commit: c399a8bb15acd06ffef54b9c1b7f0e9c36f77c86 Author: Matt Turner <mattst88 <AT> gentoo <DOT> org> AuthorDate: Sat Aug 10 04:03:09 2019 +0000 Commit: Matt Turner <mattst88 <AT> gentoo <DOT> org> CommitDate: Sat Aug 10 04:05:33 2019 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c399a8bb
sci-chemistry/coot: Remove Closes: https://bugs.gentoo.org/639760 Signed-off-by: Matt Turner <mattst88 <AT> gentoo.org> sci-chemistry/coot/Manifest | 2 - sci-chemistry/coot/coot-0.8.2-r1.ebuild | 181 --------------------- sci-chemistry/coot/files/coot-0.8.2-desktop.patch | 21 --- sci-chemistry/coot/files/coot-0.8.2-libguile.patch | 29 ---- sci-chemistry/coot/files/coot-0.8.2-libtool.patch | 39 ----- .../coot/files/coot-0.8.2-sandbox-icons.patch | 16 -- sci-chemistry/coot/metadata.xml | 8 - 7 files changed, 296 deletions(-) diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest deleted file mode 100644 index 0ef426fb410..00000000000 --- a/sci-chemistry/coot/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST coot-0.8.2-greg-data.tar.gz 8677037 BLAKE2B bb2eac183598fed429c4977f9512e90335ccb988f154a3a29985668e6d3a90a19cb77ec61e0453e7294243b8dffd9b5ef6bb318bac2280b26eab37e2de25a18a SHA512 28396a5fa64af61e8932b565c6593ed27c4708e6a59158d62c94005bea9fa8c46562b6caba97011209a40705e5ec6711b949138dd8a23bb954df2ab4dfa9bb33 -DIST coot-0.8.2.tar.gz 15772937 BLAKE2B 8ee8fb827ef4ec6470f17eea4a91db8c57699c8c3a3d7cce3388c53389ba15c90a7610d8f2592320acdaee0b6c09fe8e9452cd45857659d71d363abc3322bf6f SHA512 a323608df7b63f22eb2d1ac679fc047bba9fe23fe6366ae1d6ae29ca00a567aafb3d29840878e8c5123421037e26b6463f0bb845ef28dcbb4f3647cda2f74575 diff --git a/sci-chemistry/coot/coot-0.8.2-r1.ebuild b/sci-chemistry/coot/coot-0.8.2-r1.ebuild deleted file mode 100644 index b4fa2b21f7b..00000000000 --- a/sci-chemistry/coot/coot-0.8.2-r1.ebuild +++ /dev/null @@ -1,181 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -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" -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/${MY_P}.tar.gz - test? ( https://dev.gentoo.org/~jlec/distfiles/${P}-greg-data.tar.gz )" - -SLOT="0" -LICENSE="GPL-3" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -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/guile-2 - 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 '/export LD_LIBRARY/s:^:#:g' \ - -i src/coot.in || die - - 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 deleted file mode 100644 index c264dd5a762..00000000000 --- a/sci-chemistry/coot/files/coot-0.8.2-desktop.patch +++ /dev/null @@ -1,21 +0,0 @@ - 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 deleted file mode 100644 index cbaccefb294..00000000000 --- a/sci-chemistry/coot/files/coot-0.8.2-libguile.patch +++ /dev/null @@ -1,29 +0,0 @@ - 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 <libguile.h> - - // 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 <libguile.h> -+ - // 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 deleted file mode 100644 index 10c43ad5559..00000000000 --- a/sci-chemistry/coot/files/coot-0.8.2-libtool.patch +++ /dev/null @@ -1,39 +0,0 @@ - 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 deleted file mode 100644 index 2a9ff2d7177..00000000000 --- a/sci-chemistry/coot/files/coot-0.8.2-sandbox-icons.patch +++ /dev/null @@ -1,16 +0,0 @@ - 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; diff --git a/sci-chemistry/coot/metadata.xml b/sci-chemistry/coot/metadata.xml deleted file mode 100644 index 8937bad0b17..00000000000 --- a/sci-chemistry/coot/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata>
