From owner-svn-ports-all@freebsd.org Mon Jun 24 09:29:08 2019 Return-Path: Delivered-To: svn-ports-all@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 132F315C83AD; Mon, 24 Jun 2019 09:29:08 +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 AFE8C8D6AB; Mon, 24 Jun 2019 09:29:07 +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 9FA942EFA4; Mon, 24 Jun 2019 09:29:07 +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 x5O9T78Z006641; Mon, 24 Jun 2019 09:29:07 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id x5O9T56L006629; Mon, 24 Jun 2019 09:29:05 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201906240929.x5O9T56L006629@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 09:29:05 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r505017 - in head/biology: . viennarna viennarna/files X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/biology: . viennarna viennarna/files X-SVN-Commit-Revision: 505017 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: AFE8C8D6AB X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.95 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_SHORT(-0.95)[-0.952,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US]; NEURAL_HAM_MEDIUM(-1.00)[-0.999,0]; NEURAL_HAM_LONG(-1.00)[-1.000,0] X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 24 Jun 2019 09:29:08 -0000 Author: yuri Date: Mon Jun 24 09:29:05 2019 New Revision: 505017 URL: https://svnweb.freebsd.org/changeset/ports/505017 Log: New port: biology/viennarna: Alignment tools for the structural analysis of RNA Added: head/biology/viennarna/ head/biology/viennarna/Makefile (contents, props changed) head/biology/viennarna/distinfo (contents, props changed) head/biology/viennarna/files/ head/biology/viennarna/files/patch-RNA-Tutorial_Makefile.in (contents, props changed) head/biology/viennarna/files/patch-configure (contents, props changed) head/biology/viennarna/files/patch-examples_Makefile.in (contents, props changed) head/biology/viennarna/files/patch-src_bin_Makefile.in (contents, props changed) head/biology/viennarna/pkg-descr (contents, props changed) head/biology/viennarna/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Mon Jun 24 09:25:36 2019 (r505016) +++ head/biology/Makefile Mon Jun 24 09:29:05 2019 (r505017) @@ -164,6 +164,7 @@ SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet + SUBDIR += viennarna SUBDIR += vsearch SUBDIR += wise Added: head/biology/viennarna/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/viennarna/Makefile Mon Jun 24 09:29:05 2019 (r505017) @@ -0,0 +1,41 @@ +# $FreeBSD$ + +PORTNAME= viennarna +DISTVERSION= 2.4.13 +CATEGORIES= biology +MASTER_SITES= https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ +DISTNAME= ViennaRNA-${DISTVERSION} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Alignment tools for the structural analysis of RNA + +LICENSE= ViennaRNALicense +LICENSE_NAME= Vienna RNA License +LICENSE_FILE= ${WRKSRC}/COPYING +LICENSE_PERMS= auto-accept dist-mirror pkg-mirror + +BUILD_DEPENDS= bash:shells/bash \ + libgd>0:graphics/gd # for the static lib +LIB_DEPENDS= libgmp.so:math/gmp \ + libgsl.so:math/gsl \ + libmpfr.so:math/mpfr + +USES= compiler:c++11-lang gmake libtool localbase perl5 +USE_XORG= x11 xext # only for build + +GNU_CONFIGURE= yes +CONFIGURE_SHELL= ${PREFIX}/bin/bash +CONFIGURE_ARGS= --enable-shared --disable-static --with-gsl --with-cluster --with-kinwalker --enable-mpfr --without-python --without-python3 --without-perl + +INFO= RNAlib + +DATASDIR= ${PREFIX}/share/ViennaRNA +DOCSDIR= ${PREFIX}/share/doc/ViennaRNA +EXAMPLESDIR= ${PREFIX}/share/examples/ViennaRNA + +OPTIONS_DEFINE= DOCS EXAMPLES + +PORTDOCS= * +PORTEXAMPLES= * + +.include Added: head/biology/viennarna/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/viennarna/distinfo Mon Jun 24 09:29:05 2019 (r505017) @@ -0,0 +1,3 @@ +TIMESTAMP = 1561312270 +SHA256 (ViennaRNA-2.4.13.tar.gz) = 915c271b48536a3cc60b3109f11f7fd99dcd26d22621ee50f05e7f1c2f90cabe +SIZE (ViennaRNA-2.4.13.tar.gz) = 34094932 Added: head/biology/viennarna/files/patch-RNA-Tutorial_Makefile.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/viennarna/files/patch-RNA-Tutorial_Makefile.in Mon Jun 24 09:29:05 2019 (r505017) @@ -0,0 +1,11 @@ +--- 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 = $(tut_datadir)/qrna Added: head/biology/viennarna/files/patch-configure ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/viennarna/files/patch-configure Mon Jun 24 09:29:05 2019 (r505017) @@ -0,0 +1,11 @@ +--- configure.orig 2019-05-31 13:31:21 UTC ++++ configure +@@ -22325,7 +22325,7 @@ fi + if test "x$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;} Added: head/biology/viennarna/files/patch-examples_Makefile.