# ChangeLog for sci-biology/abyss # Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2 # (auto-generated from git log) *abyss-1.3.6 (09 Aug 2015) *abyss-1.3.4 (09 Aug 2015) *abyss-1.3.3 (09 Aug 2015) 09 Aug 2015; Robin H. Johnson +abyss-1.3.3.ebuild, +abyss-1.3.4.ebuild, +abyss-1.3.6.ebuild, +files/abyss-1.3.3-ac_prog_ar.patch, +files/abyss-1.3.3-gcc-4.7.patch, +files/abyss-1.3.4-gcc-4.7.patch, +files/abyss-1.3.6-ac_prog_ar.patch, +files/abyss-1.3.6-gcc-4.7.patch, +metadata.xml: proj/gentoo: Initial commit 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 X-Thanks: Alec Warner - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring - wrote much python to improve cvs2svn X-Thanks: Rich Freeman - validation scripts X-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed 24 Aug 2015; Justin Lecher metadata.xml: Use https by default Convert all URLs for sites supporting encrypted connections from http to https Signed-off-by: Justin Lecher 24 Aug 2015; Mike Gilbert metadata.xml: Revert DOCTYPE SYSTEM https changes in metadata.xml repoman does not yet accept the https version. This partially reverts eaaface92ee81f30a6ac66fe7acbcc42c00dc450. Bug: https://bugs.gentoo.org/552720 24 Jan 2016; Michał Górny metadata.xml: Replace all herds with appropriate projects (GLEP 67) Replace all uses of herd with appropriate project maintainers, or no maintainers in case of herds requested to be disbanded. 24 Jan 2016; Michał Górny metadata.xml: Set appropriate maintainer types in metadata.xml (GLEP 67) 08 Feb 2016; Sergei Trofimovich abyss-1.3.6.ebuild, metadata.xml: fix automagic haskell deps, bug #534412 Reported-by: Toralf Förster Bug: https://bugs.gentoo.org/534412 Package-Manager: portage-2.2.27 *abyss-1.3.6-r1 (03 Apr 2016) 03 Apr 2016; David Seifert +abyss-1.3.6-r1.ebuild, +files/abyss-1.3.6-samtoafg.patch: Latest ebuild from science-overlay * EAPI=6 Package-Manager: portage-2.2.28 03 Apr 2016; David Seifert -abyss-1.3.4.ebuild, -abyss-1.3.6.ebuild, -files/abyss-1.3.4-gcc-4.7.patch: Remove old Package-Manager: portage-2.2.28 15 May 2016; Sergei Trofimovich abyss-1.3.3.ebuild: add missing dev-libs/boost dependency Package-Manager: portage-2.2.28 *abyss-1.9.0 (18 Sep 2016) 18 Sep 2016; Sergei Trofimovich +abyss-1.9.0.ebuild, +files/abyss-1.9.0-ac_prog_ar.patch, +files/abyss-1.9.0-gcc-6.patch: bump up to 1.9.0, tweak for gcc-6, bug #594254 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}’ 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 *abyss-1.9.0-r1 (18 Sep 2016) 18 Sep 2016; Sergei Trofimovich -abyss-1.9.0.ebuild, +abyss-1.9.0-r1.ebuild: pin boost subslot, noticed by Soap Package-Manager: portage-2.3.0 *abyss-2.0.2 (06 Nov 2016) 06 Nov 2016; Sergei Trofimovich abyss-1.9.0-r1.ebuild, +abyss-2.0.2.ebuild: bump up to 2.0.2, bug #596018 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