[gentoo-commits] repo/gentoo:master commit in: sci-biology/prank/, sci-biology/prank/files/

[David Seifert]

commit: 39e97c83356a57c6181602feda6a2da0e1127f6b
Author: David Seifert  gentoo  org>
AuthorDate: Thu Jul  7 19:57:08 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Thu Jul  7 19:57:08 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=39e97c83

sci-biology/prank: update EAPI 6 -> 8

Signed-off-by: David Seifert  gentoo.org>

 .../prank/files/prank-140603-fix-c++14.patch   |  2 +-
 .../prank/files/prank-140603-makefile.patch| 28 
 sci-biology/prank/prank-140603-r1.ebuild   | 28 
 sci-biology/prank/prank-140603.ebuild  | 38 --
 4 files changed, 57 insertions(+), 39 deletions(-)

diff --git a/sci-biology/prank/files/prank-140603-fix-c++14.patch 
b/sci-biology/prank/files/prank-140603-fix-c++14.patch
index 5779207e294f..211e377d798a 100644
--- a/sci-biology/prank/files/prank-140603-fix-c++14.patch
+++ b/sci-biology/prank/files/prank-140603-fix-c++14.patch
@@ -8,7 +8,7 @@ See also: https://bugs.gentoo.org/show_bug.cgi?id=594060
  else
  {
 -cout<<"HMModel::alignmentModel: impossible 'as'"

[gentoo-commits] repo/gentoo:master commit in: sci-biology/prank/, sci-biology/prank/files/

[David Seifert]

commit: 25e5a98a39581c4c7c2b5c9f29b429baee0462b5
Author: David Seifert  gentoo  org>
AuthorDate: Tue Sep 20 18:52:11 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Tue Sep 20 21:05:59 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=25e5a98a

sci-biology/prank: Allow for compiling with GCC 6

Gentoo-bug: 594060
* EAPI=6

Package-Manager: portage-2.3.1

 sci-biology/prank/files/prank-140603-fix-c++14.patch | 14 ++
 sci-biology/prank/prank-140603.ebuild|  8 +---
 2 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/sci-biology/prank/files/prank-140603-fix-c++14.patch 
b/sci-biology/prank/files/prank-140603-fix-c++14.patch
new file mode 100644
index ..5779207
--- /dev/null
+++ b/sci-biology/prank/files/prank-140603-fix-c++14.patch
@@ -0,0 +1,14 @@
+Fix building with C++14, which errors out due to changing operator void* -> 
operator bool.
+See also: https://bugs.gentoo.org/show_bug.cgi?id=594060
+
+--- a/hmmodel.cpp
 b/hmmodel.cpp
+@@ -1499,7 +1499,7 @@
+ }
+ else
+ {
+-cout<<"HMModel::alignmentModel: impossible 'as'"<

[gentoo-commits] repo/gentoo:master commit in: sci-biology/prank/, sci-biology/prank/files/

[David Seifert]

commit: 68feaba73d3b6a368162db6bcdbbb34a03fd6b2a
Author: David Seifert  gentoo  org>
AuthorDate: Tue Sep 20 18:57:03 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Tue Sep 20 21:06:03 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=68feaba7

sci-biology/prank: Remove old ebuilds

Package-Manager: portage-2.3.1

 sci-biology/prank/Manifest |  2 --
 sci-biology/prank/files/prank-30-gcc-4.7.patch | 15 -
 sci-biology/prank/prank-100701.ebuild  | 34 ---
 sci-biology/prank/prank-30.ebuild  | 38 --
 4 files changed, 89 deletions(-)

