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-rw-r--r--academic/ViennaRNA/swig4.patch203
1 files changed, 0 insertions, 203 deletions
diff --git a/academic/ViennaRNA/swig4.patch b/academic/ViennaRNA/swig4.patch
deleted file mode 100644
index 88df2eb933..0000000000
--- a/academic/ViennaRNA/swig4.patch
+++ /dev/null
@@ -1,203 +0,0 @@
-commit c8a867dc017f58a4ffbfb2d3d976506947e5d9d6
-Author: Ronny Lorenz <ronny@tbi.univie.ac.at>
-Date: Mon May 13 08:22:42 2019 +0200
-
- SWIG: Fix install for wrappers generated by swig 4
-
- - We now default to install _RNA.*so files for Python2/3 into the RNA/
- subdirectory. This seems necessary to avoid problems when importing
- the RNA package, where the underlying loader changed from swig 3 to
- swig 4.
- - We also require swig 3.0.0 or later from now on to generate the
- wrapper code, and we drop the -modern flag
-
-diff --git a/interfaces/Python/Makefile.am b/interfaces/Python/Makefile.am
-index df279501..41be4c08 100644
---- a/interfaces/Python/Makefile.am
-+++ b/interfaces/Python/Makefile.am
-@@ -16,9 +16,8 @@ INTERFACE_FILES = $(SWIG_src) \
- $(LANG_SPECIFIC_INTERFACE_FILES)
-
- pkgpy2execdir = $(py2execdir)/RNA
--pkgpy2cmoddir = $(py2execdir)
-
--pkgpy2cmod_LTLIBRARIES = _RNA.la
-+pkgpy2exec_LTLIBRARIES = _RNA.la
- pkgpy2exec_DATA = RNA/__init__.py
-
- _RNA_la_SOURCES = $(INTERFACE_FILES) \
-@@ -73,7 +72,7 @@ $(SWIG_wrapper): $(SWIG_src) $(INTERFACE_FILES)
- $(swig_verbose)$(SWIG) -I$(top_srcdir)/src \
- -I$(srcdir) -I$(builddir) \
- $(RNA_CPPFLAGS) \
-- -python -modern -c++ \
-+ -python -c++ \
- -o $(SWIG_wrapper) \
- $(SWIG_main_src)
-
-@@ -87,27 +86,33 @@ RNA/__init__.py: $(SWIG_module_name).py
- $(AM_V_GEN)( test -d RNA || $(MKDIR_P) RNA ) && \
- cp `test -f RNA.py || echo '$(srcdir)/'`RNA.py RNA/__init__.py
-
--_RNA$(PYTHON2_SO): _RNA.la
-- $(AM_V_GEN)( $(LIBTOOL) --config > libtoolconfig.tmp ) && \
-- ( . ./libtoolconfig.tmp; cp $$objdir/_RNA$(PYTHON2_SO) . ) && \
-+RNA/_RNA$(PYTHON2_SO): _RNA.la
-+ $(AM_V_GEN)( test -d RNA || $(MKDIR_P) RNA ) && \
-+ ( $(LIBTOOL) --config > libtoolconfig.tmp ) && \
-+ ( . ./libtoolconfig.tmp; cp $$objdir/_RNA$(PYTHON2_SO) RNA ) && \
- rm -f libtoolconfig.tmp
-
--all-local: _RNA$(PYTHON2_SO)
-+CLEANFILES = \
-+ RNA/_RNA$(PYTHON2_SO) \
-+ RNA/__init__.py \
-+ RNA/__init__.pyc
-+
-+all-local: RNA/_RNA$(PYTHON2_SO)
-
- clean-local:
-- -rm -rf RNA _RNA$(PYTHON2_SO)
-+ -rm -rf RNA
-
- # Remove the .la file - RNA.la is never linked against (it's a module)
- # and Python doesn't use libltdl. Note that the library gets installed by
- # install-data, so that's where we need to hook.
