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author | Justin Lecher <jlec@gentoo.org> | 2013-12-20 13:20:09 +0100 |
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committer | Justin Lecher <jlec@gentoo.org> | 2013-12-20 13:20:09 +0100 |
commit | 490fa66ffa51dcf074eca92c85880a803e689377 (patch) | |
tree | 0d1b1895bbe062fb8827a5ec6eeefdf04f0d5fb0 | |
parent | app-text/jabref: Moved jabref-2.9.2 to x86. (diff) | |
download | sci-490fa66ffa51dcf074eca92c85880a803e689377.tar.gz sci-490fa66ffa51dcf074eca92c85880a803e689377.tar.bz2 sci-490fa66ffa51dcf074eca92c85880a803e689377.zip |
sci-libs/ghmm: Drop obsolete tools, #163; correctly support python modules; add optional support for gsl and lapack
Package-Manager: portage-2.2.7
-rw-r--r-- | sci-libs/ghmm/ChangeLog | 8 | ||||
-rw-r--r-- | sci-libs/ghmm/files/ghmm-9999-link.patch | 24 | ||||
-rw-r--r-- | sci-libs/ghmm/files/ghmm-9999-obsolete.patch | 13 | ||||
-rw-r--r-- | sci-libs/ghmm/files/ghmm-9999-out-of-source.patch | 40 | ||||
-rw-r--r-- | sci-libs/ghmm/files/ghmm-9999-respect.patch | 12 | ||||
-rw-r--r-- | sci-libs/ghmm/ghmm-9999.ebuild | 55 |
6 files changed, 138 insertions, 14 deletions
diff --git a/sci-libs/ghmm/ChangeLog b/sci-libs/ghmm/ChangeLog index a55592121..886fd6a4c 100644 --- a/sci-libs/ghmm/ChangeLog +++ b/sci-libs/ghmm/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-libs/ghmm -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 20 Dec 2013; Justin Lecher <jlec@gentoo.org> ghmm-9999.ebuild, + +files/ghmm-9999-link.patch, +files/ghmm-9999-obsolete.patch, + +files/ghmm-9999-out-of-source.patch, +files/ghmm-9999-respect.patch: + Drop obsolete tools, #163; correctly support python modules; add optional + support for gsl and lapack + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: Fixed herd entry in metadata.xml diff --git a/sci-libs/ghmm/files/ghmm-9999-link.patch b/sci-libs/ghmm/files/ghmm-9999-link.patch new file mode 100644 index 000000000..9b4e919ec --- /dev/null +++ b/sci-libs/ghmm/files/ghmm-9999-link.patch @@ -0,0 +1,24 @@ +Index: tools/Makefile.am +=================================================================== +--- tools/Makefile.am (revision 2332) ++++ tools/Makefile.am (working copy) +@@ -23,5 +23,5 @@ + smix_hmm_SOURCES = smix_hmm.c + smo2xml_SOURCES = smo2xml.c + +-LDADD = $(top_builddir)/ghmm/.libs/libghmm.a ++LDADD = $(top_builddir)/ghmm/libghmm.la + bin_SCRIPTS = ghmm-config +Index: tests/Makefile.am +=================================================================== +--- tests/Makefile.am (revision 2332) ++++ tests/Makefile.am (working copy) +@@ -34,7 +34,7 @@ + read_fa \ + mcmc + +-LDADD = $(top_builddir)/ghmm/.libs/libghmm.a ++LDADD = $(top_builddir)/ghmm/libghmm.la + + TESTS_ENVIRONMENT = GHMM_SILENT_TESTS + TESTS = root_finder_test \ diff --git a/sci-libs/ghmm/files/ghmm-9999-obsolete.patch b/sci-libs/ghmm/files/ghmm-9999-obsolete.patch new file mode 100644 index 000000000..2e6be54d0 --- /dev/null +++ b/sci-libs/ghmm/files/ghmm-9999-obsolete.patch @@ -0,0 +1,13 @@ +Index: configure.in +=================================================================== +--- configure.in (revision 2332) ++++ configure.in (working copy) +@@ -293,7 +293,7 @@ + CFLAGS="$CFLAGS $LIBXML2_CFLAGS" + + dnl final configuration +-SUBDIRS="ghmm tools tests" ++SUBDIRS="ghmm" + + dnl python wrapper can be switched on or off + AC_ARG_WITH(python, diff --git a/sci-libs/ghmm/files/ghmm-9999-out-of-source.patch b/sci-libs/ghmm/files/ghmm-9999-out-of-source.patch new file mode 100644 index 000000000..6197d9ba1 --- /dev/null +++ b/sci-libs/ghmm/files/ghmm-9999-out-of-source.patch @@ -0,0 +1,40 @@ +Index: tools/Makefile.am +=================================================================== +--- tools/Makefile.am (revision 2332) ++++ tools/Makefile.am (working copy) +@@ -12,7 +12,7 @@ + MAINTAINERCLEANFILES = Makefile.in + + BUILT_SOURCES = +-INCLUDES = -I$(top_srcdir) ++INCLUDES = -I$(top_srcdir) -I$(top_builddir)/ghmm + + bin_PROGRAMS = probdist cluster scluster smix_hmm $(OBSOLETE_TOOLS) + EXTRA_PROGRAMS = smo2xml +Index: tests/Makefile.am +=================================================================== +--- tests/Makefile.am (revision 2332) ++++ tests/Makefile.am (working copy) +@@ -15,7 +15,7 @@ + MAINTAINERCLEANFILES = Makefile.in + # stuff from dejagnu + +-INCLUDES=-I$(top_srcdir) ++INCLUDES=-I$(top_srcdir) -I$(top_builddir)/ghmm + + #these tests will not be installed + # in progress: test_sdfoba nullmodel ciscreen test_sdmodel +Index: ghmmwrapper/Makefile.am +=================================================================== +--- ghmmwrapper/Makefile.am (revision 2332) ++++ ghmmwrapper/Makefile.am (working copy) +@@ -47,7 +47,9 @@ + testdata/model_label.xml \ + testdata/tiny.txt.sqd + ++INCLUDES=-I$(top_builddir) + ++ + EXTRA_DIST = ${SWIG_INTERFACE_FILES} ${EXTENSION_C_FILES} ${PYTHON_FILES} ${PYTHON_GATO_FILES} ${TESTDATA_FILES} + + all: setup.py ghmm.py ${SWIG_INTERFACE_FILES} diff --git a/sci-libs/ghmm/files/ghmm-9999-respect.patch b/sci-libs/ghmm/files/ghmm-9999-respect.patch new file mode 100644 index 000000000..09c8721c9 --- /dev/null +++ b/sci-libs/ghmm/files/ghmm-9999-respect.patch @@ -0,0 +1,12 @@ +Index: ghmmwrapper/setup.py +=================================================================== +--- ghmmwrapper/setup.py (revision 2332) ++++ ghmmwrapper/setup.py (working copy) +@@ -48,7 +48,6 @@ + include_dirs = ['..'], + library_dirs = ['../ghmm/.libs'], + libraries = ['ghmm', 'm', 'pthread', 'xml2', 'z'], +- extra_compile_args = ["-O2", "-pipe", "-Wall"], # -g might help debugging + depends = ['wrapper_alphabet.i', 'wrapper_cmodel.i', 'wrapper_cseq.i', + 'wrapper_dmodel.i', 'wrapper_dpmodel.i', 'wrapper_dpseq.i', + 'wrapper_dseq.i', 'wrapper_xmlfile.i'] diff --git a/sci-libs/ghmm/ghmm-9999.ebuild b/sci-libs/ghmm/ghmm-9999.ebuild index 514d454af..5981be5f5 100644 --- a/sci-libs/ghmm/ghmm-9999.ebuild +++ b/sci-libs/ghmm/ghmm-9999.ebuild @@ -1,38 +1,67 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/mauvealigner/mauvealigner-9999.ebuild,v 1.1 2009/04/17 18:03:19 weaver Exp $ -EAPI="2" +EAPI=5 -ESVN_REPO_URI="https://ghmm.svn.sourceforge.net/svnroot/ghmm/trunk/ghmm" +AUTOTOOLS_AUTORECONF=true + +PYTHON_COMPAT=( python{2_6,2_7} ) -inherit subversion +inherit autotools-utils distutils-r1 subversion DESCRIPTION="General Hidden Markov Model library - efficient data structures and algorithms for HMMs" HOMEPAGE="http://ghmm.sourceforge.net/" SRC_URI="" +ESVN_REPO_URI="https://ghmm.svn.sourceforge.net/svnroot/ghmm/trunk/ghmm" LICENSE="LGPL-2.1" SLOT="0" -IUSE="" KEYWORDS="" +IUSE="gsl lapack +python static-libs" -CDEPEND="" -DEPEND="${CDEPEND}" -RDEPEND="${CDEPEND}" +RDEPEND=" + dev-libs/libxml2 + gsl? ( sci-libs/gsl ) + lapack? ( + sci-libs/clapack + virtual/lapack + )" +DEPEND="${RDEPEND}" S="${WORKDIR}/${PN}" +ESVN_BOOTSTRAP="autotools-utils_src_prepare" + +PATCHES=( + "${FILESDIR}"/${P}-out-of-source.patch + "${FILESDIR}"/${P}-link.patch + "${FILESDIR}"/${P}-respect.patch + "${FILESDIR}"/${P}-obsolete.patch +) + src_prepare() { - ./autogen.sh + use python && AUTOTOOLS_IN_SOURCE_BUILD=1 + autotools-utils_src_prepare + use python && cd "${S}"/ghmmwrapper && distutils-r1_python_prepare } src_configure() { - econf - # fixme: hack - sed -i 's|^prefix = \(.*\)|prefix = ${D}/usr|' {ghmmwrapper,HMMEd}/Makefile || die + local myeconfargs=( + --without-python + --disable-obsolete + $(use_enable gsl) + $(use_enable lapack atlas) + ) + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile + use python && cd "${S}"/ghmmwrapper && distutils-r1_src_compile } src_install() { - einstall || die + autotools-utils_src_install + use python && cd "${S}"/ghmmwrapper && distutils-r1_src_install } |