diff options
Diffstat (limited to 'sci-chemistry/coot')
| -rw-r--r-- | sci-chemistry/coot/ChangeLog | 10 | ||||
| -rw-r--r-- | sci-chemistry/coot/coot-0.7_pre4266.ebuild | 171 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/coot-0.7_pre4266-clipper-config.patch | 17 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/coot-0.7_pre4266-goocanvas.patch | 25 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/coot-0.7_pre4266-mmdb-config.patch | 18 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/coot-0.7_pre4266-ssm.patch | 56 |
6 files changed, 296 insertions, 1 deletions
diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog index 4bda510b5d15..9af9cc16646a 100644 --- a/sci-chemistry/coot/ChangeLog +++ b/sci-chemistry/coot/ChangeLog @@ -1,6 +1,14 @@ # ChangeLog for sci-chemistry/coot # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.52 2012/03/07 19:33:39 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.53 2012/07/11 20:38:49 jlec Exp $ + +*coot-0.7_pre4266 (11 Jul 2012) + + 11 Jul 2012; Justin Lecher <jlec@gentoo.org> +coot-0.7_pre4266.ebuild, + +files/coot-0.7_pre4266-clipper-config.patch, + +files/coot-0.7_pre4266-goocanvas.patch, + +files/coot-0.7_pre4266-mmdb-config.patch, +files/coot-0.7_pre4266-ssm.patch: + Version Bump, fixes compilation with gcc-4.7, #425836 07 Mar 2012; Justin Lecher <jlec@gentoo.org> coot-0.6.2.ebuild, coot-0.6.2-r1.ebuild, coot-0.7_pre4040.ebuild: diff --git a/sci-chemistry/coot/coot-0.7_pre4266.ebuild b/sci-chemistry/coot/coot-0.7_pre4266.ebuild new file mode 100644 index 000000000000..6d331ba735e8 --- /dev/null +++ b/sci-chemistry/coot/coot-0.7_pre4266.ebuild @@ -0,0 +1,171 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/coot-0.7_pre4266.ebuild,v 1.1 2012/07/11 20:38:49 jlec Exp $ + +EAPI=4 + +PYTHON_DEPEND="2" + +AUTOTOOLS_AUTORECONF="true" + +inherit autotools-utils python 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="http://www.biop.ox.ac.uk/coot/" +SRC_URI=" + http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz + test? ( http://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz )" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+openmp static-libs test" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +SCIDEPS=" + >=sci-libs/ccp4-libs-6.1 + >=sci-libs/clipper-20090520 + >=sci-libs/coot-data-2 + >=sci-libs/gsl-1.3 + >=sci-libs/mmdb-1.23 + sci-libs/ssm + <sci-libs/monomer-db-1 + sci-chemistry/reduce + <sci-chemistry/refmac-5.6 + sci-chemistry/probe" + +XDEPS=" + gnome-base/libgnomecanvas + gnome-base/librsvg:2 + media-libs/libpng + media-libs/freeglut + x11-libs/gtk+:2 + x11-libs/goocanvas:0 + x11-libs/gtkglext" + +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} + ${SCHEMEDEPS} + dev-python/pygtk:2 + >=dev-libs/gmp-4.2.2-r2 + >=net-misc/curl-7.19.6 + net-dns/libidn" +DEPEND="${RDEPEND} + >=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_set_active_version 2 + python_pkg_setup +} + +PATCHES=( + "${FILESDIR}"/${P}-clipper-config.patch + "${FILESDIR}"/${P}-goocanvas.patch + "${FILESDIR}"/${P}-mmdb-config.patch + "${FILESDIR}"/${P}-ssm.patch + ) + +src_prepare() { + sed \ + -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-$(PYTHON)-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \ + -i configure.in || die + + autotools-utils_src_prepare + + cat >> src/svn-revision.cc <<- EOF + extern "C" { + int svn_revision() { + return ${ESVN_WC_REVISION:-0}; + } + } + EOF +} + +src_configure() { + # All the --with's are used to activate various parts. + # Yes, this is broken behavior. + local myeconfargs=( + --includedir='${prefix}/include/coot' + --with-goocanvas-prefix="${EPREFIX}/usr" + --with-guile + --with-python="${EPREFIX}/usr" + --with-guile-gtk + --with-gtk2 + --with-pygtk + $(use_enable openmp) + ) + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile + python_convert_shebangs $(python_get_version) "${S}"/src/coot_gtk2.py + cp "${S}"/src/coot_gtk2.py python/coot.py || die +} + +src_test() { + source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" + mkdir "${T}"/coot_test + + export COOT_STANDARD_RESIDUES="${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="${S}/python/" + export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}" + export