From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 3C6271384B4 for ; Mon, 16 Nov 2015 06:45:20 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 5211421C1F6; Mon, 16 Nov 2015 06:45:17 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id DA34521C1F6 for ; Mon, 16 Nov 2015 06:45:16 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 78D12340634 for ; Mon, 16 Nov 2015 06:45:13 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 517EAB6E for ; Mon, 16 Nov 2015 06:45:10 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1447656299.cb5cc14f669bad5286c22ff35ce42e3c3ce05ddc.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: / X-VCS-Repository: proj/sci X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: cb5cc14f669bad5286c22ff35ce42e3c3ce05ddc X-VCS-Branch: master Date: Mon, 16 Nov 2015 06:45:10 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 285e1632-f222-4344-968c-a1e5cf2a813d X-Archives-Hash: 1b2d96bb2bc206a00d0b97f2d4f973df commit: cb5cc14f669bad5286c22ff35ce42e3c3ce05ddc Author: Justin Lecher gentoo org> AuthorDate: Mon Nov 16 06:44:59 2015 +0000 Commit: Justin Lecher gentoo org> CommitDate: Mon Nov 16 06:44:59 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cb5cc14f Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci * 'master' of git+ssh://git.gentoo.org/proj/sci: sci-chemistry/votca-csg: update live ebuild sci-biology/codonw: add original Thesis of John Peden describing codonw package in more detail sci-biology/BBmap: version bump; apply also the UnicodeToAscii.patch sci-biology/Rcorrector: add einfo() message that default kmer size 23 is suboptimal sci-biology/SEECER: add einfo() message that default kmer size 17 is suboptimal sci-biology/Rcorrector: respect CXXFLAGS sci-biology/Rcorrector: new package sci-biology/jellyfish: fix filename generated by pkgconfig sci-biology/SEECER: patch crappy shellscripts to at leats die on error; require jellyfish-1.1.11 sci-biology/SEECER: remove hardcoded paths sci-biology/BBmap-34.56: restoring previous working version sci-biology/BBmap-35.66: this version needs more cleanup, upstream will make a new release, dropping KEYWORD Update local USE description sci-libs/armadillo: Version bump; remove old .../{BBmap-34.56.ebuild => BBmap-34.97.ebuild} | 1 + .../{BBmap-34.56.ebuild => BBmap-35.66.ebuild} | 3 +- sci-biology/BBmap/ChangeLog | 6 + sci-biology/BBmap/Manifest | 3 +- sci-biology/BBmap/files/UnicodeToAscii.patch | 17 +++ sci-biology/Rcorrector/ChangeLog | 18 +++ sci-biology/Rcorrector/Rcorrector-9999.ebuild | 36 ++++++ .../jhdf5 => sci-biology/Rcorrector}/metadata.xml | 0 sci-biology/SEECER/ChangeLog | 17 +++ ...ECER-0.1.3-r1.ebuild => SEECER-0.1.3-r2.ebuild} | 19 +++- .../SEECER/files/remove-hardcoded-paths.patch | 84 ++++++++++++++ sci-biology/codonw/ChangeLog | 5 + sci-biology/codonw/Manifest | 1 + sci-biology/codonw/codonw-1.4.4-r2.ebuild | 5 +- sci-biology/jellyfish/ChangeLog | 4 + sci-biology/jellyfish/jellyfish-1.1.11.ebuild | 3 +- sci-chemistry/votca-csg/ChangeLog | 3 + sci-chemistry/votca-csg/votca-csg-9999.ebuild | 2 +- sci-libs/armadillo/ChangeLog | 7 ++ sci-libs/armadillo/Manifest | 3 +- sci-libs/armadillo/armadillo-5.500.2.ebuild | 121 --------------------- ...llo-5.400.2.ebuild => armadillo-6.200.3.ebuild} | 2 +- 22 files changed, 226 insertions(+), 134 deletions(-)