From 673d602fa0469af10478c8090c69a00fdfef9b40 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Tue, 15 Sep 2015 15:47:49 +0200 Subject: [PATCH] sci-chemistry/coot: Version Bump Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher --- sci-chemistry/coot/Manifest | 2 + sci-chemistry/coot/coot-0.8.2.ebuild | 176 ++++++++++++++++++ .../coot/files/coot-0.8.2-desktop.patch | 21 +++ .../coot/files/coot-0.8.2-libguile.patch | 29 +++ .../coot/files/coot-0.8.2-libtool.patch | 39 ++++ .../coot/files/coot-0.8.2-sandbox-icons.patch | 16 ++ 6 files changed, 283 insertions(+) create mode 100644 sci-chemistry/coot/coot-0.8.2.ebuild create mode 100644 sci-chemistry/coot/files/coot-0.8.2-desktop.patch create mode 100644 sci-chemistry/coot/files/coot-0.8.2-libguile.patch create mode 100644 sci-chemistry/coot/files/coot-0.8.2-libtool.patch create mode 100644 sci-chemistry/coot/files/coot-0.8.2-sandbox-icons.patch diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest index 3b897f1a8159..7942eee0ff2a 100644 --- a/sci-chemistry/coot/Manifest +++ b/sci-chemistry/coot/Manifest @@ -1,6 +1,8 @@ DIST coot-0.7.1.tar.gz 16663581 SHA256 2310d48f7581283ee20eeb355d5fcef90e8d36bc032684b7b47f7c61e89ea0a9 SHA512 dad758b227231543cacd9b34ca00a0bff18bdc208c10529bbf2e504db9f17a3f1bbf610a52c21fe6046e443222667a3703dc962241debff87058ac041bbcec2e WHIRLPOOL 7c57f1161016a74449a9fee1202ada82044d17d957002c67c59f2eb9776f676eb525b605a1973b9bc479e15b40df5478e3b3fad9594433fee73bfc544d5d6b52 DIST coot-0.7.2.tar.gz 16859099 SHA256 67fbb702559be850f3198c11038fa2c25c692ef8a284e88bbf6a0e941cf3dadd SHA512 84ced967ab661a36ae61a529c1e7fdef121283795fe2300946277c8ba0724724a0190806434257cae01302542efd628cb57d0f35f24968b061cb04faf43daefa WHIRLPOOL ef379156fdfafc275fa953c01b81a06bf75dbf51cc84d6669fa92aef4449e507f45429ad599b455ca3b6b53f9944116adfe42e7ef50e2c56396624f3b5ea5f79 DIST coot-0.7.tar.gz 16172237 SHA256 e3d61d326ee906eb77081a6f646024cc6c5c92281f9508da3086fb937fb05aa2 SHA512 27fe0485240adcb7f370cf2daf116d8ea1c8e80e297c0975f1b2d2f78d4a5cd9314e06537e680993d465ef551ceba46a2b402c63acfabcbf599cca6bdb8f843f WHIRLPOOL cc919a7ec3731cfd482bb906c7fd9dc98d9ce2ba2f6bbaa91facf5e5195e27b3fe3f0e03e93668a1524bc2b2306ec23951e1db5033315ed1f26456768a5ac2a7 +DIST coot-0.8.2.tar.gz 15772937 SHA256 2f5961ded7f2cf06b887560afe964c239aba94f9c4bf8a2a80b3ca4fbc471eee SHA512 a323608df7b63f22eb2d1ac679fc047bba9fe23fe6366ae1d6ae29ca00a567aafb3d29840878e8c5123421037e26b6463f0bb845ef28dcbb4f3647cda2f74575 WHIRLPOOL d84d23aa49404dce63649bd6c5f8149e95ad5776ec4fa6ebdfcf44ebabef56c3a29376da7a1d5f8ee6f8013158a7f5c74f5bd74066036ca750bc3ff7de084791 +DIST coot-greg-data.tar.gz 8677037 SHA256 d936795853406f3c2a3dfd6f37a07a7df677e96b2d023d9302668aa49b7f06cb SHA512 28396a5fa64af61e8932b565c6593ed27c4708e6a59158d62c94005bea9fa8c46562b6caba97011209a40705e5ec6711b949138dd8a23bb954df2ab4dfa9bb33 WHIRLPOOL cb85234ece76314661bcfa424904224ac554c41fc63655857f3ba1bd2f0bf8e457c55dd1f42ffecffb9a8582ff759277b0fb9a40ca2393bf47b6a09fdd04ce1e DIST greg-data-0.7.1.tar.gz 8142259 SHA256 6f3e1c1bc540c8355583ce2e1807cc9f6a2f7b466384382a843942f96b1d31a1 SHA512 6ce97b72f3f984c0d2dc1eb4a259412761736bfaec23867eba46919b6c6444698dc0b0e717c1a095aa713b2a4726d4229aed5964d89a74f7c1f2aa058f4891bf WHIRLPOOL 