From: "Justin Lecher" <jlec@gentoo.org>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
Date: Wed, 29 Jun 2011 13:32:38 +0000 (UTC) [thread overview]
Message-ID: <767b48f97d415ca52c9aa904172fc1e24f5d5533.jlec@gentoo> (raw)
commit: 767b48f97d415ca52c9aa904172fc1e24f5d5533
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 29 13:32:19 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 29 13:32:19 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=767b48f9
Imported changes from tree
(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-chemistry/coot/ChangeLog | 5 ++
sci-chemistry/coot/coot-9999.ebuild | 46 ++++++++++----------
sci-chemistry/coot/files/9999-clipper-config.patch | 17 +++++++
sci-chemistry/coot/files/9999-mmdb-config.patch | 18 ++++++++
sci-chemistry/coot/files/9999-test.patch | 16 +++++++
sci-chemistry/coot/metadata.xml | 8 ++--
6 files changed, 83 insertions(+), 27 deletions(-)
diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 2d688c2..c4d7981 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 29 Jun 2011; Justin Lecher <jlec@gentoo.org>
+ +files/9999-clipper-config.patch, +files/9999-mmdb-config.patch,
+ coot-9999.ebuild, +files/9999-test.patch, metadata.xml:
+ Imported changes from tree
+
15 Jun 2011; Justin Lecher <jlec@gentoo.org> -files/9999-align.patch,
coot-9999.ebuild:
Updated to current HEAD
diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index 5561140..ecb5ff0 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI="3"
+EAPI=3
PYTHON_DEPEND="2"
@@ -23,16 +23,17 @@ SRC_URI="test? ( http://www.biop.ox.ac.uk/coot/devel/greg-data.tar.gz )"
SLOT="0"
LICENSE="GPL-3"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
+IUSE="+openmp test"
SCIDEPS="
>=sci-libs/ccp4-libs-6.1
>=sci-libs/clipper-20090520
>=sci-libs/coot-data-2
>=sci-libs/gsl-1.3
- sci-libs/mmdb
+ >=sci-libs/mmdb-1.23
+ <sci-libs/monomer-db-1
sci-chemistry/reduce
- sci-chemistry/refmac
+ <sci-chemistry/refmac-5.6
sci-chemistry/probe"
XDEPS="
@@ -67,14 +68,20 @@ DEPEND="${RDEPEND}
S="${WORKDIR}"
pkg_setup() {
+ if use openmp; then
+ tc-has-openmp || die "Please use an OPENMP capable compiler"
+ fi
python_set_active_version 2
}
PATCHES=(
+ "${FILESDIR}"/${PV}-clipper-config.patch
"${FILESDIR}"/${PV}-lidia.patch
"${FILESDIR}"/${PV}-goocanvas.patch
"${FILESDIR}"/${PV}-include.patch
"${FILESDIR}"/${PV}-gl.patch
+ "${FILESDIR}"/${PV}-mmdb-config.patch
+ "${FILESDIR}"/${PV}-test.patch
)
