{"bugs":[{"bugid":549644,"firstseen":"2016-06-16T16:08:01.789616","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/emboss: try to install mimetype information"},{"bugid":712504,"firstseen":"2020-03-30T23:04:59.676975","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/emboss-6.6.0-r2 : embossversion.c: error: _USE_FORTIFY_LEVEL undeclared (first use in this function)"},{"bugid":920917,"firstseen":"2023-12-29T09:57:50.692537","severity":"normal","status":"CONFIRMED","summary":"sci-biology\/emboss-6.6.0-r3 - ajreg.c: error: assignment to struct real_pcre from incompatible pointer type pcre {aka struct real_pcre8_or_16 } [-Winc"}],"categories":[{"categoryid":452,"name":"dev-db","summary":"The dev-db category contains libraries and utilities for database related programming."},{"categoryid":406,"name":"dev-java","summary":"The dev-java category contains libraries and utilities relevant to the Java programming language."},{"categoryid":393,"name":"dev-libs","summary":"The dev-libs category contains various miscellaneous programming libraries."},{"categoryid":372,"name":"games-action","summary":"The games-action category contains action games."},{"categoryid":438,"name":"media-libs","summary":"The media-libs category contains media-related 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":381,"name":"sys-libs","summary":"The sys-libs category contains various system-level libraries."},{"categoryid":330,"name":"x11-libs","summary":"The x11-libs category contains various X11-related libraries."}],"changelog":[{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"e37c8c78ba4264d7f0051c483761fc2e82d77726","committime":"2024-03-30T19:49:32","packageid":54441,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/927976\nSigned-off-by: David Seifert ","commitid":"92cb387a0aa19b2cf594e25dcfa91a60f85c57e9","committime":"2024-03-30T19:36:42","packageid":54441,"repoid":1,"summary":"sci-biology\/emboss: avoid file collision with dev-texlive\/texlive-latexextra"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"c120ca34bbbcc47eb73dc5d0ebdd66ff32cc7057","committime":"2024-01-17T17:18:56","packageid":54441,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Signed-off-by: Michał Górny ","commitid":"f13cf85499a8a168c211d6c185a7b61e82faf692","committime":"2024-01-17T15:07:30","packageid":54441,"repoid":1,"summary":"Move {sys-devel → dev-build}\/cons"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"8256296f6742425e9c5a09628fba8c65ebc515b6","committime":"2022-02-13T23:36:42","packageid":54441,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Signed-off-by: David Seifert ","commitid":"d4378caa9f3a31d8baf594d0b7452ccc98dd5bd2","committime":"2022-02-13T23:28:30","packageid":54441,"repoid":1,"summary":"sci-biology\/emboss: update EAPI 7 -> 8"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"2944eaae39acf59eae4dd732eee8d9ffe0d393e0","committime":"2021-08-01T18:51:37","packageid":54441,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"* Also fix `-Wimplicit-function-declaration`\n\nCloses: https:\/\/bugs.gentoo.org\/695380\nSigned-off-by: David Seifert ","commitid":"9753c0fb02f9a8c76aeac1e2efd80793cb501416","committime":"2021-08-01T18:31:32","packageid":54441,"repoid":1,"summary":"sci-biology\/emboss: Fix C99 `bool` clash"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"1a334f07bd5eadd8140d9e464257ab6a17399971","committime":"2021-03-12T16:10:46","packageid":54441,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"asturm@gentoo.org","authorname":"Andreas Sturmlechner","body":"Bug: https:\/\/bugs.gentoo.org\/770262\nPackage-Manager: Portage-3.0.17, Repoman-3.0.2\nSigned-off-by: Andreas Sturmlechner ","commitid":"c4919007b325c1ab3852e60f64926ff98984d16f","committime":"2021-03-12T10:06:50","packageid":54441,"repoid":1,"summary":"sci-biology\/emboss: EAPI-7 bump, minor style"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"25093d6359f778b8d1052f66ba9e26fc29ded21a","committime":"2017-02-28T20:35:29","packageid":54441,"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":54441,"repoid":1,"summary":"Drop $Id$ per council decision in bug #611234."