diff --git a/sci-biology/prank/Manifest b/sci-biology/prank/Manifest
index 55e1e6d..ca8dbd6 100644
--- a/sci-biology/prank/Manifest
+++ b/sci-biology/prank/Manifest
@@ -1,3 +1 @@
 DIST prank.source.140603.tgz 150346 SHA256 
9a48064132c01b6dba1eec90279172bf6c13d96b3f1b8dd18297b1a53d17dec6 SHA512 
25e5f99a3822ff31436406f9ba1c781ba375959e1ed452c1e7416898d5246183510ec6d2bc715ff1495a779e42d7bd1d49ad1c332e1bd5982dad8c744ad999c7
 WHIRLPOOL 
5884563e6035b7e5a06b064035980e9fcee1cafcf559d86c8b9c8fc23628c7e9d1ba3e153a06f7322bb536120adcc6c8d169381f95d0a491b57836ada35a0de6
-DIST prank.src.100701.tgz 115444 SHA256 
2ba63fc8f998a86e6fc688170b03f831eeb8d8deda95cbf0986e8a3a3b09ec79 SHA512 
e656cef120313fdaa16c16c16a2b2539d0ac9095ed04153d9452a9218148da414b5950cfc50c09be5e1fc9a218a83b74513c53a3cef5705dc26be39a90abe116
 WHIRLPOOL 
001ae1a9efdc00cef397f2abe2483902f659ef10e7b4d0b42a05aeb76e874086c0143b39637e91a69708d3d2926962b4367579be58e0f3dd8e4dcb9b62082169
-DIST prank.src.30.tgz 10 SHA256 
61473a6b7b199f2d05e35a31adf813a2813decc9aa1429de118b62a51d7aac14 SHA512 
94f382bd71d6a58fe9b87b436bdec97ed297ebf88f3074d8e2971a24dcdc4509e737161aa057be0ac15783c1cfe7ca6d0a09ad80d0247b92426134097d4b400c
 WHIRLPOOL 
37b96f3dc0e53f7d0b70ddfc5664dc65eff4dbec322788d391c32f5d74103663b547825dcc58fe5da3b5b44086c36fcf00a3a2253e696d6212baa3958d13fc5b

diff --git a/sci-biology/prank/files/prank-30-gcc-4.7.patch 
b/sci-biology/prank/files/prank-30-gcc-4.7.patch
deleted file mode 100644
index d7defbc..
--- a/sci-biology/prank/files/prank-30-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- src/check_version.cpp |1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/src/check_version.cpp b/src/check_version.cpp
-index e968a05..6dfa062 100644
 a/src/check_version.cpp
-+++ b/src/check_version.cpp
-@@ -8,6 +8,7 @@
- #include 
- #include 
- #include 
-+#include 
- 
- using namespace std;
- 

diff --git a/sci-biology/prank/prank-100701.ebuild 
b/sci-biology/prank/prank-100701.ebuild
deleted file mode 100644
index 913ff56..
--- a/sci-biology/prank/prank-100701.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit toolchain-funcs
-
-DESCRIPTION="Probabilistic Alignment Kit"
-HOMEPAGE="http://wasabiapp.org/software/prank/;
-SRC_URI="http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.${PV}.tgz;
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-S=${WORKDIR}/${PN}
-
-src_prepare() {
-   sed -i -e "s/\$(LINK)/& \$(LDFLAGS)/" Makefile || die
-}
-
-src_compile() {
-   emake \
-   LINK="$(tc-getCXX)" \
-   CXX="$(tc-getCXX)" \
-   CFLAGS="${CFLAGS}" \
-   CXXFLAGS="${CXXFLAGS}"
-}
-
-src_install() {
-   dobin prank
-}

diff --git a/sci-biology/prank/prank-30.ebuild 
b/sci-biology/prank/prank-30.ebuild
deleted file mode 100644
index d0d1ae0..
--- a/sci-biology/prank/prank-30.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils multilib toolchain-funcs
-
-DESCRIPTION="Probabilistic Alignment Kit"
-HOMEPAGE="http://wasabiapp.org/software/prank/;
-SRC_URI="https://prank-msa.googlecode.com/files/prank.src.${PV}.tgz;
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/prank-msa/src"
-
-src_prepare() {
-   epatch "${FILESDIR}"/${P}-gcc-4.7.patch
-   sed \
-   -e "s/\$(LINK)/& \$(LDFLAGS)/" \
-   -e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \
-   -i Makefile || die
-}
-
-src_compile() {
-   emake \
-   LINK="$(tc-getCXX)" \
-   CXX="$(tc-getCXX)" \
-   CFLAGS="${CFLAGS}" \
-   CXXFLAGS="${CXXFLAGS}"
-}
-
-src_install() {
-   dobin prank
-}