Date: Mon, 24 Jun 2019 19:30:15 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r505049 - in head/biology/viennarna: . files Message-ID: <201906241930.x5OJUFgp021964@repo.freebsd.org>
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Author: yuri Date: Mon Jun 24 19:30:15 2019 New Revision: 505049 URL: https://svnweb.freebsd.org/changeset/ports/505049 Log: 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. Added: head/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am (contents, props changed) head/biology/viennarna/files/patch-examples_Makefile.am (contents, props changed) Deleted: head/biology/viennarna/files/patch-RNA-Tutorial_Makefile.in head/biology/viennarna/files/patch-configure head/biology/viennarna/files/patch-examples_Makefile.in Modified: head/biology/viennarna/Makefile Modified: head/biology/viennarna/Makefile ============================================================================== --- head/biology/viennarna/Makefile Mon Jun 24 18:37:56 2019 (r505048) +++ head/biology/viennarna/Makefile Mon Jun 24 19:30:15 2019 (r505049) @@ -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 Added: head/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am Mon Jun 24 19:30:15 2019 (r505049) @@ -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 Added: head/biology/viennarna/files/patch-examples_Makefile.am ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/viennarna/files/patch-examples_Makefile.am Mon Jun 24 19:30:15 2019 (r505049) @@ -0,0 +1,8 @@ +--- 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 + pkgperlexampledir = $(pkgexampledir)/perl5 + pkgpythonexampledir = $(pkgexampledir)/python
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