},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"e97b8c8ed5df03f1a539438e22e9ab351550f476","committime":"2017-02-19T19:02:03","packageid":54441,"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\/3937","commitid":"b40760bd69c57dae5c57650ee8507e5ac0d54b1c","committime":"2017-02-19T18:41:38","packageid":54441,"repoid":1,"summary":"sci-biology\/emboss: Remove old"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: portage-2.3.1\nCloses: https:\/\/github.com\/gentoo\/gentoo\/pull\/3937","commitid":"80392a26afc1e58165ac311b55d54d64ef2fa553","committime":"2017-02-19T18:41:33","packageid":54441,"repoid":1,"summary":"sci-biology\/emboss: Port to emboss-r2.eclass"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"e276789fbac1f63ee217f1146713347048bdbfe3","committime":"2017-02-06T21:38:43","packageid":54441,"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":"06033e6b1c4f28f88b1135fa26de456bb7ddf22f","committime":"2017-02-06T20:48:01","packageid":54441,"repoid":1,"summary":"sci-biology\/emboss: Remove ppc from KEYWORDS"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"d71c845f5ed1c6329eddf38d5a94b0bb55c50ff7","committime":"2016-07-28T21:42:01","packageid":54441,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"wizardedit@gentoo.org","authorname":"Austin English","body":"Gentoo-Bug: https:\/\/bugs.gentoo.org\/589918\n\nPackage-Manager: portage-2.3.0","commitid":"38ae04afecd43fd2a719b34977d8cf660cf409c2","committime":"2016-07-28T21:35:04","packageid":54441,"repoid":1,"summary":"sci-biology\/emboss: add a blocker for games-action\/xbomber #589918"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"8af61953b0e2cbf7e2e0de8453a9775238a8c916","committime":"2016-04-26T19:04:02","packageid":54441,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"jlec@gentoo.org","authorname":"Justin Lecher","body":"Move to readme.gentoo-r1.eclass\n\nGentoo-Bug: https:\/\/bugs.gentoo.org\/show_bug.cgi?id=579728\n\nPackage-Manager: portage-2.2.28\nSigned-off-by: Justin Lecher ","commitid":"38938220c8b6fde207fb7054dbdd8987bfa5085d","committime":"2016-04-26T18:48:22","packageid":54441,"repoid":1,"summary":"sci-biology\/emboss: Clean up of files dir"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"10f3170d7e5797d299afffa28b4f11a7dd75735f","committime":"2015-08-27T14:06:55","packageid":54441,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"jlec@gentoo.org","authorname":"Justin Lecher","body":"obsolets multiple bugs\n\nGentoo-Bug: https:\/\/bugs.gentoo.org\/show_bug.cgi?id=542274\nGentoo-Bug: https:\/\/bugs.gentoo.org\/show_bug.cgi?id=534418\nGentoo-Bug: https:\/\/bugs.gentoo.org\/show_bug.cgi?id=521604\nGentoo-Bug: https:\/\/bugs.gentoo.org\/show_bug.cgi?id=514014\nGentoo-Bug: https:\/\/bugs.gentoo.org\/show_bug.cgi?id=493724\nGentoo-Bug: https:\/\/bugs.gentoo.org\/show_bug.cgi?id=406279\nGentoo-Bug: https:\/\/bugs.gentoo.org\/show_bug.cgi?id=393311\nGentoo-Bug: https:\/\/bugs.gentoo.org\/show_bug.cgi?id=382321\nGentoo-Bug: https:\/\/bugs.gentoo.org\/show_bug.cgi?id=378443\n\nPackage-Manager: portage-2.2.20.1\nSigned-off-by: Justin Lecher ","commitid":"08fae0a30263fd06fe51ac5b75301d574be9e1be","committime":"2015-08-27T13:47:31","packageid":54441,"repoid":1,"summary":"sci-biology\/emboss: Drop old"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"fba66cde604bc5daea3c49b51bdcbbf4a525a10a","committime":"2015-08-26T19:46:30","packageid":54441,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mrueg@gentoo.org","authorname":"Manuel Rüger","body":"This commit reverts 0d040c84fbb38ead35451769d2b65a33af2fbf2a.\n\nPackage-Manager: portage-2.2.20.1\nRepoMan-Options: --force","commitid":"0db67f06dd6358a4c5294cc79450616900e9160a","committime":"2015-08-26T17:21:50","packageid":54441,"repoid":1,"summary":"sci-biology\/emboss: Restore old version."},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"fa50b97ea7abd5a16f4ff7d844ad532097b1e28f","committime":"2015-08-26T14:46:41","packageid":54441,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"zlogene@gentoo.org","authorname":"Mikle Kolyada","body":"Package-Manager: portage-2.2.20.1","commitid":"0d040c84fbb38ead35451769d2b65a33af2fbf2a","committime":"2015-08-26T14:23:48","packageid":54441,"repoid":1,"summary":"sci-biology\/emboss: Drop old"},{"authoremail":"zlogene@gentoo.org","authorname":"Mikle Kolyada","body":"Package-Manager: portage-2.2.20.1","commitid":"7b735875e325586d7418d4c7813658089652f227","committime":"2015-08-26T14:22:31","packageid":54441,"repoid":1,"summary":"sci-biology\/emboss: x86 stable wrt bug #529038"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA 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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":54441,"repoid":1,"summary":"proj\/gentoo: Initial