src_unpack() {
@@ -85,12 +92,6 @@ src_unpack() {
src_prepare() {
base_src_prepare
- # Link against single-precision fftw
- sed -i \
- -e "s:\}fftw:}sfftw:g" \
- -e "s:\}rfftw:}srfftw:g" \
- "${S}"/macros/clipper.m4
-
cat >> src/svn-revision.cc <<- EOF
extern "C" {
int svn_revision() {
@@ -107,17 +108,15 @@ src_configure() {
# Yes, this is broken behavior.
econf \
--includedir='${prefix}/include/coot' \
- --with-gtkcanvas-prefix="${EPREFIX}"/usr \
- --with-clipper-prefix="${EPREFIX}"/usr \
- --with-mmdb-prefix="${EPREFIX}"/usr \
- --with-ssmlib-prefix="${EPREFIX}"/usr \
- --with-gtkgl-prefix="${EPREFIX}"/usr \
+ --with-gtkcanvas-prefix="${EPREFIX}/usr" \
+ --with-ssmlib-prefix="${EPREFIX}/usr" \
+ --with-gtkgl-prefix="${EPREFIX}/usr" \
--with-guile \
- --with-python="${EPREFIX}"/usr \
+ --with-python="${EPREFIX}/usr" \
--with-guile-gtk \
--with-gtk2 \
--with-pygtk \
- --enable-openmp
+ $(use_enable openmp)
}
src_compile() {
@@ -133,16 +132,16 @@ src_test() {
export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
export COOT_SCHEME_DIR="${S}/scheme/"
export COOT_RESOURCES_FILE="${S}/cootrc"
- export COOT_PIXMAPS_DIR="${S}/pixmaps"
- export COOT_DATA_DIR="${S}"
- export COOT_PYTHON_DIR="${S}/python"
+ export COOT_PIXMAPS_DIR="${S}/pixmaps/"
+ export COOT_DATA_DIR="${S}/"
+ export COOT_PYTHON_DIR="${S}/python/"
export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
- export PYTHONHOME="${EPREFIX}"/usr
- export CCP4_SCR="${T}"/coot_test
+ export PYTHONHOME="${EPREFIX}"/usr/
+ export CCP4_SCR="${T}"/coot_test/
export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/"
export SYMINFO="${S}/syminfo.lib"
- export COOT_TEST_DATA_DIR="${S}"/data/greg-data
+ export COOT_TEST_DATA_DIR="${S}"/data/greg-data/
cat > command-line-greg.scm <<- EOF
(use-modules (ice-9 greg))
@@ -169,4 +168,5 @@ src_test() {
einfo "SYMINFO ${SYMINFO}"
"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
+ "${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die
}
diff --git a/sci-chemistry/coot/files/9999-clipper-config.patch b/sci-chemistry/coot/files/9999-clipper-config.patch
new file mode 100644
index 0000000..311b5e8
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-clipper-config.patch
@@ -0,0 +1,17 @@
+ macros/clipper.m4 | 3 +++
+ 1 files changed, 3 insertions(+), 0 deletions(-)
+
+diff --git a/macros/clipper.m4 b/macros/clipper.m4
+index 0bf087a..d0e8b6b 100644
+--- a/macros/clipper.m4
++++ b/macros/clipper.m4
+@@ -98,6 +98,9 @@ case $ac_cv_build_alias in
+ ;;
+ esac
+
++CLIPPER_CXXFLAGS=`clipper-config --cflags`
++CLIPPER_LDOPTS=`clipper-config --libs`
++
+ AC_MSG_CHECKING([for Clipper])
+
+ LIBS="$save_LIBS $CLIPPER_LDOPTS"
diff --git a/sci-chemistry/coot/files/9999-mmdb-config.patch b/sci-chemistry/coot/files/9999-mmdb-config.patch
new file mode 100644
index 0000000..1d7cbd4
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-mmdb-config.patch
@@ -0,0 +1,18 @@
+ macros/mmdb.m4 | 4 ++++
+ 1 files changed, 4 insertions(+), 0 deletions(-)
+
+diff --git a/macros/mmdb.m4 b/macros/mmdb.m4
+index b477597..d05cf66 100644
+--- a/macros/mmdb.m4
++++ b/macros/mmdb.m4
+@@ -86,6 +86,10 @@ else
+ ac_MMDB_LDOPTS="-lmmdb -lm"
+ fi
+
++PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2])
++ac_MMDB_LDOPTS="${MMDB_LIBS}"
++ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}"
++
+ AC_MSG_CHECKING([for MMDB])
+
+ LIBS="$save_LIBS $ac_MMDB_LDOPTS"
diff --git a/sci-chemistry/coot/files/9999-test.patch b/sci-chemistry/coot/files/9999-test.patch
new file mode 100644
index 0000000..8cb79e6
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-test.patch
@@ -0,0 +1,16 @@
+ src/testing.cc | 4 +++-
+ 1 files changed, 3 insertions(+), 1 deletions(-)
+
+diff --git a/src/testing.cc b/src/testing.cc
+index f767bf6..097b9b9 100644
+--- a/src/testing.cc
++++ b/src/testing.cc
+@@ -86,6 +86,8 @@ std::string greg_test(const std::string &file_name) {
+ const char *c = getenv("COOT_TEST_DATA_DIR");
+ if (c) {
+ dd = c;
++ dd += "/";
++ dd += file_name;
+ } else {
+ const char *d = getenv("HOME");
+ if (d) {
diff --git a/sci-chemistry/coot/metadata.xml b/sci-chemistry/coot/metadata.xml
index d7156cf..702e073 100644
--- a/sci-chemistry/coot/metadata.xml
+++ b/sci-chemistry/coot/metadata.xml
@@ -1,10 +1,10 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
-<herd>sci</herd>
-<maintainer>
- <email>sci@gentoo.org</email>
-</maintainer>
+ <herd>sci</herd>
+ <maintainer>
+ <email>sci@gentoo.org</email>
+ </maintainer>
<maintainer>
<email>jlec@gentoo.org</email>
<name>Justin Lecher</name>
next reply other threads:[~2011-06-29 13:32 UTC|newest]
Thread overview: 24+ messages / expand[flat|nested] mbox.gz Atom feed top
2011-06-29 13:32 Justin Lecher [this message]
-- strict thread matches above, loose matches on Subject: below --
2020-09-22 13:40 [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/ Aisha Tammy
2015-09-15 13:34 Justin Lecher
2014-06-30 19:02 Justin Lecher
2013-11-25 18:48 Justin Lecher
2013-10-02 6:49 Justin Lecher
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2013-08-27 6:58 Justin Lecher
2013-07-22 13:29 Justin Lecher
2013-06-02 16:48 Justin Lecher
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2012-03-21 11:20 Justin Lecher
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2011-10-11 20:50 Justin Lecher
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2011-06-02 8:39 Justin Lecher
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2011-04-29 10:05 Justin Lecher
2011-03-03 14:23 Justin Lecher
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