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path: root/sci-biology/abyss
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* sci-biology/abyss: mark as LTO-unsafeEli Schwartz2024-03-081-1/+6
| | | | | | Closes: https://bugs.gentoo.org/862252 Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/abyss: remove useless sedEli Schwartz2024-03-081-2/+1
| | | | | | | | It seds out something that hasn't existed since 2012: https://github.com/bcgsc/abyss/commit/ded065d3b257e72ceb70ad3f6dd399019b00b46e Signed-off-by: Eli Schwartz <eschwartz93@gmail.com> Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/abyss: fix metadata indentationSam James2022-07-301-10/+10
| | | | Signed-off-by: Sam James <sam@gentoo.org>
* sci-biology/abyss: drop version 2.0.3Andrew Ammerlaan2022-01-133-76/+0
| | | | | | | Closes: https://bugs.gentoo.org/741154 Closes: https://bugs.gentoo.org/715718 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* sci-biology/abyss: add version 2.3.4Andrew Ammerlaan2022-01-132-0/+58
| | | | | | Closes: https://bugs.gentoo.org/646478 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
* **/metadata.xml: Replace http by https in DOCTYPE elementUlrich Müller2021-09-111-1/+1
| | | | | Bug: https://bugs.gentoo.org/552720 Signed-off-by: Ulrich Müller <ulm@gentoo.org>
* sci-biology/abyss: drop haskell@ from maintainersSergei Trofimovich2021-07-241-4/+0
| | | | | Package-Manager: Portage-3.0.20, Repoman-3.0.3 Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>
* */*: Normalize metadata.xml filesMichał Górny2021-03-161-1/+1
| | | | | | | | | | | Normalize quoting, replace '>' with entities, replace unnecessary entities, remove trailing empty lines. Done via: find -name metadata.xml -exec xml ed -P -L -d //none {} + Signed-off-by: Michał Górny <mgorny@gentoo.org>
* sci-biology/abyss: switch from virtual/libffiSergei Trofimovich2020-06-211-1/+1
| | | | | Package-Manager: Portage-2.3.101, Repoman-2.3.22 Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>
* sci-biology/abyss: drop oldSergei Trofimovich2020-06-213-110/+0
| | | | | Package-Manager: Portage-2.3.101, Repoman-2.3.22 Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>
* sci-biology/abyss: disable CFLAGS QA check on samtobreakSergei Trofimovich2020-05-251-0/+8
| | | | | | | | | | | | GHC uses it's own native code generator. Portage's QA check generates false positive because it assumes presence of GCC-specific sections. Workaround false positiove by disabling the check, bug #677600. Bug: https://bugs.gentoo.org/677600 Package-Manager: Portage-2.3.100, Repoman-2.3.22 Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>
* sci-biology/abyss: respect AR override, bug #725300Sergei Trofimovich2020-05-252-0/+67
| | | | | | | | | | Use AM_PROG_AR to default to standard AR discovery instead of make's 'ar'. Reported-by: Agostino Sarubbo Closes: https://bugs.gentoo.org/725300 Package-Manager: Portage-2.3.100, Repoman-2.3.22 Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>
* sci-biology/abyss: bump up to 2.0.3Sergei Trofimovich2018-03-152-0/+55
| | | | Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-biology/*: Update Manifest hashesMichał Górny2017-12-101-1/+1
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* Globally add missing remote ID references to metadata.xmlJustin Lecher2017-04-291-2/+5
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Drop $Id$ per council decision in bug #611234.Robin H. Johnson2017-02-281-1/+0
| | | | Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
* sci-biology/abyss: only openmpi is supportedMartin Mokrejš2017-01-151-7/+16
| | | | Closes: https://github.com/gentoo/gentoo/pull/3414
* sci-biology/abyss: Remove oldDavid Seifert2016-12-2011-310/+0
| | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/3183
* sci-biology/abyss: bump up to 2.0.2, bug #596018Sergei Trofimovich2016-11-063-1/+49
| | | | | | | | | Fixes gcc-6 and boost-1.62 build failures. Reported-by: Toralf Förster Bug: https://bugs.gentoo.org/596018 Package-Manager: portage-2.3.2
* sci-biology/abyss: pin boost subslot, noticed by SoapSergei Trofimovich2016-09-181-1/+1
| | | | Package-Manager: portage-2.3.0
* sci-biology/abyss: bump up to 1.9.0, tweak for gcc-6, bug #594254Sergei Trofimovich2016-09-184-0/+106
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | On gcc-6 build failed as: ``` In file included from AssemblyAlgorithms.cpp:4:0: ../DataLayer/FastaReader.h: In member function ‘FastaReader::operator void*() const’: ../DataLayer/FastaReader.h:49:35: error: cannot convert ‘std::istream {aka std::basic_istream<char>}’ to ‘void*’ ... operator void*() const { return m_in; } ^~~~ ``` In the following source: ```c++ static bool existFile(const char* f) { ifstream file(f); return file; } ``` c++98 provides file->operator void*() c++11 provides file->explicit operator bool() Hence the failure on c++11. The change adds explicit casts around ifstream. Reported-by: Toralf Förster Bug: https://bugs.gentoo.org/594254 Package-Manager: portage-2.3.0
* sci-biology/abyss: add missing dev-libs/boost dependencySergei Trofimovich2016-05-151-0/+1
| | | | Package-Manager: portage-2.2.28
* sci-biology/abyss: Remove oldDavid Seifert2016-04-034-120/+0
| | | | Package-Manager: portage-2.2.28
* sci-biology/abyss: Latest ebuild from science-overlayDavid Seifert2016-04-032-0/+94
| | | | | | * EAPI=6 Package-Manager: portage-2.2.28
* sci-biology/abyss: fix automagic haskell deps, bug #534412Sergei Trofimovich2016-02-082-4/+22
| | | | | | | Reported-by: Toralf Förster Bug: https://bugs.gentoo.org/534412 Package-Manager: portage-2.2.27
* Set appropriate maintainer types in metadata.xml (GLEP 67)Michał Górny2016-01-241-1/+1
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* Replace all herds with appropriate projects (GLEP 67)Michał Górny2016-01-241-1/+4
| | | | | Replace all uses of herd with appropriate project maintainers, or no maintainers in case of herds requested to be disbanded.
* Revert DOCTYPE SYSTEM https changes in metadata.xmlMike Gilbert2015-08-241-1/+1
| | | | | | | repoman does not yet accept the https version. This partially reverts eaaface92ee81f30a6ac66fe7acbcc42c00dc450. Bug: https://bugs.gentoo.org/552720
* Use https by defaultJustin Lecher2015-08-241-1/+1
| | | | | | Convert all URLs for sites supporting encrypted connections from http to https Signed-off-by: Justin Lecher <jlec@gentoo.org>
* proj/gentoo: Initial commitRobin H. Johnson2015-08-0810-0/+223
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed