biology/viennarna: Make it less/not prone to failures due to hardcoded C++ library name

configure and Makefile.in provided in tarballs have -lstdc++ hard-coded in them.
The previous version of the port patches these to be -lc++, which still might fail on gcc systems, depending on which C++ library is used.

This change adds USES=autoreconf which makes it to regenerate configure and Makefile.in and hopefully have the proper C++ library in these files.

GNU libtool links with the C compiler, not with the C++ compiler, in this project. This is what I think triggers link failures due to a wrong C++
library getting into the link lines. GNU libtool likely chooses C compiler because this project has its 'main' functions in .c files,
but also includes C++ object modules. This likely causes GNU tools confusion and it uses the C compiler to link and fails due to wrong C++ libraries added there.

5 files changed, 15 insertions, 29 deletions

diff --git a/biology/viennarna/Makefile b/biology/viennarna/Makefile
index 0b7521b7a9b9..6a9ac252d81b 100644
--- a/biology/viennarna/Makefile
+++ b/biology/viennarna/Makefile
@@ -20,7 +20,7 @@ LIB_DEPENDS=	libgmp.so:math/gmp \
 		libgsl.so:math/gsl \
 		libmpfr.so:math/mpfr
 
-USES=		compiler:c++11-lang gmake libtool localbase perl5
+USES=		autoreconf compiler:c++11-lang gmake libtool localbase perl5 pkgconfig # w/out autoreconf -lstdc++ is present in configure and Makefiles and this causes link failure
 USE_XORG=	x11 xext # only for build
 
 GNU_CONFIGURE=	yes
diff --git a/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am b/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am
new file mode 100644
index 000000000000..170cccfc6eb7
--- /dev/null
+++ b/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am
@@ -0,0 +1,11 @@
+--- RNA-Tutorial/Makefile.am.orig	2019-06-24 18:48:09 UTC
++++ RNA-Tutorial/Makefile.am
+@@ -95,7 +95,7 @@ vrna_htmltutorial_uninst:
+ 
+ if WITH_TUTORIAL_PDF
+ 
+-tut_datadir         = $(pkgdatadir)/tutorial
++tut_datadir         = $(prefix)/share/doc/ViennaRNA/tutorial
+ tut_programsdir     = $(tut_datadir)/programs
+ tut_alifoldzdir     = $(tut_datadir)/alifoldz
+ tut_qrnadir         = $(tut_datadir)/qrna
diff --git a/biology/viennarna/files/patch-RNA-Tutorial_Makefile.in b/biology/viennarna/files/patch-RNA-Tutorial_Makefile.in
deleted file mode 100644
index 98d93d82be86..000000000000
--- a/biology/viennarna/files/patch-RNA-Tutorial_Makefile.in
+++ /dev/null
@@ -1,11 +0,0 @@
---- RNA-Tutorial/Makefile.in.orig	2019-06-24 07:18:45 UTC
-+++ RNA-Tutorial/Makefile.in
-@@ -459,7 +459,7 @@ clean_tutorial_html = rm -f *.html *.css *.4ct *.4tc *
- @WITH_TUTORIAL_BUILD_TRUE@@WITH_TUTORIAL_PDFLATEX_FALSE@@WITH_TUTORIAL_PDF_TRUE@@WITH_TUTORIAL_TRUE@CONVERT_TUT_TO_PDF = $(TUTORIAL_CMD_DVIPDF) tutorial.dvi;
- html_DATA = $(TUTORIAL_FILES_HTML)
- pdf_DATA = $(TUTORIAL_FILES_PDF)
--@WITH_TUTORIAL_PDF_TRUE@tut_datadir = $(pkgdatadir)/tutorial
-+@WITH_TUTORIAL_PDF_TRUE@tut_datadir = $(prefix)/share/doc/ViennaRNA/tutorial
- @WITH_TUTORIAL_PDF_TRUE@tut_programsdir = $(tut_datadir)/programs
- @WITH_TUTORIAL_PDF_TRUE@tut_alifoldzdir = $(tut_datadir)/alifoldz
- @WITH_TUTORIAL_PDF_TRUE@tut_qrnadir = $(tut_datadir)/qrna
diff --git a/biology/viennarna/files/patch-configure b/biology/viennarna/files/patch-configure
deleted file mode 100644
index bbcd28ef6c87..000000000000
--- a/biology/viennarna/files/patch-configure
+++ /dev/null
@@ -1,11 +0,0 @@
---- configure.orig	2019-05-31 13:31:21 UTC
-+++ configure
-@@ -22325,7 +22325,7 @@ fi
- if test "x$enable_static_executables" = "xyes"; then
- 
-     SAVED_LDFLAGS=$LDFLAGS
--    LDFLAGS="$LDFLAGS -static -lstdc++"
-+    LDFLAGS="$LDFLAGS -static -lc++"
- 
-     { $as_echo "$as_me:${as_lineno-$LINENO}: Checking possiblity to build statically linked executables using C++ compiler" >&5
- $as_echo "$as_me: Checking possiblity to build statically linked executables using C++ compiler" >&6;}
diff --git a/biology/viennarna/files/patch-examples_Makefile.in b/biology/viennarna/files/patch-examples_Makefile.am
index 7b408df151cd..b74a80c994ca 100644
--- a/biology/viennarna/files/patch-examples_Makefile.in
+++ b/biology/viennarna/files/patch-examples_Makefile.am
@@ -1,9 +1,6 @@
---- examples/Makefile.in.orig	2019-06-24 07:09:07 UTC
-+++ examples/Makefile.in
-@@ -441,7 +441,7 @@ target_alias = @target_alias@
- top_build_prefix = @top_build_prefix@
- top_builddir = @top_builddir@
- top_srcdir = @top_srcdir@
+--- examples/Makefile.am.orig	2019-06-24 18:49:57 UTC
++++ examples/Makefile.am
+@@ -1,4 +1,4 @@
 -pkgexampledir = $(pkgdatadir)/examples
 +pkgexampledir = $(prefix)/share/examples/ViennaRNA
  pkgexampledatadir = $(pkgexampledir)/data