* [gentoo-commits] proj/sci:master commit in: sci-chemistry/rosetta/
@ 2013-06-11 14:25 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2013-06-11 14:25 UTC (permalink / raw
To: gentoo-commits
commit: 6e3e2802c51bba8a1d0505716235d07ddd95206a
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 11 14:20:53 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 11 14:22:52 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6e3e2802
sci-chemistry/rosetta: Add patches from www.csrosetta.org
Package-Manager: portage-2.2.0_alpha179
---
sci-chemistry/rosetta/ChangeLog | 4 ++++
sci-chemistry/rosetta/metadata.xml | 1 +
sci-chemistry/rosetta/rosetta-3.4.ebuild | 4 ++--
3 files changed, 7 insertions(+), 2 deletions(-)
diff --git a/sci-chemistry/rosetta/ChangeLog b/sci-chemistry/rosetta/ChangeLog
index 02eb379..181dbc8 100644
--- a/sci-chemistry/rosetta/ChangeLog
+++ b/sci-chemistry/rosetta/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 11 Jun 2013; Justin Lecher <jlec@gentoo.org> rosetta-3.4.ebuild,
+ metadata.xml:
+ Add patches from www.csrosetta.org
+
21 Mar 2013; Justin Lecher <jlec@gentoo.org> rosetta-3.4.ebuild:
Fix for mpi
diff --git a/sci-chemistry/rosetta/metadata.xml b/sci-chemistry/rosetta/metadata.xml
index 96d9d63..b8a4661 100644
--- a/sci-chemistry/rosetta/metadata.xml
+++ b/sci-chemistry/rosetta/metadata.xml
@@ -9,6 +9,7 @@
<flag name="boinc">compile rosetta as a rosetta@home client</flag>
<flag name="boost">compile rosetta with boost supported code</flag>
<flag name="float">Build with floats rather than doubles</flag>
+ <flag name="lange">Apply patches from www.csrosetta.org</flag>
</use>
<upstream>
<bugs-to>general-support@mail.rosettacommons.org</bugs-to>
diff --git a/sci-chemistry/rosetta/rosetta-3.4.ebuild b/sci-chemistry/rosetta/rosetta-3.4.ebuild
index 518e746..3a5ec2f 100644
--- a/sci-chemistry/rosetta/rosetta-3.4.ebuild
+++ b/sci-chemistry/rosetta/rosetta-3.4.ebuild
@@ -145,8 +145,8 @@ src_install() {
newbin ${BIN} ${BIN%%.*} || die "could not install rosetta program files"
done
- mv "${ED}"/usr/bin/cluster{,-${PN}} || die
- mv "${ED}"/usr/bin/benchmark{,-${PN}} || die
+ [[ -e "${ED}"/usr/bin/cluster ]] && ( mv "${ED}"/usr/bin/cluster{,-${PN}} || die )
+ [[ -e "${ED}"/usr/bin/benchmark ]] && ( mv "${ED}"/usr/bin/benchmark{,-${PN}} || die )
}
my_filter_option() {
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-chemistry/rosetta/
@ 2013-06-11 14:25 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2013-06-11 14:25 UTC (permalink / raw
To: gentoo-commits
commit: d09462138f4920e500c9540237cbe25b07214695
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 11 14:22:26 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 11 14:22:52 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d0946213
sci-chemistry/rosetta: Fix: Ebuild calls die in a subshell
Package-Manager: portage-2.2.0_alpha179
---
sci-chemistry/rosetta/ChangeLog | 3 +++
sci-chemistry/rosetta/rosetta-3.4.ebuild | 9 +++++++--
2 files changed, 10 insertions(+), 2 deletions(-)
diff --git a/sci-chemistry/rosetta/ChangeLog b/sci-chemistry/rosetta/ChangeLog
index 181dbc8..89adc6e 100644
--- a/sci-chemistry/rosetta/ChangeLog
+++ b/sci-chemistry/rosetta/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 11 Jun 2013; Justin Lecher <jlec@gentoo.org> rosetta-3.4.ebuild:
+ Fix: Ebuild calls die in a subshell
+
11 Jun 2013; Justin Lecher <jlec@gentoo.org> rosetta-3.4.ebuild,
metadata.xml:
Add patches from www.csrosetta.org
diff --git a/sci-chemistry/rosetta/rosetta-3.4.ebuild b/sci-chemistry/rosetta/rosetta-3.4.ebuild
index 3a5ec2f..7a9cead 100644
--- a/sci-chemistry/rosetta/rosetta-3.4.ebuild