65db8c976f481a765e1301526cc7af6939ceb4c1cc26f3c1d5e628512a9c34bc4a10e8380d10ab4773976def9b3e07cf84b2cdc1da821750118c405b2f8b34d4 DIST greg-data-0.7.2.tar.gz 8142259 SHA256 6f3e1c1bc540c8355583ce2e1807cc9f6a2f7b466384382a843942f96b1d31a1 SHA512 6ce97b72f3f984c0d2dc1eb4a259412761736bfaec23867eba46919b6c6444698dc0b0e717c1a095aa713b2a4726d4229aed5964d89a74f7c1f2aa058f4891bf WHIRLPOOL 65db8c976f481a765e1301526cc7af6939ceb4c1cc26f3c1d5e628512a9c34bc4a10e8380d10ab4773976def9b3e07cf84b2cdc1da821750118c405b2f8b34d4 DIST greg-data-0.7.tar.gz 8202091 SHA256 b82743b1d3c2d3acaa4adb4901368d46e0638733364963ad62044f79111f21f7 SHA512 71ab00869df074660103b824130776ceeaad398b1df8bbc30c9fc41660cc08a66998a406c5cfc93f4605cc5052aae414bd79b6e6de2ae46acd9c6997dbd5361b WHIRLPOOL 87deff25e864f55b316f432b9a9b595e23352720d08257e2b69bbe7946bf8ab5d1fcc9d13205354a0edd3fbea89422952df5f6fa0c05f9707167b544494b2c14 diff --git a/sci-chemistry/coot/coot-0.8.2.ebuild b/sci-chemistry/coot/coot-0.8.2.ebuild new file mode 100644 index 000000000000..0c45a43ef2b2 --- /dev/null +++ b/sci-chemistry/coot/coot-0.8.2.ebuild @@ -0,0 +1,176 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +AUTOTOOLS_AUTORECONF="true" + +inherit autotools-utils python-single-r1 toolchain-funcs versionator + +MY_S2_PV=$(replace_version_separator 2 - ${PV}) +MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1} +MY_S_P=${MY_S2_P}-${PR/r/revision-} +MY_PV=${PV} +MY_P=${PN}-${MY_PV} + +DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation" +HOMEPAGE="https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/" +SRC_URI="http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/${MY_P}.tar.gz + test? ( https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/data/greg-data.tar.gz -> ${PN}-greg-data.tar.gz )" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="" +IUSE="+openmp static-libs test" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +SCIDEPS=" + sci-libs/libccp4 + sci-libs/clipper + >=sci-libs/coot-data-2 + >=sci-libs/gsl-1.3 + sci-libs/fftw:2.1= + sci-libs/mmdb:2 + sci-libs/monomer-db + sci-libs/ssm + sci-chemistry/reduce + sci-chemistry/probe" + +XDEPS=" + gnome-base/libgnomecanvas + gnome-base/librsvg:2 + media-libs/libpng:0= + media-libs/freeglut + x11-libs/gtk+:2 + x11-libs/goocanvas:0 + x11-libs/gtkglext + virtual/opengl" + +SCHEMEDEPS=" + dev-scheme/net-http + dev-scheme/guile-gui + >=dev-scheme/guile-lib-0.1.6 + dev-scheme/guile-www + >=x11-libs/guile-gtk-2.1" + +RDEPEND=" + ${SCIDEPS} + ${XDEPS} + ${SCHEMEDEPS} + ${PYTHON_DEPS} + dev-db/sqlite:3 + dev-libs/boost:0=[python,${PYTHON_USEDEP}] + dev-libs/glib:2 + >=dev-libs/gmp-4.2.2-r2:0= + dev-python/pygobject:2[${PYTHON_USEDEP}] + dev-python/pygtk:2[${PYTHON_USEDEP}] + >=net-misc/curl-7.19.6 + net-dns/libidn + sys-libs/readline:0= + " +DEPEND="${RDEPEND} + virtual/pkgconfig + >=sys-devel/libtool-2.4-r2 + dev-lang/swig + sys-devel/bc + test? ( dev-scheme/greg )" + +S="${WORKDIR}/${MY_P}" + +pkg_setup() { + if use openmp; then + tc-has-openmp || die "Please use an OPENMP capable compiler" + fi + python-single-r1_pkg_setup +} + +PATCHES=( + "${FILESDIR}"/${P}-desktop.patch + "${FILESDIR}"/${P}-sandbox-icons.patch + "${FILESDIR}"/${P}-libtool.patch + "${FILESDIR}"/${P}-libguile.patch +) + +src_unpack() { + default + if use test; then + cd "${S}" || die + ln -sf ../greg-data || die + fi +} + +src_prepare() { + sed \ + -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \ + -i configure.ac || die + + autotools-utils_src_prepare +} + +src_configure() { + # All the --with's are used to activate various parts. + # Yes, this is broken behavior. + local myeconfargs=( + --with-goocanvas-prefix="${EPREFIX}/usr" + --with-guile="${EPREFIX}/usr" + --with-python="${EPREFIX}/usr" + --with-guile-gtk + --with-pygtk="${EPREFIX}/usr" + --with-sqlite3 + --with-boost="${EPREFIX}/usr" + ) + autotools-utils_src_configure +} + +src_test() { + source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" + mkdir "${T}"/coot_test || die + + 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 PYTHONPATH="${COOT_PYTHON_DIR}:${S}/src:${PYTHONPATH}" + export PYTHONHOME="${EPREFIX}"/usr/ + export CCP4_SCR="${T}"/coot_test/ + export CLIBD_MON="${EPREFIX}/usr/share/data/monomers/" + export COOT_REF_STRUCTS="${EPREFIX}/usr/share/data/monomers/" + export SYMINFO="${S}/syminfo.lib" + + export COOT_TEST_DATA_DIR="${S}"/greg-data/ + + cat > command-line-greg.scm <<- EOF + (use-modules (ice-9 greg)) + (set! greg-tools (list "greg-tests")) + (set! greg-debug #t) + (set! greg-verbose 5) + (let ((r (greg-test-run))) + (if r + (coot-real-exit 0) + (coot-real-exit 1))) + EOF + + einfo "Running test with following paths ..." + einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES" + einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR" + einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE" + einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR" + einfo "COOT_DATA_DIR $COOT_DATA_DIR" + einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR" + einfo "PYTHONPATH $PYTHONPATH" + einfo "PYTHONHOME $PYTHONHOME" + einfo "CCP4_SCR ${CCP4_SCR}" + einfo "CLIBD_MON ${CLIBD_MON}" + einfo "SYMINFO ${SYMINFO}" + + "${S}"/src/coot-bin --no-graphics --script command-line-greg.scm || die + "${S}"/src/coot-bin --no-graphics --script python-tests/coot_unittest.py || die +} diff --git a/sci-chemistry/coot/files/coot-0.8.2-desktop.patch b/sci-chemistry/coot/files/coot-0.8.2-desktop.patch new file mode 100644 index 000000000000..c264dd5a7628 --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.8.2-desktop.patch @@ -0,0 +1,21 @@ + coot.desktop | 7 +++---- + 1 file changed, 3 insertions(+), 4 deletions(-) + +diff --git a/coot.desktop b/coot.desktop +index 74aecf3..8668018 100644 +--- a/coot.desktop ++++ b/coot.desktop +@@ -1,10 +1,9 @@ + [Desktop Entry] + Type=Application +-Encoding=UTF-8 + Name=Coot + Comment=Macromolecular model builder + Exec=coot +-Icon=coot.png ++Icon=coot + Terminal=true +-Categories=Science;Graphics +-MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile ++Categories=Science;Graphics; ++MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile; diff --git a/sci-chemistry/coot/files/coot-0.8.2-libguile.patch b/sci-chemistry/coot/files/coot-0.8.2-libguile.patch new file mode 100644 index 000000000000..cbaccefb2947 --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.8.2-libguile.patch @@ -0,0 +1,29 @@ + src/graphics-info-modelling.cc | 1 + + src/graphics-info.cc | 2 ++ + 2 files changed, 3 insertions(+) + +diff --git a/src/graphics-info-modelling.cc b/src/graphics-info-modelling.cc +index 05a63ad..4b7d129 