}],"dependencies":[{"block":false,"categoryid":318,"description":"Metapackage for a suite of sparse matrix tools","ebuildids":[777090,853615],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci@gentoo.org","maintainername":"Gentoo Science Project","name":"suitesparse","packageid":42578,"summary":"SuiteSparse is a suite of sparse matrix libraries from University of Florida Computer Science Department. Currently, this includes: * AMD: symmetric approximate minimum degree * BTF: permutation to block triangular form * CAMD: symmetric approximate minimum degree * CCOLAMD: constrained column approximate minimum degree * COLAMD: column approximate minimum degree * CHOLMOD: sparse supernodal Cholesky factorization and update\/downdate * CSparse: a concise sparse matrix package * CXSparse: an extended version of CSparse * KLU: sparse LU factorization, for circuit simulation * LDL: a simple LDL^T factorization * SPQR: multifrontal sparse QT factorization * UMFPACK: sparse multifrontal LU factorization * SuiteSparse_config: common configuration for all but CSparse The Gentoo package does not include the suitesparse MATLAB tools from upstream, from the packages above and the following MATLAB-only packages: * RBio: MATLAB toolbox for reading\/writing sparse matrices * LINFACTOR: solve Ax=b using LU or CHOL * MESHND: 2D and 3D mesh generation and nested dissection * SSMULT: sparse matrix times sparse matrix"},{"block":false,"categoryid":393,"description":"Boost Libraries for C++","ebuildids":[777090,853615],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"cpp@gentoo.org","maintainername":"Gentoo C++ Project","name":"boost","packageid":45155},{"block":false,"categoryid":318,"description":"The GNU Scientific Library","ebuildids":[777090,853615],"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."},{"block":false,"categoryid":452,"description":"C++ API interface to the MySQL database","ebuildids":[777090,853615],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"mysql-bugs@gentoo.org","maintainername":"MySQL","name":"mysql++","packageid":49708},{"block":false,"categoryid":452,"description":"SQL database engine","ebuildids":[777090,853615],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"arfrever.fta@gmail.com","maintainername":"Arfrever Frehtes Taifersar Arahesis","name":"sqlite","packageid":50388},{"block":false,"categoryid":353,"description":"Utilities for analysing and manipulating the SAM\/BAM alignment formats","ebuildids":[777090,853615],"firstseen":"2010-12-22T14:41:05.491029","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"samtools","packageid":56631},{"block":false,"categoryid":317,"description":"Mixed Integer Linear Programming (MILP) solver","ebuildids":[777090,853615],"firstseen":"2011-07-24T14:38:52.845929","maintainer":"office@gentoo.org","maintainername":"Gentoo Office project","name":"lpsolve","packageid":57658},{"block":false,"categoryid":353,"description":"A programmer's API and an end-user's toolkit for handling BAM files","ebuildids":[777090,853615],"firstseen":"2012-02-26T14:35:52.932489","maintainer":"mmokrejs@gmail.com","maintainername":"Martin Mokrejs","name":"bamtools","packageid":58945,"summary":"BAM (Binary Alignment\/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files."},{"block":false,"categoryid":318,"description":"C library for high-throughput sequencing data formats","ebuildids":[777090,853615],"firstseen":"2014-09-21T13:51:26.076524","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"htslib","packageid":62539},{"block":false,"categoryid":452,"description":"C client library for MariaDB\/MySQL","ebuildids":[777090,853615],"firstseen":"2015-07-18T13:39:36.291834","maintainer":"mysql-bugs@gentoo.org","maintainername":"MySQL","name":"mysql-connector-c","packageid":63873},{"block":false,"categoryid":396,"description":"Virtual for libz.so providers","ebuildids":[777090,853615],"firstseen":"2025-11-04T07:31:41.418357","name":"zlib","packageid":78605}],"depending":[],"ebuilds":[{"archs":["~amd64","~x86"],"ebuildid":853615,"firstseen":"2025-02-11T01:49:48.646762","license":"Artistic","moddate":"2026-03-28T18:04:21","packageid":54585,"repoid":1,"slot":"0","uses":["doc","test"],"version":"3.5.0"},{"archs":["amd64","~x86"],"ebuildid":777090,"firstseen":"2023-02-04T17:48:35.903574","license":"Artistic","moddate":"2026-03-22T20:20:57","packageid":54585,"repoid":1,"slot":"0","uses":["doc"],"version":"3.4.0-r3"}],"masks":[],"package":{"categoryid":353,"description":"Eukaryotic gene predictor","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"augustus","packageid":54585},"rdependencies":[{"block":false,"categoryid":318,"description":"Metapackage for a suite of sparse matrix tools","ebuildids":[777090,853615],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci@gentoo.org","maintainername":"Gentoo Science Project","name":"suitesparse","packageid":42578,"summary":"SuiteSparse is a suite of sparse matrix libraries from University of Florida Computer Science Department. 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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."},{"block":false,"categoryid":452,"description":"C++ API interface to the MySQL database","ebuildids":[777090,853615],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"mysql-bugs@gentoo.org","maintainername":"MySQL","name":"mysql++","packageid":49708},{"block":false,"categoryid":452,"description":"SQL database engine","ebuildids":[777090,853615],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"arfrever.fta@gmail.com","maintainername":"Arfrever Frehtes Taifersar Arahesis","name":"sqlite","packageid":50388},{"block":false,"categoryid":353,"description":"Utilities for analysing and manipulating the SAM\/BAM alignment formats","ebuildids":[777090,853615],"firstseen":"2010-12-22T14:41:05.491029","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"samtools","packageid":56631},{"block":false,"categoryid":317,"description":"Mixed Integer Linear Programming (MILP) solver","ebuildids":[777090,853615],"firstseen":"2011-07-24T14:38:52.845929","maintainer":"office@gentoo.org","maintainername":"Gentoo Office project","name":"lpsolve","packageid":57658},{"block":false,"categoryid":353,"description":"A programmer's API and an end-user's toolkit for handling BAM files","ebuildids":[777090,853615],"firstseen":"2012-02-26T14:35:52.932489","maintainer":"mmokrejs@gmail.com","maintainername":"Martin Mokrejs","name":"bamtools","packageid":58945,"summary":"BAM (Binary Alignment\/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files."},{"block":false,"categoryid":318,"description":"C library for high-throughput sequencing data formats","ebuildids":[777090,853615],"firstseen":"2014-09-21T13:51:26.076524","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"htslib","packageid":62539},{"block":false,"categoryid":452,"description":"C client library for MariaDB\/MySQL","ebuildids":[777090,853615],"firstseen":"2015-07-18T13:39:36.291834","maintainer":"mysql-bugs@gentoo.org","maintainername":"MySQL","name":"mysql-connector-c","packageid":63873},{"block":false,"categoryid":396,"description":"Virtual for libz.so providers","ebuildids":[777090,853615],"firstseen":"2025-11-04T07:31:41.418357","name":"zlib","packageid":78605}],"repos":[{"branch":"master","lastcommit":"1f58741385367db432e79500a838ced67b2a773d","name":"gentoo","path":"\/usr\/portage","repoid":1,"upstream":"origin"}],"tracked":false,"urls":["https:\/\/bioinf.uni-greifswald.de\/augustus\/"],"uses":[{"description":"Add extra documentation (API, Javadoc, etc). It is recommended to enable per package instead of globally","isdefault":false,"use":"doc"},{"description":"Enable dependencies and\/or preparations necessary to run tests (usually controlled by FEATURES=test but can be toggled independently)","isdefault":false,"use":"test"}]}