commit"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"4fd0a9fa186b0fc4ddc85fa2926486febd5d436c","committime":"2015-07-26T21:45:13","packageid":54441,"repoid":1,"summary":"2015-07-26 21:43:13 UTC"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"a637bd65b7fef8e2be4e7fc6e9097479372e0e2e","committime":"2015-06-19T16:38:33","packageid":54441,"repoid":1,"summary":"2015-06-19 16:35:30 UTC"}],"dependencies":[{"block":false,"categoryid":393,"description":"Stream-oriented XML parser library","ebuildids":[821091],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"freedesktop-bugs@gentoo.org","maintainername":"Gentoo Freedesktop Project","name":"expat","packageid":44320},{"block":false,"categoryid":318,"description":"Multi-language scientific plotting library","ebuildids":[821091],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci@gentoo.org","maintainername":"Gentoo Science Project","name":"plplot","packageid":45584,"summary":"PLplot is a library of functions that are useful for making scientific plots. It can be used from within compiled languages such as C, C++, FORTRAN and Java, as well as interactively from interpreted languages such as Octave, Python, Perl and Tcl. It is capable of producing standard x-y plots, semilog plots, log-log plots, contour plots, 3D surface plots, mesh plots, bar charts and pie charts. Multiple graphs may be composited, and it also supports a large variety of output file devices such as Postscript, PNG, JPEG, LaTeX and others. It is also possible to to use interactive devices such as xwin, tk and xterm as output devices. PLplot also offers support for extended characters inculding the Greek alphabet and a host of mathematical symbols."},{"block":false,"categoryid":393,"description":"Perl-compatible regular expression library","ebuildids":[821091],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"base-system@gentoo.org","maintainername":"Gentoo Base System","name":"libpcre","packageid":46794},{"block":false,"categoryid":330,"description":"X.Org X Toolkit Intrinsics library","ebuildids":[821091],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"x11@gentoo.org","maintainername":"X11","name":"libXt","packageid":47667},{"block":false,"categoryid":438,"description":"C\/C++ library for PDF generation","ebuildids":[821091],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci@gentoo.org","maintainername":"Gentoo Science Project","name":"libharu","packageid":48308,"summary":"Haru PDF library is a ANSI\/C library for generating PDF files. It supports the following features: 1. Generating PDF files with lines, text, images. 2. Outline, text annotation, link annotation. 3. Compressing document with deflate-decode. 4. Embedding PNG, Jpeg images. 5. Embedding Type1 font and TrueType font. 6. Creating encrypted PDF files. 7. Using various character sets (ISO8859-1~16, MSCP1250~8, KOI8-R). 8. Supporting CJK fonts and encodings."},{"block":false,"categoryid":438,"description":"Graphics library for fast image creation","ebuildids":[821091],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"vapier@gentoo.org","maintainername":"Gentoo Graphics Project","name":"gd","packageid":53143,"summary":"gd is a graphics library. It allows your code to quickly draw images complete with lines, arcs, text, multiple colors, cut and paste from other images, and flood fills, and write out the result as a PNG or JPEG file. This is particularly useful in World Wide Web applications, where PNG and JPEG are two of the formats accepted for inline images by most browsers. gd is not a paint program. If you are looking for a paint program, you are looking in the wrong place. If you are not a programmer, you are looking in the wrong place, unless you are installing a required library in order to run an application. gd does not provide for every possible desirable graphics operation. It is not necessary or desirable for gd to become a kitchen-sink graphics package, but version 2.0 does include most frequently requested features, including both truecolor and palette images, resampling (smooth resizing of truecolor images) and so forth."