100644 +--- a/src/graphics-info-modelling.cc ++++ b/src/graphics-info-modelling.cc +@@ -102,6 +102,7 @@ + + #include "utils/coot-utils.hh" + ++#include + + // Idealize the geometry without considering the map. + // +diff --git a/src/graphics-info.cc b/src/graphics-info.cc +index e2f9d52..76b6769 100644 +--- a/src/graphics-info.cc ++++ b/src/graphics-info.cc +@@ -92,6 +92,8 @@ + #include "cc-interface-scripting.hh" + #endif + ++#include ++ + // A few non-class members - should be somewhere else, I guess. + // + void initialize_graphics_molecules() { diff --git a/sci-chemistry/coot/files/coot-0.8.2-libtool.patch b/sci-chemistry/coot/files/coot-0.8.2-libtool.patch new file mode 100644 index 000000000000..10c43ad55594 --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.8.2-libtool.patch @@ -0,0 +1,39 @@ + configure.ac | 2 +- + lbg/Makefile.am | 11 ----------- + 2 files changed, 1 insertion(+), 12 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 73d6ed7..b04dcd6 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -69,7 +69,7 @@ AC_LIB_PREPARE_MULTILIB + + AC_SUBST(COOT_STDTYPES) + +-EXPORT_DYNAMIC_FLAG_SPEC=$export_dynamic_flag_spec ++eval EXPORT_DYNAMIC_FLAG_SPEC=\"$export_dynamic_flag_spec\" + AC_SUBST(EXPORT_DYNAMIC_FLAG_SPEC) + + +diff --git a/lbg/Makefile.am b/lbg/Makefile.am +index 1277afe..a79ebe0 100644 +--- a/lbg/Makefile.am ++++ b/lbg/Makefile.am +@@ -43,17 +43,6 @@ pkginclude_HEADERS = lbg.hh wmolecule.hh flev-annotations.hh graphics-c-interfa + lbg-drag-and-drop.hh qed-interface.hh alerts.hh pi-stacking.hh + pkgincludedir = $(includedir)/coot/lbg + +-# 20140521 +-# lidia_LDFLAGS = -Wl,--export-dynamic +-# +-# Now we use EXPORT_DYNAMIC_FLAG_SPEC which usually evaluates to ${wl}--export-dynamic +-# (but not for MacOSX, where it Does The Right Thing (hopefully)). +-# We manually set the value of wl here, but maybe the Right Thing To Do for that is +-# run (eval) $($LIBTOOL --config | grep ^wl). How do I do that here though? +-# I don't understand. Maybe the setting of wl should be done in configure? But then +-# I have to force the output of libtool. Bleugh. Hmm... +-# Anyway, thankyou Gary Vaughan. +-wl=-Wl, + lidia_LDFLAGS = $(EXPORT_DYNAMIC_FLAG_SPEC) + + # res spec output operator means we include libcoot-coord-utils diff --git a/sci-chemistry/coot/files/coot-0.8.2-sandbox-icons.patch b/sci-chemistry/coot/files/coot-0.8.2-sandbox-icons.patch new file mode 100644 index 000000000000..2a9ff2d7177c --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.8.2-sandbox-icons.patch @@ -0,0 +1,16 @@ + pixmaps/icons/Makefile.am | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/pixmaps/icons/Makefile.am b/pixmaps/icons/Makefile.am +index 0c183ae..dddc11a 100644 +--- a/pixmaps/icons/Makefile.am ++++ b/pixmaps/icons/Makefile.am +@@ -11,6 +11,6 @@ install-data-local: + CONTEXT=` echo $$icon | cut -d_ -f2`; \ + SIZE=` echo $$icon | cut -d_ -f3`; \ + ICONFILE=`echo $$icon | cut -d_ -f4`; \ +- mkdir -p $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \ +- $(INSTALL_DATA) $(srcdir)/$$icon $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \ ++ mkdir -p $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \ ++ $(INSTALL_DATA) $(srcdir)/$$icon $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \ + done; -- 2.26.2