academic/ViennaRNA: Updated for version 2.4.12.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

4 files changed, 235 insertions, 13 deletions

diff --git a/academic/ViennaRNA/README b/academic/ViennaRNA/README
index 84581ebcf2fff..a8fb799e7974b 100644
--- a/academic/ViennaRNA/README
+++ b/academic/ViennaRNA/README
@@ -26,3 +26,16 @@ They are not maintained any more and not built by default.
 The code very rarely uses static arrays, and all programs should work for 
 sequences up to a length of 32,700 (if you have huge amounts of memory that
 is).
+
+For those who wish to link the Vienna package their own C, perl or python programs,
+the RNAlib Reference Manual can be assessed at:
+
+https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/index.html
+
+or downloaded from:
+
+https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/RNAlib-$VERSION.pdf
+
+For further info see:
+
+https://www.tbi.univie.ac.at/RNA/documentation.html
diff --git a/academic/ViennaRNA/ViennaRNA.SlackBuild b/academic/ViennaRNA/ViennaRNA.SlackBuild
index 2165d6da28327..9de92bfa6e872 100644
--- a/academic/ViennaRNA/ViennaRNA.SlackBuild
+++ b/academic/ViennaRNA/ViennaRNA.SlackBuild
@@ -23,7 +23,7 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=ViennaRNA
-VERSION=${VERSION:-2.4.11}
+VERSION=${VERSION:-2.4.12}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
@@ -68,6 +68,11 @@ find . \
  -exec chmod 755 {} \; -o \
  \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
  -exec chmod 644 {} \;
+ 
+patch -p 1 < $CWD/swig4.patch
+
+#needed to make patches compile
+autoreconf
 
 # You can configure some ViennaRNA features that are (not) compiled by default.
 # See the README.md for details. You can enable/disable a these features by
@@ -95,19 +100,20 @@ find . \
 # - SVM Z-score filter in RNALfold
 # - GNU Scientific Library for RNApvmin
 
-cluster=""       ; [ "${CLUS:-no}" != "no" ]       && cluster="--with-cluster"
-kinwalker=""     ; [ "${KINW:-no}" != "no" ]       && kinwalker="--with-kinwalker"
-forester=""      ; [ "${FORE:-yes}" != "yes" ]     && forester="--without-forester"
-kinfold=""       ; [ "${KINF:-yes}" != "yes" ]     && kinwalk="--without-kinfold"
-rnalocmin=""     ; [ "${RLOC:-yes}" != "yes" ]     && rnalocmin="--without-rnalocmin"
+cluster=""       ; [ "${CLUSTER:-yes}" != "no" ]      && cluster="--with-cluster"
+kinwalker=""     ; [ "${KINWALKER:-yes}" != "no" ]       && kinwalker="--with-kinwalker"
+# Default enabled features:
+forester=""      ; [ "${FORESTER:-yes}" != "yes" ]     && forester="--without-forester"
+kinfold=""       ; [ "${KINFOLD:-yes}" != "yes" ]     && kinwalk="--without-kinfold"
+rnalocmin=""     ; [ "${RNALOCMIN:-yes}" != "yes" ]     && rnalocmin="--without-rnalocmin"
 perl=""          ; [ "${PERL:-yes}" != "yes" ]     && perl="--without-perl"
-python=""        ; [ "${PYTH:-yes}" != "yes" ]     && python="--without-python"
-python3=""       ; [ "${PYT3:-yes}" != "yes" ]     && python3="--without-python3"
+python=""        ; [ "${PYTHON:-yes}" != "yes" ]     && python="--without-python"
+python3=""       ; [ "${PYTHON3:-yes}" != "yes" ]     && python3="--without-python3"
 swig=""          ; [ "${SWIG:-yes}" != "yes" ]     && swig="--without-swig"
 simd=""          ; [ "${SIMD:-yes}" != "yes" ]     && simd="--disable-simd"
 lto=""           ; [ "${LTO:-yes}" != "yes" ]      && lto="--disable-lto"
-openmp=""        ; [ "${OMP:-yes}" != "yes" ]      && openmp="--disable-openmp"
-pthreads=""      ; [ "${PTHR:-yes}" != "yes" ]     && pthreads="--disable-pthreads"
+openmp=""        ; [ "${OPENMP:-yes}" != "yes" ]      && openmp="--disable-openmp"
+pthreads=""      ; [ "${PTHREADS:-yes}" != "yes" ]     && pthreads="--disable-pthreads"
 svm=""           ; [ "${SVM:-yes}" != "yes" ]      && svm="--without-svm"
 gsl=""           ; [ "${GSL:-yes}" != "yes" ]      && gsl="--without-gsl"
 
diff --git a/academic/ViennaRNA/ViennaRNA.info b/academic/ViennaRNA/ViennaRNA.info
index ffde773320486..1432a46dc11da 100644
--- a/academic/ViennaRNA/ViennaRNA.info
+++ b/academic/ViennaRNA/ViennaRNA.info
@@ -1,8 +1,8 @@
 PRGNAM="ViennaRNA"
-VERSION="2.4.11"
+VERSION="2.4.12"
 HOMEPAGE="https://www.tbi.univie.ac.at/RNA"
-DOWNLOAD="https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.11.tar.gz"
-MD5SUM="114ea7450ef994404754abdc6cb45353"
+DOWNLOAD="https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.12.tar.gz"
+MD5SUM="db37ca5c863375d61488e6d7248c7176"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES="grace gri"
diff --git a/academic/ViennaRNA/swig4.patch b/academic/ViennaRNA/swig4.patch
new file mode 100644
index 0000000000000..88df2eb933001
--- /dev/null
+++ b/academic/ViennaRNA/swig4.patch
@@ -0,0 +1,203 @@
+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