commit: 1e58b1ab68dc2345b4eb70e4324a151f5ae4d2d7
Author: Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 2 20:27:51 2014 +0000
Commit: Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Mon Jun 2 20:27:51 2014 +0000
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1e58b1ab
sci-libs/ghmm: fix issue #223, patch applying failure
---
sci-libs/ghmm/ChangeLog | 6 +++++-
sci-libs/ghmm/files/ghmm-9999-clapack.patch | 11 +++++++++++
sci-libs/ghmm/files/ghmm-9999-respect.patch | 8 +++-----
sci-libs/ghmm/ghmm-9999.ebuild | 1 +
4 files changed, 20 insertions(+), 6 deletions(-)
diff --git a/sci-libs/ghmm/ChangeLog b/sci-libs/ghmm/ChangeLog
index 886fd6a..1220db1 100644
--- a/sci-libs/ghmm/ChangeLog
+++ b/sci-libs/ghmm/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-libs/ghmm
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 02 Jun 2014; Jauhien Piatlicki <jauh...@gentoo.org> ghmm-9999.ebuild,
+ +files/ghmm-9999-clapack.patch, files/ghmm-9999-respect.patch:
+ fix issue #223
+
20 Dec 2013; Justin Lecher <j...@gentoo.org> ghmm-9999.ebuild,
+files/ghmm-9999-link.patch, +files/ghmm-9999-obsolete.patch,
+files/ghmm-9999-out-of-source.patch, +files/ghmm-9999-respect.patch:
diff --git a/sci-libs/ghmm/files/ghmm-9999-clapack.patch
b/sci-libs/ghmm/files/ghmm-9999-clapack.patch
new file mode 100644
index 0000000..d36cb2a
--- /dev/null
+++ b/sci-libs/ghmm/files/ghmm-9999-clapack.patch
@@ -0,0 +1,11 @@
+--- ghmm/matrixop.c
++++ ghmm/matrixop.c
+@@ -45,7 +45,7 @@
+ #endif
+
+ #ifdef DO_WITH_ATLAS
+-#include <clapack.h>
++#include <clapack/clapack.h>
+ #endif
+
+
/*============================================================================*/
diff --git a/sci-libs/ghmm/files/ghmm-9999-respect.patch
b/sci-libs/ghmm/files/ghmm-9999-respect.patch
index 09c8721..cc70a07 100644
--- a/sci-libs/ghmm/files/ghmm-9999-respect.patch
+++ b/sci-libs/ghmm/files/ghmm-9999-respect.patch
@@ -1,12 +1,10 @@
-Index: ghmmwrapper/setup.py
-===================================================================
---- ghmmwrapper/setup.py (revision 2332)
-+++ ghmmwrapper/setup.py (working copy)
+--- ghmmwrapper/setup.py
++++ ghmmwrapper/setup.py
@@ -48,7 +48,6 @@
include_dirs = ['..'],
library_dirs = ['../ghmm/.libs'],
libraries = ['ghmm', 'm', 'pthread', 'xml2',
'z'],
- extra_compile_args = ["-O2", "-pipe",
"-Wall"], # -g might help debugging
- depends = ['wrapper_alphabet.i',
'wrapper_cmodel.i', 'wrapper_cseq.i',
+ depends = ['wrapper_alphabet.i',
'wrapper_bayes.i', 'wrapper_cmodel.i', 'wrapper_cseq.i',
'wrapper_dmodel.i',
'wrapper_dpmodel.i', 'wrapper_dpseq.i',
'wrapper_dseq.i',
'wrapper_xmlfile.i']
diff --git a/sci-libs/ghmm/ghmm-9999.ebuild b/sci-libs/ghmm/ghmm-9999.ebuild
index a8bcf5d..54b46f2 100644
--- a/sci-libs/ghmm/ghmm-9999.ebuild
+++ b/sci-libs/ghmm/ghmm-9999.ebuild
@@ -34,6 +34,7 @@ S="${WORKDIR}/${PN}"
ESVN_BOOTSTRAP="autotools-utils_src_prepare"
PATCHES=(
+ "${FILESDIR}"/${P}-clapack.patch
"${FILESDIR}"/${P}-out-of-source.patch
"${FILESDIR}"/${P}-link.patch
"${FILESDIR}"/${P}-respect.patch
