* [gentoo-commits] repo/gentoo:master commit in: sci-biology/prank/, sci-biology/prank/files/
@ 2016-09-20 21:07 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2016-09-20 21:07 UTC (permalink / raw
To: gentoo-commits
commit: 68feaba73d3b6a368162db6bcdbbb34a03fd6b2a
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 20 18:57:03 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Tue Sep 20 21:06:03 2016 +0000
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-111130-gcc-4.7.patch | 15 ---------
sci-biology/prank/prank-100701.ebuild | 34 -------------------
sci-biology/prank/prank-111130.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.111130.tgz 133330 SHA256 61473a6b7b199f2d05e35a31adf813a2813decc9aa1429de118b62a51d7aac14 SHA512 94f382bd71d6a58fe9b87b436bdec97ed297ebf88f3074d8e2971a24dcdc4509e737161aa057be0ac15783c1cfe7ca6d0a09ad80d0247b92426134097d4b400c WHIRLPOOL 37b96f3dc0e53f7d0b70ddfc5664dc65eff4dbec322788d391c32f5d74103663b547825dcc58fe5da3b5b44086c36fcf00a3a2253e696d6212baa3958d13fc5b
diff --git a/sci-biology/prank/files/prank-111130-gcc-4.7.patch b/sci-biology/prank/files/prank-111130-gcc-4.7.patch
deleted file mode 100644
index d7defbc..00000000
--- a/sci-biology/prank/files/prank-111130-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 <string>
- #include <sstream>
- #include <iostream>
-+#include <unistd.h>
-
- 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..00000000
--- 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-111130.ebuild b/sci-biology/prank/prank-111130.ebuild
deleted file mode 100644
index d0d1ae0..00000000
--- a/sci-biology/prank/prank-111130.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
-}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/prank/, sci-biology/prank/files/
@ 2016-09-20 21:07 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2016-09-20 21:07 UTC (permalink / raw
To: gentoo-commits
commit: 25e5a98a39581c4c7c2b5c9f29b429baee0462b5
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 20 18:52:11 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Tue Sep 20 21:05:59 2016 +0000
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 00000000..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'"<<cout;
++ cout<<"HMModel::alignmentModel: impossible 'as'"<<bool(cout);
+ exit(-1);
+ }
+
diff --git a/sci-biology/prank/prank-140603.ebuild b/sci-biology/prank/prank-140603.ebuild
index a18b7ab..ca22fff 100644
--- a/sci-biology/prank/prank-140603.ebuild
+++ b/sci-biology/prank/prank-140603.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=4
+EAPI=6
-inherit eutils multilib toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="Probabilistic Alignment Kit"
HOMEPAGE="http://wasabiapp.org/software/prank/"
@@ -16,12 +16,14 @@ IUSE=""
KEYWORDS="~amd64 ~x86"
S="${WORKDIR}/${PN}-msa/src"
+PATCHES=( "${FILESDIR}/${PN}-140603-fix-c++14.patch" )
src_prepare() {
sed \
-e "s/\$(LINK)/& \$(LDFLAGS)/" \
-e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \
-i Makefile || die
+ default
}
src_compile() {
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/prank/, sci-biology/prank/files/
@ 2022-07-07 19:58 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2022-07-07 19:58 UTC (permalink / raw
To: gentoo-commits
commit: 39e97c83356a57c6181602feda6a2da0e1127f6b
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 7 19:57:08 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Jul 7 19:57:08 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=39e97c83
sci-biology/prank: update EAPI 6 -> 8
Signed-off-by: David Seifert <soap <AT> 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'"<<cout;
-+ cout<<"HMModel::alignmentModel: impossible 'as'"<<bool(cout);
++ cout<<"HMModel::alignmentModel: impossible 'as'";
exit(-1);
}
diff --git a/sci-biology/prank/files/prank-140603-makefile.patch b/sci-biology/prank/files/prank-140603-makefile.patch
new file mode 100644
index 000000000000..eeb74df89b4c
--- /dev/null
+++ b/sci-biology/prank/files/prank-140603-makefile.patch
@@ -0,0 +1,28 @@
+--- a/Makefile
++++ b/Makefile
+@@ -4,14 +4,8 @@
+
+ ####### Compiler, tools and options
+
+-CC = gcc
+-CXX = g++
+-DEFINES =
+-CFLAGS = -m64 -pipe -O3 $(DEFINES)
+-CXXFLAGS = -m64 -pipe -O3 $(DEFINES)
+-INCPATH = -I. -I/usr/include
+-LINK = g++
+-LFLAGS = -m64
++INCPATH = $(CPPFLAGS) -I.
++LINK = $(CXX)
+ LIBS = $(SUBLIBS)
+ AR = ar cqs
+ RANLIB =
+@@ -136,7 +130,7 @@
+ all: Makefile $(TARGET) $(MANPAGES)
+
+ $(TARGET): $(OBJECTS)
+- $(LINK) $(LFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS)
++ $(LINK) $(LDFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS)
+
+
+ clean:compiler_clean
diff --git a/sci-biology/prank/prank-140603-r1.ebuild b/sci-biology/prank/prank-140603-r1.ebuild
new file mode 100644
index 000000000000..9128cf9cf99b
--- /dev/null
+++ b/sci-biology/prank/prank-140603-r1.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Probabilistic Alignment Kit"
+HOMEPAGE="http://wasabiapp.org/software/prank/"
+SRC_URI="http://wasabiapp.org/download/${PN}/${PN}.source.${PV}.tgz"
+S="${WORKDIR}/${PN}-msa/src"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-makefile.patch
+ "${FILESDIR}"/${P}-fix-c++14.patch
+)
+
+src_configure() {
+ tc-export CXX
+}
+
+src_install() {
+ dobin prank
+}
diff --git a/sci-biology/prank/prank-140603.ebuild b/sci-biology/prank/prank-140603.ebuild
deleted file mode 100644
index a29e425f43bf..000000000000
--- a/sci-biology/prank/prank-140603.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Probabilistic Alignment Kit"
-HOMEPAGE="http://wasabiapp.org/software/prank/"
-SRC_URI="http://wasabiapp.org/download/${PN}/${PN}.source.${PV}.tgz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/${PN}-msa/src"
-PATCHES=( "${FILESDIR}/${PN}-140603-fix-c++14.patch" )
-
-src_prepare() {
- sed \
- -e "s/\$(LINK)/& \$(LDFLAGS)/" \
- -e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \
- -i Makefile || die
- default
-}
-
-src_compile() {
- emake \
- LINK="$(tc-getCXX)" \
- CXX="$(tc-getCXX)" \
- CFLAGS="${CFLAGS}" \
- CXXFLAGS="${CXXFLAGS}"
-}
-
-src_install() {
- dobin ${PN}
-}
^ permalink raw reply related [flat|nested] 3+ messages in thread
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