},{"block":false,"categoryid":381,"description":"Standard (de)compression library","ebuildids":[821091],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"base-system@gentoo.org","maintainername":"Gentoo Base System","name":"zlib","packageid":55408},{"block":false,"categoryid":452,"description":"PostgreSQL RDBMS","ebuildids":[821091],"firstseen":"2014-10-12T13:39:23.431369","maintainer":"pgsql-bugs@gentoo.org","maintainername":"PostgreSQL and Related Package Development","name":"postgresql","packageid":62608},{"block":false,"categoryid":452,"description":"C client library for MariaDB\/MySQL","ebuildids":[821091],"firstseen":"2015-07-18T13:39:36.291834","maintainer":"mysql-bugs@gentoo.org","maintainername":"MySQL","name":"mysql-connector-c","packageid":63873}],"depending":[{"block":false,"categoryid":353,"description":"A protein motif fingerprint database","ebuildids":[753656],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"prints","packageid":42374,"summary":"A protein motif fingerprint database maintained at the University of Manchester. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT\/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours."},{"block":false,"categoryid":353,"description":"A protein families and domains database","ebuildids":[753657],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"prosite","packageid":42442,"summary":"A protein families and domains database maintained at the Swiss Institude for Bioinformatics. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins."},{"block":false,"categoryid":353,"description":"EMBOSS integrated version of Simple menu of EMBOSS applications","ebuildids":[740084,740084],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"embassy-emnu","packageid":42614},{"block":false,"categoryid":353,"description":"A restriction enzyme database","ebuildids":[755560],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"rebase","packageid":42753,"summary":"The Restriction Enzyme data BASE is a collection of information about restriction enzymes and related proteins. It is maintained by New England Biolabs. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. More recently, putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed."},{"block":true,"categoryid":372,"description":"Bomberman clone w\/multiplayer support","ebuildids":[616100],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"games@gentoo.org","maintainername":"Gentoo Games Project","name":"xbomber","packageid":42995},{"block":false,"categoryid":353,"description":"EMBOSS integrated version of Protein domain analysis add-on package","ebuildids":[740081,740081],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"embassy-domainatrix","packageid":43298},{"block":false,"categoryid":353,"description":"EMBOSS integrated version of Protein domain search add-on package","ebuildids":[740083,740083],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"embassy-domsearch","packageid":43581},{"block":false,"categoryid":353,"description":"EMBOSS integrated version of MSE - Multiple Sequence Screen Editor","ebuildids":[740088,740088],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"embassy-mse","packageid":43957},{"block":false,"categoryid":353,"description":"EMBOSS integrated version of The Phylogeny Inference Package","ebuildids":[740089,740089],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"embassy-phylipnew","packageid":44837},{"block":false,"categoryid":353,"description":"EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA","ebuildids":[740085,740085],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"embassy-esim4","packageid":46542},{"block":false,"categoryid":353,"description":"Amino acid indices and similarity matrices","ebuildids":[753651],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"aaindex","packageid":46645,"summary":"Amino acid indices and similarity matrices maintained at Kyoto University. An amino acid index is a set of 20 numerical values representing any of the different physicochemical and biological properties of amino acids. The AAindex1 section of the Amino Acid Index Database is a collection of published indices together with the result of cluster analysis using the correlation coefficient as the distance between two indices. This section currently contains 494 indices. Another important feature of amino acids that can be represented numerically is the similarity between amino acids. Thus, a similarity matrix, also called a mutation matrix, is a set of 210 numerical values, 20 diagonal and 20x19\/2 off-diagonal elements, used for sequence alignments and similarity searches. The AAindex2 section of the Amino Acid Index Database is a collection of published amino acid mutation matrices together with the result of cluster analysis. 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