+++ b/sci-chemistry/rosetta/rosetta-3.4.ebuild
@@ -145,8 +145,13 @@ src_install() {
newbin ${BIN} ${BIN%%.*} || die "could not install rosetta program files"
done
- [[ -e "${ED}"/usr/bin/cluster ]] && ( mv "${ED}"/usr/bin/cluster{,-${PN}} || die )
- [[ -e "${ED}"/usr/bin/benchmark ]] && ( mv "${ED}"/usr/bin/benchmark{,-${PN}} || die )
+ if [[ -e "${ED}"/usr/bin/cluster ]]; then
+ mv "${ED}"/usr/bin/cluster{,-${PN}} || die
+ fi
+
+ if [[ -e "${ED}"/usr/bin/benchmark ]]; then
+ mv "${ED}"/usr/bin/benchmark{,-${PN}} || die
+ fi
}
my_filter_option() {
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-chemistry/rosetta/
@ 2013-03-21 16:11 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2013-03-21 16:11 UTC (permalink / raw
To: gentoo-commits
commit: 304951199eb3ec037cc33c7c9a9a69423b42b211
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 21 16:11:06 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Mar 21 16:11:06 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=30495119
sci-chemistry/rosetta: Fix for mpi
Package-Manager: portage-2.2.0_alpha166
---
sci-chemistry/rosetta/ChangeLog | 3 +++
sci-chemistry/rosetta/rosetta-3.4.ebuild | 7 +++++--
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/sci-chemistry/rosetta/ChangeLog b/sci-chemistry/rosetta/ChangeLog
index 22a7697..02eb379 100644
--- a/sci-chemistry/rosetta/ChangeLog
+++ b/sci-chemistry/rosetta/ChangeLog
@@ -3,6 +3,9 @@
# $Header: $
21 Mar 2013; Justin Lecher <jlec@gentoo.org> rosetta-3.4.ebuild:
+ Fix for mpi
+
+ 21 Mar 2013; Justin Lecher <jlec@gentoo.org> rosetta-3.4.ebuild:
Use system path
21 Mar 2013; Justin Lecher <jlec@gentoo.org> rosetta-3.4.ebuild,
diff --git a/sci-chemistry/rosetta/rosetta-3.4.ebuild b/sci-chemistry/rosetta/rosetta-3.4.ebuild
index 37fc74e..6ffe8df 100644
--- a/sci-chemistry/rosetta/rosetta-3.4.ebuild
+++ b/sci-chemistry/rosetta/rosetta-3.4.ebuild
@@ -80,13 +80,16 @@ src_prepare() {
-e "/program_path/s:#::g" \
-i tools/build/user.settings || die
+ tc-export CC CXX
+
if use mpi; then
sed \
-e 's:mpiCC:mpicxx:g' \
-i tools/build/basic.settings || die
+ sed \
+ -e "/cxx/d" \
+ -i tools/build/user.settings || die
fi
-
- tc-export CC CXX
}
src_configure() {
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-chemistry/rosetta/
@ 2013-03-21 16:11 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2013-03-21 16:11 UTC (permalink / raw
To: gentoo-commits
commit: 8a9ac80d7ce5e17562dd971aa2f571df79e0909f
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 21 09:20:40 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Mar 21 09:20:40 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8a9ac80d
sci-chemistry/rosetta: Use system path
Package-Manager: portage-2.2.0_alpha166
---
sci-chemistry/rosetta/ChangeLog | 3 +++
sci-chemistry/rosetta/rosetta-3.4.ebuild | 1 +
2 files changed, 4 insertions(+), 0 deletions(-)
diff --git a/sci-chemistry/rosetta/ChangeLog b/sci-chemistry/rosetta/ChangeLog
index aedc45e..22a7697 100644
--- a/sci-chemistry/rosetta/ChangeLog
+++ b/sci-chemistry/rosetta/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 21 Mar 2013; Justin Lecher <jlec@gentoo.org> rosetta-3.4.ebuild:
+ Use system path
+
21 Mar 2013; Justin Lecher <jlec@gentoo.org> rosetta-3.4.ebuild,
metadata.xml:
Rename USE custom-flags -> custom-cflags
diff --git a/sci-chemistry/rosetta/rosetta-3.4.ebuild b/sci-chemistry/rosetta/rosetta-3.4.ebuild
index 53d3d52..37fc74e 100644
--- a/sci-chemistry/rosetta/rosetta-3.4.ebuild
+++ b/sci-chemistry/rosetta/rosetta-3.4.ebuild
@@ -77,6 +77,7 @@ src_prepare() {
-e "s:GENTOO_CXXFLAGS:${myCXXFLAGS}:g" \
