commit: 9e7fe2f9babe9a495f94e299f4bab5aea1e48db7
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 6 09:30:51 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 6 09:30:51 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9e7fe2f9
sci-biology/bambus: EAPI bump
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/bambus/bambus-2.33.ebuild | 16 ++++++++-------
.../bambus/files/TigrFoundation-all-patches.patch | 24 +++++++++++-----------
2 files changed, 21 insertions(+), 19 deletions(-)
diff --git a/sci-biology/bambus/bambus-2.33.ebuild
b/sci-biology/bambus/bambus-2.33.ebuild
index 4391801b0..e92c8c8da 100644
--- a/sci-biology/bambus/bambus-2.33.ebuild
+++ b/sci-biology/bambus/bambus-2.33.ebuild
@@ -1,10 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
+inherit perl-module toolchain-funcs
DESCRIPTION="Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS
bundle"
HOMEPAGE="
@@ -17,7 +16,6 @@ SRC_URI="
LICENSE="Artistic"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
RDEPEND="
sci-biology/tigr-foundation-libs
@@ -26,8 +24,13 @@ RDEPEND="
dev-perl/GraphViz"
DEPEND="${RDEPEND}"
+PATCHES=(
+ "${FILESDIR}"/TigrFoundation-all-patches.patch
+)
+
src_prepare() {
-# epatch "${FILESDIR}"/amos-2.0.8-gcc44.patch
+ default
+# eapply "${FILESDIR}"/amos-2.0.8-gcc44.patch
sed -e 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' -i
Makefile || die
sed -e 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' -i Makefile
|| die
sed \
@@ -64,7 +67,6 @@ src_prepare() {
#rm -rf src/TIGR_Foundation_CC || die "Failed to rm -rf
src/TIGR_Foundation_CC/, we use it from sci-biology/tigr-foundation-libs"
#sed -i 's:TIGR_Foundation_CC::' src/Makefile || die "Failed to zap
last pointer to local copy of tigr-foundation-libs"
cd src/TIGR_Foundation_CC || die "Failed to cd src/TIGR_Foundation_CC/"
- epatch "${FILESDIR}"/TigrFoundation-all-patches.patch || die
sed -e "s:/export/usr/local:${ED}/usr:g" -i Makefile || die
}
diff --git a/sci-biology/bambus/files/TigrFoundation-all-patches.patch
b/sci-biology/bambus/files/TigrFoundation-all-patches.patch
index 57ad86e2e..11501494f 100644
--- a/sci-biology/bambus/files/TigrFoundation-all-patches.patch
+++ b/sci-biology/bambus/files/TigrFoundation-all-patches.patch
@@ -1,5 +1,5 @@
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/ConfigFile.cc.old 2010-12-04
17:07:50.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/ConfigFile.cc 2010-12-04
17:07:25.000000000 +0100
+--- a/src/TIGR_Foundation_CC/ConfigFile.cc 2010-12-04 17:07:50.000000000
+0100
++++ b/src/TIGR_Foundation_CC/ConfigFile.cc 2010-12-04 17:07:25.000000000
+0100
@@ -33,6 +33,7 @@
* different values.
*/
@@ -8,8 +8,8 @@
#include "ConfigFile.hh"
//! Constructor
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/Logger.hh.old 2010-12-04
17:20:19.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/Logger.hh 2010-12-04
17:20:49.000000000 +0100
+--- a/src/TIGR_Foundation_CC/Logger.hh 2010-12-04 17:20:19.000000000 +0100
++++ b/src/TIGR_Foundation_CC/Logger.hh 2010-12-04 17:20:49.000000000 +0100
@@ -15,6 +15,7 @@
#include <list>
#include <string>
@@ -18,8 +18,8 @@
#include <time.h>
#include <pwd.h>
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/OptionResult.hh.old
2010-12-04 17:21:35.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/OptionResult.hh 2010-12-04
17:22:02.000000000 +0100
+--- a/src/TIGR_Foundation_CC/OptionResult.hh 2010-12-04 17:21:35.000000000
+0100
++++ b/src/TIGR_Foundation_CC/OptionResult.hh 2010-12-04 17:22:02.000000000
+0100
@@ -12,6 +12,7 @@
#define OPTIONRESULT_HH 1
@@ -28,8 +28,8 @@
#include <map>
#include "Exceptions.hh"
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/Options.hh.old 2010-12-04
17:22:37.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/Options.hh 2010-12-04
17:23:01.000000000 +0100
+--- a/src/TIGR_Foundation_CC/Options.hh 2010-12-04 17:22:37.000000000
+0100
++++ b/src/TIGR_Foundation_CC/Options.hh 2010-12-04 17:23:01.000000000
+0100
@@ -11,6 +11,7 @@
#ifndef OPTIONS_HH
#define OPTIONS_HH 1
@@ -38,8 +38,8 @@
#include <list>
#include <map>
#include <set>
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/FileSystem.cc.old 2010-12-04
17:24:02.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/FileSystem.cc 2010-12-04
17:24:12.000000000 +0100
+--- a/src/TIGR_Foundation_CC/FileSystem.cc 2010-12-04 17:24:02.000000000
+0100
++++ b/src/TIGR_Foundation_CC/FileSystem.cc 2010-12-04 17:24:12.000000000
+0100
@@ -55,7 +55,7 @@
{
// Check to see if path was given
@@ -49,8 +49,8 @@
if (end_of_path)
{
---- /tmp/autoEditor-1.20/TigrFoundation-2.0/Options.cc.old 2010-12-04
17:24:53.000000000 +0100
-+++ /tmp/autoEditor-1.20/TigrFoundation-2.0/Options.cc 2010-12-04
17:25:15.000000000 +0100
+--- a/src/TIGR_Foundation_CC/Options.cc 2010-12-04 17:24:53.000000000
+0100
++++ b/src/TIGR_Foundation_CC/Options.cc 2010-12-04 17:25:15.000000000
+0100
@@ -25,6 +25,7 @@
* written to stderr is prefixed with (stderr).
*/