- install-data-hook:
-- rm -f $(DESTDIR)$(pkgpy2cmoddir)/_RNA.la
-+ rm -f $(DESTDIR)$(pkgpy2execdir)/_RNA.la
-
- # Because we don't install the .la file, "make uninstall" doesn't work and
- # we need to remove the file ourselves.
- uninstall-local:
-- eval `grep '^dlname=' $(pkgpy2cmod_LTLIBRARIES)` ; \
-- rm -f $(DESTDIR)$(pkgpy2cmoddir)/"$$dlname"
-+ eval `grep '^dlname=' $(pkgpy2exec_LTLIBRARIES)` ; \
-+ rm -f $(DESTDIR)$(pkgpy2execdir)/"$$dlname"
-
- ## remove all generated content
- maintainer-clean-local:
-diff --git a/interfaces/Python3/Makefile.am b/interfaces/Python3/Makefile.am
-index de9b049e..67824a99 100644
---- a/interfaces/Python3/Makefile.am
-+++ b/interfaces/Python3/Makefile.am
-@@ -17,10 +17,9 @@ INTERFACE_FILES = $(SWIG_src) \
- $(LANG_SPECIFIC_INTERFACE_FILES)
-
- pkgpyexecdir = $(py3execdir)/RNA
--pkgpycmoddir = $(py3execdir)
- pkgpycachedir = $(pkgpyexecdir)/__pycache__
-
--pkgpycmod_LTLIBRARIES = _RNA.la
-+pkgpyexec_LTLIBRARIES = _RNA.la
- pkgpyexec_DATA = RNA/__init__.py
- pkgpycache_DATA = RNA/__pycache__/__init__.@PYTHON3_CACHE_TAG@.pyc \
- RNA/__pycache__/__init__.@PYTHON3_CACHE_OPT1_EXT@
-@@ -75,7 +74,7 @@ $(SWIG_wrapper): $(SWIG_src) $(INTERFACE_FILES)
- -I$(srcdir) -I$(builddir) \
- -DPY3 \
- $(RNA_CPPFLAGS) \
-- -python -modern -py3 -c++ \
-+ -python -py3 -c++ \
- -o $(SWIG_wrapper) \
- $(SWIG_main_src)
-
-@@ -91,42 +90,43 @@ RNA/__init__.py: $(SWIG_module_name).py
-
- # We "import _RNA" first so that if we fail to import the glue library
- # we don't generate a broken .pyc or .pyo.
--RNA/__pycache__/__init__.@PYTHON3_CACHE_TAG@.pyc: RNA/__init__.py _RNA$(PYTHON3_SO)
-+RNA/__pycache__/__init__.@PYTHON3_CACHE_TAG@.pyc: RNA/__init__.py RNA/_RNA$(PYTHON3_SO)
- $(AM_V_GEN)( PYTHONPATH="RNA:$$PYTHONPATH" $(PYTHON3) -c "import _RNA" ; \
- PYTHONPATH=".:$$PYTHONPATH" $(PYTHON3) -c "import RNA" )
-
--RNA/__pycache__/__init__.@PYTHON3_CACHE_OPT1_EXT@: RNA/__init__.py _RNA$(PYTHON3_SO)
-+RNA/__pycache__/__init__.@PYTHON3_CACHE_OPT1_EXT@: RNA/__init__.py RNA/_RNA$(PYTHON3_SO)
- $(AM_V_GEN)( PYTHONPATH="RNA:$$PYTHONPATH" $(PYTHON3) -O -c "import _RNA" ; \
- PYTHONPATH=".:$$PYTHONPATH" $(PYTHON3) -O -c "import RNA" )
-
--_RNA$(PYTHON3_SO): _RNA.la
-- $(AM_V_GEN)( $(LIBTOOL) --config > libtoolconfig.tmp ) && \
-- ( . ./libtoolconfig.tmp; cp $$objdir/_RNA$(PYTHON3_SO) . ) && \
-+RNA/_RNA$(PYTHON3_SO): _RNA.la
-+ $(AM_V_GEN)( test -d RNA || $(MKDIR_P) RNA ) && \
-+ ( $(LIBTOOL) --config > libtoolconfig.tmp ) && \
-+ ( . ./libtoolconfig.tmp; cp $$objdir/_RNA$(PYTHON3_SO) RNA ) && \
- rm -f libtoolconfig.tmp
-
- CLEANFILES = \
-- _RNA$(PYTHON3_SO) \
-+ RNA/_RNA$(PYTHON3_SO) \
- RNA/__init__.py \
- RNA/__pycache__/__init__.@PYTHON3_CACHE_TAG@.pyc \
- RNA/__pycache__/__init__.@PYTHON3_CACHE_OPT1_EXT@\
- $(srcdir)/*.pyc
-
--all-local: _RNA$(PYTHON3_SO)
-+all-local: RNA/_RNA$(PYTHON3_SO)
-
- clean-local:
-- -rm -rf RNA _RNA$(PYTHON3_SO)
-+ -rm -rf RNA
-
- # Remove the .la file - RNA.la is never linked against (it's a module)
- # and Python doesn't use libltdl. Note that the library gets installed by
- # install-data, so that's where we need to hook.