-e "s:GENTOO_LDFLAGS:${myCXXFLAGS} ${myLDFLAGS}:g" \
-e "s:GENTOO_LIBDIR:$(get_libdir):g" \
+ -e "/program_path/s:#::g" \
-i tools/build/user.settings || die
if use mpi; then
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-chemistry/rosetta/
@ 2013-03-21 6:54 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2013-03-21 6:54 UTC (permalink / raw
To: gentoo-commits
commit: e1d6d9a585a1a3d0ea69e9760fe9e419510db12f
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 21 06:54:13 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Mar 21 06:54:13 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e1d6d9a5
sci-chemistry/rosetta: Rename USE custom-flags -> custom-cflags
Package-Manager: portage-2.2.0_alpha166
---
sci-chemistry/rosetta/ChangeLog | 4 ++++
sci-chemistry/rosetta/metadata.xml | 1 -
sci-chemistry/rosetta/rosetta-3.4.ebuild | 4 ++--
3 files changed, 6 insertions(+), 3 deletions(-)
diff --git a/sci-chemistry/rosetta/ChangeLog b/sci-chemistry/rosetta/ChangeLog
index e13d7f3..aedc45e 100644
--- a/sci-chemistry/rosetta/ChangeLog
+++ b/sci-chemistry/rosetta/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 21 Mar 2013; Justin Lecher <jlec@gentoo.org> rosetta-3.4.ebuild,
+ metadata.xml:
+ Rename USE custom-flags -> custom-cflags
+
*rosetta-3.4 (19 Mar 2013)
19 Mar 2013; Justin Lecher <jlec@gentoo.org> -files/3.0-boinc.patch,
diff --git a/sci-chemistry/rosetta/metadata.xml b/sci-chemistry/rosetta/metadata.xml
index 3468184..96d9d63 100644
--- a/sci-chemistry/rosetta/metadata.xml
+++ b/sci-chemistry/rosetta/metadata.xml
@@ -9,7 +9,6 @@
<flag name="boinc">compile rosetta as a rosetta@home client</flag>
<flag name="boost">compile rosetta with boost supported code</flag>
<flag name="float">Build with floats rather than doubles</flag>
- <flag name="custom-flags">Use your own flags</flag>
</use>
<upstream>
<bugs-to>general-support@mail.rosettacommons.org</bugs-to>
diff --git a/sci-chemistry/rosetta/rosetta-3.4.ebuild b/sci-chemistry/rosetta/rosetta-3.4.ebuild
index e38bbcf..53d3d52 100644
--- a/sci-chemistry/rosetta/rosetta-3.4.ebuild
+++ b/sci-chemistry/rosetta/rosetta-3.4.ebuild
@@ -18,7 +18,7 @@ SRC_URI="${MY_P}.tgz"
LICENSE="|| ( rosetta-academic rosetta-commercial )"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="boinc +boost custom-flags debug doc float mpi +openmp X"
+IUSE="boinc +boost custom-cflags debug doc float mpi +openmp X"
REQUIRED_USE="?? ( mpi boinc )"
@@ -48,7 +48,7 @@ src_prepare() {
local myCXXFLAGS
local myLDFLAGS
- use custom-flags || \
+ use custom-cflags || \
export CXXFLAGS="-O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -pipe"
epatch \
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-chemistry/rosetta/
@ 2011-06-24 17:09 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2011-06-24 17:09 UTC (permalink / raw
To: gentoo-commits
commit: 63fc336691bf8a86452153436749be4626f0f0a0
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 24 13:08:02 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 24 13:08:02 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=63fc3366
Sort inherit and/or USE
(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-chemistry/rosetta/rosetta-3.0-r1.ebuild | 4 +-
sci-chemistry/rosetta/rosetta-3.0.ebuild | 128 ---------------------------
2 files changed, 2 insertions(+), 130 deletions(-)
diff --git a/sci-chemistry/rosetta/rosetta-3.0-r1.ebuild b/sci-chemistry/rosetta/rosetta-3.0-r1.ebuild
index 1e26712..da1d226 100644
--- a/sci-chemistry/rosetta/rosetta-3.0-r1.ebuild
+++ b/sci-chemistry/rosetta/rosetta-3.0-r1.ebuild
@@ -6,7 +6,7 @@
EAPI="2"
-inherit versionator eutils multilib
