sci-biology / mira

Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina

Official package sites : http://www.chevreux.org/projects_mira.html ·

v4.0.2 :: 0 :: gentoo

Modified
License
GPL-2
Keywords
amd64 x86 ~amd64-linux ~x86-linux ~x86-macos
USE flags
doc

General

doc
Add extra documentation (API, Javadoc, etc). It is recommended to enable per package instead of globally

app-editors / vim-core : vim and gvim shared files

app-portage / elt-patches : Collection of patches for libtool.eclass

dev-libs / boost : Boost Libraries for C++

dev-libs / expat : Stream-oriented XML parser library

dev-util / google-perftools : Fast, multi-threaded malloc() and nifty performance analysis tools

sys-devel / autoconf : Used to create autoconfiguration files

sys-devel / automake : Used to generate Makefile.in from Makefile.am

sys-devel / flex : The Fast Lexical Analyzer

sys-devel / libtool : A shared library tool for developers

dev-libs / boost : Boost Libraries for C++

dev-util / google-perftools : Fast, multi-threaded malloc() and nifty performance analysis tools

585942
sci-biology/mira-4.0.2 : ads.C:76:58: error: ‘pow’ was not declared in this scope
Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
T. Malfatti · gentoo
media-libs/portaudio: Version bump
Lars Wendler · gentoo
sci-biology/mira: Bump to EAPI-6. Ebuild cleanup.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Nicholas Vinson · gentoo
sci-biology/mira: Update flex-2.6.3 fix; add cmath header
Another round of testing discovered that caf_flexer.cc is also a pre-generated lexer. The commit updates the ebuild to remove that file as well. The file abs.C fails to find the pow() function. Modern versions of C++ store the header for that function in cmath. The file is updated to include that header. Gentoo-bug: 585942 Package-Manager: Portage-2.3.3, Repoman-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/3442
Lars Wendler · gentoo
sci-biology/mira: Adjusted sys-devel/flex dependency.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Nicholas Vinson · gentoo
sci-biology/mira: Force rebuild of lexer C++ source files
Upstream ships pregenerated C++ source files for its lexers. These files fail to compile under newer versions of GCC. This update forces them to be rebuilt by removing them before compilaiton starts. Package-Manager: Portage-2.3.3, Repoman-2.3.1
Mike Frysinger · gentoo
sourceforge: switch to https:// URIs
David Seifert · gentoo
sci-biology/mira: Add missing <sys-devel/flex-2.6.0 dependency
Gentoo-Bug: 574172 * Fix GCC5 explicit conversion of 'nullptr' to 'bool' * Fix overlong DESCRIPTION Package-Manager: portage-2.2.27
Justin Lecher · gentoo
sci-biology/mira: Add missing USE dep for boost[threads]
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=558092 Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
Robin H. Johnson · gentoo
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 <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