- install-data-hook:
-- rm -f $(DESTDIR)$(pkgpycmoddir)/_RNA.la
-+ rm -f $(DESTDIR)$(pkgpyexecdir)/_RNA.la
-
- # Because we don't install the .la file, "make uninstall" doesn't work and
- # we need to remove the file ourselves.
- uninstall-local:
-- eval `grep '^dlname=' $(pkgpycmod_LTLIBRARIES)` ; \
-- rm -f $(DESTDIR)$(pkgpycmoddir)/"$$dlname"
-+ eval `grep '^dlname=' $(pkgpyexec_LTLIBRARIES)` ; \
-+ rm -f $(DESTDIR)$(pkgpyexecdir)/"$$dlname"
-
- ## remove all generated content
- maintainer-clean-local:
-diff --git a/interfaces/RNA.i b/interfaces/RNA.i
-index fb2260d6..6ae86641 100644
---- a/interfaces/RNA.i
-+++ b/interfaces/RNA.i
-@@ -1,4 +1,9 @@
-+#ifdef SWIGPYTHON
-+%module(moduleimport="from . import _RNA") RNA
-+#else
- %module RNA
-+#endif
-+
- //%pragma(perl5) modulecode="@EXPORT=qw(fold);"
- %pragma(perl5) include="RNA.pod"
-
-diff --git a/m4/ac_rna_swig.m4 b/m4/ac_rna_swig.m4
-index 98583bed..29ea398f 100644
---- a/m4/ac_rna_swig.m4
-+++ b/m4/ac_rna_swig.m4
-@@ -9,13 +9,12 @@ AC_DEFUN([RNA_ENABLE_SWIG_INTERFACES],[
-
- AS_IF([test "x$with_swig" != "xno"],[
- wants_swig="yes"
-- AX_PKG_SWIG(2.0.0, [has_swig="yes"], [has_swig="no"])
-+ AX_PKG_SWIG(3.0.0, [has_swig="yes"], [has_swig="no"])
- ],[
- wants_swig="no"
- ])
-
- AM_CONDITIONAL(HAS_SWIG, test "x$has_swig" != "xno")
--
- RNA_ENABLE_SWIG_PERL
- RNA_ENABLE_SWIG_PYTHON
- RNA_ENABLE_SWIG_PYTHON3
-@@ -55,10 +54,6 @@ AC_DEFUN([RNA_ENABLE_SWIG_PERL],[
- AC_MSG_ERROR([Perl is required to build.])
- [enable_perl_status="Perl is required to build."]
- fi
--# AX_PERL_EXT_FLAGS([PERLXS_CFLAGS], [PERLXS_LDFLAGS])
--# AX_PERL_EXT_LINK_CHECK([with_perl])
--# AC_SUBST([PERLXS_CFLAGS])
--# AC_SUBST([PERLXS_LDFLAGS])
- ])
-
- # prepare all files for perl interface
generated by cgit v1.2.3-80-g2a13 (git 2.46.2) at 2024-10-04 08:26:01 +0000