PYTHONHOME="${EPREFIX}"/usr/ + export CCP4_SCR="${T}"/coot_test/ + export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/" + export SYMINFO="${S}/syminfo.lib" + + export COOT_TEST_DATA_DIR="${WORKDIR}"/data/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-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/coot-0.7_pre4266-clipper-config.patch b/sci-chemistry/coot/files/coot-0.7_pre4266-clipper-config.patch new file mode 100644 index 000000000000..311b5e88d84e --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.7_pre4266-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 $CLIPPER_LDOPTS" diff --git a/sci-chemistry/coot/files/coot-0.7_pre4266-goocanvas.patch b/sci-chemistry/coot/files/coot-0.7_pre4266-goocanvas.patch new file mode 100644 index 000000000000..ce0d4a00abba --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.7_pre4266-goocanvas.patch @@ -0,0 +1,25 @@ +Index: macros/goo-canvas.m4 +=================================================================== +--- macros/goo-canvas.m4 (revision 3307) ++++ macros/goo-canvas.m4 (working copy) +@@ -56,9 +56,9 @@ + fi + fi + +-AC_MSG_CHECKING([for Goocanvas]) ++PKG_CHECK_MODULES(GOOCANVAS, goocanvas) + +-LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS" ++LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS" + CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS" + # + # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will +@@ -76,7 +76,7 @@ + if test x$have_goocanvas = xyes; then + + GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS" +- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS" ++ GOOCANVAS_LIBS="$GOOCANVAS_LIBS" + + ifelse([$1], , :, [$1]) + diff --git a/sci-chemistry/coot/files/coot-0.7_pre4266-mmdb-config.patch b/sci-chemistry/coot/files/coot-0.7_pre4266-mmdb-config.patch new file mode 100644 index 000000000000..b3b66ab65786 --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.7_pre4266-mmdb-config.patch @@ -0,0 +1,18 @@ +Index: macros/mmdb.m4 +=================================================================== +--- macros/mmdb.m4 (revision 3579) ++++ macros/mmdb.m4 (working copy) +@@ -86,8 +86,12 @@ + ac_MMDB_LDOPTS="-lmmdb -lm" + fi + +-AC_MSG_CHECKING([for MMDB]) ++PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2]) ++ac_MMDB_LDOPTS="${MMDB_LIBS}" ++ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}" + ++AC_MSG_CHECKING([for CISPEP in MMDB]) ++ + LIBS="$save_LIBS $ac_MMDB_LDOPTS" + CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS" + # diff --git a/sci-chemistry/coot/files/coot-0.7_pre4266-ssm.patch b/sci-chemistry/coot/files/coot-0.7_pre4266-ssm.patch new file mode 100644 index 000000000000..c801da72410a --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.7_pre4266-ssm.patch @@ -0,0 +1,56 @@ + macros/mmdb-ssm.m4 | 42 +----------------------------------------- + 1 files changed, 1 insertions(+), 41 deletions(-) + +diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4 +index 1937a16..6ef547c 100644 +--- a/macros/mmdb-ssm.m4 ++++ b/macros/mmdb-ssm.m4 +@@ -22,47 +22,7 @@ + AC_DEFUN([AM_WITH_MMDBSSM], + [AC_PROVIDE([AM_USE_MMDBSSM]) + +- +-AC_ARG_WITH(ssmlib-prefix, +- AC_HELP_STRING( [--with-ssmlib-prefix=PFX], [Prefix where SSMLib has been installed] ), +- [ with_ssmlib_prefix="$withval" ], +- with_ssmlib_prefix="") +- +-AC_MSG_CHECKING([for SSMLib]) +- +-if test x$with_ssmlib_prefix != x; then +- +- MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB" +- MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm" +- +-ac_mmdb_dirs=' +-. +-include +-include/ssm +-include/mmdb +-lib +-src +-lib/src +-lib/src/mmdb' +- +- for ac_dir in $ac_mmdb_dirs; do +- if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then +- ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir" +- break +- fi +- done +- +- MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS" +- +-else +- +- MMDBSSM_CXXFLAGS="" +- MMDBSSM_LIBS="" +- with_ssmlib_prefix=no +- +-fi +- +-AC_MSG_RESULT([$with_ssmlib_prefix]) ++PKG_CHECK_MODULES([MMDBSSM],[ssm]) + + AC_SUBST(MMDBSSM_CXXFLAGS) + AC_SUBST(MMDBSSM_LIBS) |