From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id B75E4138359 for ; Tue, 22 Sep 2020 13:40:57 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id DA385E086A; Tue, 22 Sep 2020 13:40:56 +0000 (UTC) Received: from smtp.gentoo.org (mail.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id B3D00E086A for ; Tue, 22 Sep 2020 13:40:56 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 44508340DD4 for ; Tue, 22 Sep 2020 13:40:55 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id AD8DB33A for ; Tue, 22 Sep 2020 13:40:53 +0000 (UTC) From: "Aisha Tammy" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Aisha Tammy" Message-ID: <1600781727.ac002458a28fad508b966a6e7ce571603fb6b603.epsilon-0@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/ X-VCS-Repository: proj/sci X-VCS-Files: sci-chemistry/coot/coot-9999.ebuild sci-chemistry/coot/files/coot-9999-desktop.patch sci-chemistry/coot/files/coot-9999-libguile.patch sci-chemistry/coot/files/coot-9999-libtool.patch sci-chemistry/coot/files/coot-9999-sandbox-icons.patch sci-chemistry/coot/metadata.xml X-VCS-Directories: sci-chemistry/coot/ sci-chemistry/coot/files/ X-VCS-Committer: epsilon-0 X-VCS-Committer-Name: Aisha Tammy X-VCS-Revision: ac002458a28fad508b966a6e7ce571603fb6b603 X-VCS-Branch: master Date: Tue, 22 Sep 2020 13:40:53 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 20b16ee6-4d58-4515-970b-462245c1d850 X-Archives-Hash: bfbdeda024e8f806e13e9c7eae7975da commit: ac002458a28fad508b966a6e7ce571603fb6b603 Author: Aisha Tammy aisha cc> AuthorDate: Tue Sep 22 13:35:27 2020 +0000 Commit: Aisha Tammy aisha cc> CommitDate: Tue Sep 22 13:35:27 2020 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ac002458 sci-chemistry/coot: drop package maintainer AWOL Package-Manager: Portage-3.0.7, Repoman-3.0.1 Signed-off-by: Aisha Tammy aisha.cc> sci-chemistry/coot/coot-9999.ebuild | 177 --------------------- sci-chemistry/coot/files/coot-9999-desktop.patch | 21 --- sci-chemistry/coot/files/coot-9999-libguile.patch | 29 ---- sci-chemistry/coot/files/coot-9999-libtool.patch | 39 ----- .../coot/files/coot-9999-sandbox-icons.patch | 16 -- sci-chemistry/coot/metadata.xml | 12 -- 6 files changed, 294 deletions(-) diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild deleted file mode 100644 index f13e9b681..000000000 --- a/sci-chemistry/coot/coot-9999.ebuild +++ /dev/null @@ -1,177 +0,0 @@ -# Copyright 1999-2018 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools git-r3 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="test? ( https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/data/greg-data.tar.gz )" -EGIT_REPO_URI="https://github.com/pemsley/coot.git" - -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:0 - sys-libs/readline:0= - " -DEPEND="${RDEPEND} - virtual/pkgconfig - >=sys-devel/libtool-2.4-r2 - dev-lang/swig - sys-devel/bc - test? ( dev-scheme/greg )" - -pkg_setup() { - if use openmp; then - tc-has-openmp || die "Please use an OPENMP capable compiler" - fi - python-single-r1_pkg_setup -} - -PATCHES=( - "${FILESDIR}"/${P}-desktop.patch - "${FILESDIR}"/${P}-sandbox-icons.patch - "${FILESDIR}"/${P}-libtool.patch - "${FILESDIR}"/${P}-libguile.patch -) - -src_unpack() { - git-r3_src_unpack - if use test; then - cd "${S}" || die - unpack ${A} - ln -sf . "${S}"/coot-ccp4 || 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-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \ - -i configure.ac || die - - default - eautoreconf -} - -src_configure() { - # All the --with's are used to activate various parts. - # Yes, this is broken behavior. - local myeconfargs=( - --with-goocanvas-prefix="${EPREFIX}/usr" - --with-guile="${EPREFIX}/usr" - --with-python="${EPREFIX}/usr" - --with-guile-gtk - --with-pygtk="${EPREFIX}/usr" - --with-sqlite3 - --with-boost="${EPREFIX}/usr" - ) - econf ${myeconfargs[@]} -} - -src_test() { - source "${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-9999-desktop.patch b/sci-chemistry/coot/files/coot-9999-desktop.patch deleted file mode 100644 index c264dd5a7..000000000 --- a/sci-chemistry/coot/files/coot-9999-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-9999-libguile.patch b/sci-chemistry/coot/files/coot-9999-libguile.patch deleted file mode 100644 index cbaccefb2..000000000 --- a/sci-chemistry/coot/files/coot-9999-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 - - // 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-9999-libtool.patch b/sci-chemistry/coot/files/coot-9999-libtool.patch deleted file mode 100644 index 10c43ad55..000000000 --- a/sci-chemistry/coot/files/coot-9999-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-9999-sandbox-icons.patch b/sci-chemistry/coot/files/coot-9999-sandbox-icons.patch deleted file mode 100644 index 2a9ff2d71..000000000 --- a/sci-chemistry/coot/files/coot-9999-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 79d42af98..000000000 --- a/sci-chemistry/coot/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - - jlec@gentoo.org - Justin Lecher - - - sci-chemistry@gentoo.org - Gentoo Chemistry Project - -