commit: e1144b215d807165cb00d2fbadfadeea27c9f5b7 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Mon May 25 21:46:08 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Mon May 25 21:46:08 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e1144b21
version bump to 3.02b which has the glimmer-3.02-glibc210.patch applied Package-Manager: portage-2.2.18 sci-biology/glimmer/ChangeLog | 10 +++++++++ .../glimmer/files/glimmer-3.02-glibc210.patch | 24 ---------------------- ...fix.patch => glimmer-3.02b-jobserver-fix.patch} | 0 ...2-ldflags.patch => glimmer-3.02b-ldflags.patch} | 0 ...ct.patch => glimmer-3.02b-rename_extract.patch} | 0 ...glimmer-3.02-r3.ebuild => glimmer-3.02b.ebuild} | 6 +++--- 6 files changed, 13 insertions(+), 27 deletions(-) diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog index 95afa54..c3157e4 100644 --- a/sci-biology/glimmer/ChangeLog +++ b/sci-biology/glimmer/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.10 2013/03/11 15:17:43 jlec Exp $ +*glimmer-3.02b (25 May 2015) + + 25 May 2015; Martin Mokrejs <[email protected]> + +files/glimmer-3.02b-jobserver-fix.patch, +files/glimmer-3.02b-ldflags.patch, + +files/glimmer-3.02b-rename_extract.patch, +glimmer-3.02b.ebuild, + -files/glimmer-3.02-glibc210.patch, -files/glimmer-3.02-jobserver-fix.patch, + -files/glimmer-3.02-ldflags.patch, -files/glimmer-3.02-rename_extract.patch, + -glimmer-3.02-r3.ebuild: + version bump to 3.02b which has the glimmer-3.02-glibc210.patch applied + 25 May 2015; Martin Mokrejs <[email protected]> files/glimmer-3.02-rename_extract.patch: updated patch with a fixed target name glimmer_extract diff --git a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch deleted file mode 100644 index f6051ec..0000000 --- a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff -durr glimmer3.02-orig/src/Common/gene.cc glimmer3.02/src/Common/gene.cc ---- glimmer3.02-orig/src/Common/gene.cc 2009-12-28 13:34:21.577437056 +0000 -+++ glimmer3.02/src/Common/gene.cc 2009-12-28 13:36:06.914974685 +0000 -@@ -443,7 +443,7 @@ - // Return a subscript corresponding to character ch . - - { -- char * p; -+ const char * p; - - p = strchr (CONVERSION_STRING, tolower (ch)); - if (p == NULL) -diff -durr glimmer3.02-orig/src/ICM/icm.cc glimmer3.02/src/ICM/icm.cc ---- glimmer3.02-orig/src/ICM/icm.cc 2009-12-28 13:34:21.577437056 +0000 -+++ glimmer3.02/src/ICM/icm.cc 2009-12-28 13:36:44.649451803 +0000 -@@ -1981,7 +1981,7 @@ - // model) for character ch . - - { -- char * p; -+ const char * p; - - p = strchr (ALPHA_STRING, tolower (Filter (ch))); - if (p == NULL) diff --git a/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch b/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch similarity index 100% rename from sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch rename to sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch diff --git a/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch similarity index 100% rename from sci-biology/glimmer/files/glimmer-3.02-ldflags.patch rename to sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch diff --git a/sci-biology/glimmer/files/glimmer-3.02-rename_extract.patch b/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch similarity index 100% rename from sci-biology/glimmer/files/glimmer-3.02-rename_extract.patch rename to sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch diff --git a/sci-biology/glimmer/glimmer-3.02-r3.ebuild b/sci-biology/glimmer/glimmer-3.02b.ebuild similarity index 90% rename from sci-biology/glimmer/glimmer-3.02-r3.ebuild rename to sci-biology/glimmer/glimmer-3.02b.ebuild index 94a2fa0..cc3411f 100644 --- a/sci-biology/glimmer/glimmer-3.02-r3.ebuild +++ b/sci-biology/glimmer/glimmer-3.02b.ebuild @@ -10,7 +10,7 @@ MY_PV=${PV//./} DESCRIPTION="An HMM-based microbial gene finding system from TIGR" HOMEPAGE="http://ccb.jhu.edu/software/glimmer"; -SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz"; +SRC_URI="http://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz"; LICENSE="Artistic" SLOT="0" @@ -22,7 +22,8 @@ RDEPEND="app-shells/tcsh !app-crypt/pkcrack !media-libs/libextractor" -S="${WORKDIR}/${PN}${PV}" +#S="${WORKDIR}/${PN}${PV}" +S="${WORKDIR}/${PN}3.02" src_prepare() { sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \ @@ -32,7 +33,6 @@ src_prepare() { # GCC 4.3 include fix sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die # avoid file collision on /usr/bin/extract #247394 - epatch "${FILESDIR}/${P}-glibc210.patch" epatch "${FILESDIR}/${P}-jobserver-fix.patch" epatch "${FILESDIR}/${P}-ldflags.patch" epatch "${FILESDIR}/${P}-rename_extract.patch"
