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author | Andrew Ammerlaan <andrewammerlaan@riseup.net> | 2021-01-05 15:59:31 +0100 |
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committer | Andrew Ammerlaan <andrewammerlaan@riseup.net> | 2021-01-05 19:01:30 +0100 |
commit | a312e72300ff482275764d9541e537a926956566 (patch) | |
tree | 4af14cbeff21e3f4c2cc93c6f024043103691448 /sci-libs/ghmm | |
parent | sci-libs/fast5: version bump, add keywords, bump py targets (diff) | |
download | sci-a312e72300ff482275764d9541e537a926956566.tar.gz sci-a312e72300ff482275764d9541e537a926956566.tar.bz2 sci-a312e72300ff482275764d9541e537a926956566.zip |
sci-libs/ghmm: drop package, py2 only latest update 2015
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
Diffstat (limited to 'sci-libs/ghmm')
-rw-r--r-- | sci-libs/ghmm/files/ghmm-9999-clapack.patch | 11 | ||||
-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 | 10 | ||||
-rw-r--r-- | sci-libs/ghmm/ghmm-9999.ebuild | 67 | ||||
-rw-r--r-- | sci-libs/ghmm/metadata.xml | 11 |
7 files changed, 0 insertions, 176 deletions
diff --git a/sci-libs/ghmm/files/ghmm-9999-clapack.patch b/sci-libs/ghmm/files/ghmm-9999-clapack.patch deleted file mode 100644 index d36cb2ab5..000000000 --- a/sci-libs/ghmm/files/ghmm-9999-clapack.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ghmm/matrixop.c -+++ ghmm/matrixop.c -@@ -45,7 +45,7 @@ - #endif - - #ifdef DO_WITH_ATLAS --#include <clapack.h> -+#include <clapack/clapack.h> - #endif - - /*============================================================================*/ diff --git a/sci-libs/ghmm/files/ghmm-9999-link.patch b/sci-libs/ghmm/files/ghmm-9999-link.patch deleted file mode 100644 index 9b4e919ec..000000000 --- a/sci-libs/ghmm/files/ghmm-9999-link.patch +++ /dev/null @@ -1,24 +0,0 @@ -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 = $(top_builddir)/ghmm/libghmm.la - - TESTS_ENVIRONMENT = GHMM_SILENT_TESTS - TESTS = root_finder_test \ diff --git a/sci-libs/ghmm/files/ghmm-9999-obsolete.patch b/sci-libs/ghmm/files/ghmm-9999-obsolete.patch deleted file mode 100644 index 2e6be54d0..000000000 --- a/sci-libs/ghmm/files/ghmm-9999-obsolete.patch +++ /dev/null @@ -1,13 +0,0 @@ -Index: configure.in -=================================================================== ---- configure.in (revision 2332) -+++ configure.in (working copy) -@@ -293,7 +293,7 @@ - CFLAGS="$CFLAGS $LIBXML2_CFLAGS" - - dnl final configuration --SUBDIRS="ghmm tools tests" -+SUBDIRS="ghmm" - - dnl python wrapper can be switched on or off - AC_ARG_WITH(python, diff --git a/sci-libs/ghmm/files/ghmm-9999-out-of-source.patch b/sci-libs/ghmm/files/ghmm-9999-out-of-source.patch deleted file mode 100644 index 6197d9ba1..000000000 --- a/sci-libs/ghmm/files/ghmm-9999-out-of-source.patch +++ /dev/null @@ -1,40 +0,0 @@ -Index: tools/Makefile.am -=================================================================== ---- tools/Makefile.am (revision 2332) -+++ tools/Makefile.am (working copy) -@@ -12,7 +12,7 @@ - MAINTAINERCLEANFILES = Makefile.in - - BUILT_SOURCES = --INCLUDES = -I$(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 ${SWIG_INTERFACE_FILES} diff --git a/sci-libs/ghmm/files/ghmm-9999-respect.patch b/sci-libs/ghmm/files/ghmm-9999-respect.patch deleted file mode 100644 index cc70a0780..000000000 --- a/sci-libs/ghmm/files/ghmm-9999-respect.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- ghmmwrapper/setup.py -+++ ghmmwrapper/setup.py -@@ -48,7 +48,6 @@ - include_dirs = ['..'], - library_dirs = ['../ghmm/.libs'], - libraries = ['ghmm', 'm', 'pthread', 'xml2', 'z'], -- extra_compile_args = ["-O2", "-pipe", "-Wall"], # -g might help debugging - depends = ['wrapper_alphabet.i', 'wrapper_bayes.i', 'wrapper_cmodel.i', 'wrapper_cseq.i', - 'wrapper_dmodel.i', 'wrapper_dpmodel.i', 'wrapper_dpseq.i', - 'wrapper_dseq.i', 'wrapper_xmlfile.i'] diff --git a/sci-libs/ghmm/ghmm-9999.ebuild b/sci-libs/ghmm/ghmm-9999.ebuild deleted file mode 100644 index 012fc6499..000000000 --- a/sci-libs/ghmm/ghmm-9999.ebuild +++ /dev/null @@ -1,67 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -AUTOTOOLS_AUTORECONF=true - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools-utils distutils-r1 subversion - -DESCRIPTION="General Hidden Markov Model library" -HOMEPAGE="http://ghmm.sourceforge.net/" -SRC_URI="" -ESVN_REPO_URI="https://ghmm.svn.sourceforge.net/svnroot/ghmm/trunk/ghmm" - -LICENSE="LGPL-2.1" -SLOT="0" -KEYWORDS="" -IUSE="gsl lapack +python static-libs" - -RDEPEND=" - dev-libs/libxml2 - gsl? ( sci-libs/gsl ) - lapack? ( - sci-libs/clapack - virtual/lapack - )" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${PN}" - -ESVN_BOOTSTRAP="autotools-utils_src_prepare" - -PATCHES=( - "${FILESDIR}"/${P}-clapack.patch - "${FILESDIR}"/${P}-out-of-source.patch - "${FILESDIR}"/${P}-link.patch - "${FILESDIR}"/${P}-respect.patch - "${FILESDIR}"/${P}-obsolete.patch -) - -src_prepare() { - use python && AUTOTOOLS_IN_SOURCE_BUILD=1 - autotools-utils_src_prepare - use python && cd "${S}"/ghmmwrapper && distutils-r1_python_prepare -} - -src_configure() { - 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() { - autotools-utils_src_install - use python && cd "${S}"/ghmmwrapper && distutils-r1_src_install -} diff --git a/sci-libs/ghmm/metadata.xml b/sci-libs/ghmm/metadata.xml deleted file mode 100644 index 5fc8aa771..000000000 --- a/sci-libs/ghmm/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">ghmm</remote-id> - </upstream> -</pkgmetadata> |