sci-biology / abyss

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

Official package sites : http://www.bcgsc.ca/platform/bioinfo/software/abyss/ ·

v2.0.3 :: 0 :: gentoo

Modified
License
abyss
Keywords
~amd64 ~x86
USE flags
misc-haskell mpi openmp

v2.0.2-r1 :: 0 :: gentoo

Modified
License
abyss
Keywords
~amd64 ~x86
USE flags
misc-haskell mpi openmp

General

misc-haskell
Missing description
mpi
Add MPI (Message Passing Interface) layer to the apps that support it
openmp
Build support for the OpenMP (support parallel computing), requires >=sys-devel/gcc-4.2 built with USE="openmp"

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

dev-cpp / sparsehash : An extremely memory-efficient hash_map implementation

dev-haskell / mmap : Memory mapped files for POSIX and Windows

dev-lang / ghc : The Glasgow Haskell Compiler

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

dev-libs / gmp : Library for arbitrary-precision arithmetic on different type of numbers

sys-cluster / openmpi : A high-performance message passing library (MPI)

sys-devel / autoconf : Used to create autoconfiguration files

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

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

virtual / libffi : A virtual for the Foreign Function Interface implementation

dev-cpp / sparsehash : An extremely memory-efficient hash_map implementation

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

dev-libs / gmp : Library for arbitrary-precision arithmetic on different type of numbers

sys-cluster / openmpi : A high-performance message passing library (MPI)

virtual / libffi : A virtual for the Foreign Function Interface implementation

646478
sci-biology/abyss-2.0.2-r1 - add USE=sqlite and other ebuild tweaks
Sergei Trofimovich · gentoo
sci-biology/abyss: bump up to 2.0.3
Package-Manager: Portage-2.3.24, Repoman-2.3.6
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
Martin Mokrejš · gentoo
sci-biology/abyss: only openmpi is supported
Closes: https://github.com/gentoo/gentoo/pull/3414
David Seifert · gentoo
sci-biology/abyss: Remove old
Package-Manager: Portage-2.3.3, Repoman-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/3183
Sergei Trofimovich · gentoo
sci-biology/abyss: 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
Sergei Trofimovich · gentoo
sci-biology/abyss: pin boost subslot, noticed by Soap
Package-Manager: portage-2.3.0
Sergei Trofimovich · gentoo
sci-biology/abyss: 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<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
Sergei Trofimovich · gentoo
sci-biology/abyss: add missing dev-libs/boost dependency
Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/abyss: Remove old
Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/abyss: Latest ebuild from science-overlay
* EAPI=6 Package-Manager: portage-2.2.28
Sergei Trofimovich · gentoo
sci-biology/abyss: fix automagic haskell deps, bug #534412
Reported-by: Toralf Förster Bug: https://bugs.gentoo.org/534412 Package-Manager: portage-2.2.27
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