From owner-svn-ports-head@freebsd.org Mon Jun 24 19:30:16 2019 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id CA80315D718C; Mon, 24 Jun 2019 19:30:16 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 7002A846D5; Mon, 24 Jun 2019 19:30:16 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 461F257D7; Mon, 24 Jun 2019 19:30:16 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id x5OJUGss021967; Mon, 24 Jun 2019 19:30:16 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id x5OJUFgp021964; Mon, 24 Jun 2019 19:30:15 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201906241930.x5OJUFgp021964@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Mon, 24 Jun 2019 19:30:15 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r505049 - in head/biology/viennarna: . files X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/biology/viennarna: . files X-SVN-Commit-Revision: 505049 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: 7002A846D5 X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.98 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-0.999,0]; NEURAL_HAM_SHORT(-0.98)[-0.976,0]; NEURAL_HAM_LONG(-1.00)[-1.000,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US] X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 24 Jun 2019 19:30:17 -0000 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