+inherit eutils multilib versionator
MY_P="${PN}$(get_major_version)_source"
@@ -17,7 +17,7 @@ SRC_URI="${MY_P}.tgz"
LICENSE="|| ( rosetta-academic rosetta-commercial )"
SLOT="0"
KEYWORDS=""
-IUSE="boinc boost X mpi debug doc"
+IUSE="boinc boost debug doc mpi X"
RESTRICT="fetch"
RDEPEND="mpi? ( virtual/mpi )
diff --git a/sci-chemistry/rosetta/rosetta-3.0.ebuild b/sci-chemistry/rosetta/rosetta-3.0.ebuild
deleted file mode 100644
index c4056e8..0000000
--- a/sci-chemistry/rosetta/rosetta-3.0.ebuild
+++ /dev/null
@@ -1,128 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit versionator eutils multilib
-
-MY_P="${PN}$(get_major_version)_source"
-
-DESCRIPTION="Prediction and design of protein structures, folding mechanisms, and protein-protein interactions"
-HOMEPAGE="http://www.rosettacommons.org/"
-SRC_URI="${MY_P}.tgz"
-
-LICENSE="|| ( rosetta-academic rosetta-commercial )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="boost X mpi debug"
-RESTRICT="fetch"
-
-RDEPEND="mpi? ( virtual/mpi )
- boost? ( dev-libs/boost )
- sci-libs/rosetta-db"
-DEPEND="${RDEPEND}
- >=dev-util/scons-0.96.1
- doc? ( app-doc/doxygen )
- X? ( media-libs/freeglut )"
-
-MYCONF=""
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_nofetch() {
- einfo "Go to ${HOMEPAGE} and get ${A}"
- einfo "which must be placed in ${DISTDIR}"
-}
-
-src_prepare() {
- local myCXXFLAGS
- local myLDFLAGS
-
- epatch "${FILESDIR}"/${PV}-platform.patch
- epatch "${FILESDIR}"/${PV}-fix-scons-warnings.patch
- epatch "${FILESDIR}"/${PV}-user-settings.patch
- epatch "${FILESDIR}"/${PV}-fix-valgrind.patch
- rm bin/* -f
-
- for i in ${CXXFLAGS}; do
- myCXXFLAGS="${myCXXFLAGS} \"${i/-/}\","
- done
-
- for i in ${LDFLAGS}; do
- myLDFLAGS="${myLDFLAGS} \"${i/-/}\","
- done
-
- sed -e "s:GENTOO_CXXFLAGS:${myCXXFLAGS}:g" \
- -e "s:GENTOO_LDFLAGS:${myCXXFLAGS} ${myLDFLAGS}:g" \
- -e "s:GENTOO_LIBDIR:$(get_libdir):g" \
- -i tools/build/user.settings
-
- use mpi && \
- sed -e 's:mpiCC:mpicxx:g' \
- -i tools/build/basic.settings
-}
-
-src_configure() {
- local myextras=""
- local mycxx=""
-
- use boost && EXTRAS=$(my_list_append "${EXTRAS}" "boost")
- use X && EXTRAS=$(my_list_append "${EXTRAS}" "graphics")
- use mpi && EXTRAS=$(my_list_append "${EXTRAS}" "mpi")
-
- COMPILER=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
- mycxx="cxx=${COMPILER}"
-
- test -n "${EXTRAS}" && myextras="extras=${EXTRAS}"
-
- if use debug; then
- MODE="debug"
- else
- MODE="release"
- fi
-
- MAKEOPTS=$(my_filter_option "${MAKEOPTS}" "--load-average[=0-9.]*")
- MAKEOPTS=$(my_filter_option "${MAKEOPTS}" "-l[0-9.]*")
-
- MYCONF="${MAKEOPTS} mode=${MODE} ${myextras} ${mycxx}"
-}
-
-src_compile() {
- einfo "running 'scons bin cat=src ${MYCONF}' ..."
- scons bin cat=src ${MYCONF} || die "scons bin cat=src ${MYCONF} failed"
-}
-
-src_install() {
- local BIT
-
- use amd64 && BIT="64"
- use x86 && BIT="32"
-
- dolib.so build/src/${MODE}/linux/2.6/${BIT}/x86/${COMPILER}/${EXTRAS//,/-}/*.so || \
- die "failed to install libs"
-
- cd bin
- for BIN in *; do
- newbin ${BIN} ${BIN%%.*} || die "could not install rosetta program files"
- done
-
- mv "${D}"/usr/bin/cluster{,-${PN}}
- mv "${D}"/usr/bin/benchmark{,-${PN}}
-}
-
-my_filter_option() {
- local value="$1"
- local exp="$2"
- local result=`echo ${value} | sed -e s/${exp}//g`
- echo "${result}"
- return 0;
-}
-
-my_list_append() {
- local old_value="$1"
- local new_value="$2"
- test -n "${old_value}" && old_value="${old_value},"
- echo "${old_value}${new_value}"
- return 0;
-}
^ permalink raw reply related [flat|nested] 6+ messages in thread
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