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/viennarna/files/patch-examples_Makefile.in Mon Jun 24 09:29:05 2019 (r505017) @@ -0,0 +1,11 @@ +--- 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@ +-pkgexampledir = $(pkgdatadir)/examples ++pkgexampledir = $(prefix)/share/examples/ViennaRNA + pkgexampledatadir = $(pkgexampledir)/data + pkgperlexampledir = $(pkgexampledir)/perl5 + pkgpythonexampledir = $(pkgexampledir)/python Added: head/biology/viennarna/files/patch-src_bin_Makefile.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/viennarna/files/patch-src_bin_Makefile.in Mon Jun 24 09:29:05 2019 (r505017) @@ -0,0 +1,13 @@ +--- src/bin/Makefile.in.orig 2019-06-24 04:33:32 UTC ++++ src/bin/Makefile.in +@@ -104,8 +104,8 @@ bin_PROGRAMS = RNAfold$(EXEEXT) RNAeval$(EXEEXT) RNAhe + RNAparconv$(EXEEXT) RNAPKplex$(EXEEXT) RNAplex$(EXEEXT) \ + RNAsnoop$(EXEEXT) RNApvmin$(EXEEXT) + @VRNA_AM_SWITCH_MPFR_TRUE@am__append_4 = $(MPFR_LIBS) +-@VRNA_AM_SWITCH_SVM_TRUE@am__append_5 = -lstdc++ +-@VRNA_AM_SWITCH_SVM_TRUE@am__append_6 = -lstdc++ ++@VRNA_AM_SWITCH_SVM_TRUE@am__append_5 = -lc++ ++@VRNA_AM_SWITCH_SVM_TRUE@am__append_6 = -lc++ + subdir = src/bin + ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 + am__aclocal_m4_deps = $(top_srcdir)/m4/ac_rna.m4 \ Added: head/biology/viennarna/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/viennarna/pkg-descr Mon Jun 24 09:29:05 2019 (r505017) @@ -0,0 +1,15 @@ +LocARNA is a collection of alignment tools for the structural analysis of RNA. +Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common +structures for your RNAs. In this way, LocARNA performs Sankoff-like alignment +and is in particular suited for analyzing sets of related RNAs without known +common structure. + +LocARNA distinguishes itself from many other Sankoff-style multiple alignment +programs by its performance and low memory complexity, high accuracy, and +richness of features. As unique features, it offers structure-local alignment, +flexible structure and anchor constraints, and provides efficient computation of +reliabilities in sequence-structure alignment. The package offers a robust core +of features and is used as experimental platform for the incorporation of new +features in RNA sequence-structure alignment. + +WWW: https://github.com/s-will/LocARNA Added: head/biology/viennarna/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/viennarna/pkg-plist Mon Jun 24 09:29:05 2019 (r505017) @@ -0,0 +1,225 @@ +bin/AnalyseDists +bin/AnalyseSeqs +bin/Kinfold +bin/RNA2Dfold +bin/RNALalifold +bin/RNALfold +bin/RNAPKplex +bin/RNAaliduplex +bin/RNAalifold +bin/RNAcofold +bin/RNAdistance +bin/RNAduplex +bin/RNAeval +bin/RNAfold +bin/RNAforester +bin/RNAheat +bin/RNAinverse +bin/RNAlocmin +bin/RNApaln +bin/RNAparconv +bin/RNApdist +bin/RNAplex +bin/RNAplfold +bin/RNAplot +bin/RNApvmin +bin/RNAsnoop +bin/RNAsubopt +bin/RNAup +bin/b2ct +bin/ct2db +bin/kinwalker +bin/popt +include/ViennaRNA/2Dfold.h +include/ViennaRNA/2Dpfold.h +include/ViennaRNA/LPfold.h +include/ViennaRNA/Lfold.h +include/ViennaRNA/MEA.h +include/ViennaRNA/PKplex.h +include/ViennaRNA/PS_dot.h +include/ViennaRNA/ProfileAln.h +include/ViennaRNA/RNAstruct.h +include/ViennaRNA/ali_plex.h +include/ViennaRNA/alifold.h +include/ViennaRNA/aln_util.h +include/ViennaRNA/alphabet.h +include/ViennaRNA/boltzmann_sampling.h +include/ViennaRNA/centroid.h +include/ViennaRNA/char_stream.h +include/ViennaRNA/cofold.h +include/ViennaRNA/combinatorics.h +include/ViennaRNA/commands.h +include/ViennaRNA/concentrations.h +include/ViennaRNA/constraints.h +include/ViennaRNA/constraints/SHAPE.h +include/ViennaRNA/constraints/basic.h +include/ViennaRNA/constraints/hard.h +include/ViennaRNA/constraints/ligand.h +include/ViennaRNA/constraints/soft.h +include/ViennaRNA/constraints_SHAPE.h +include/ViennaRNA/constraints_hard.h +include/ViennaRNA/constraints_ligand.h +include/ViennaRNA/constraints_soft.h +include/ViennaRNA/convert_epars.h +include/ViennaRNA/data_structures.h +include/ViennaRNA/datastructures/basic.h +include/ViennaRNA/datastructures/char_stream.h +include/ViennaRNA/datastructures/hash_tables.h +include/ViennaRNA/datastructures/heap.h +include/ViennaRNA/datastructures/lists.h +include/ViennaRNA/datastructures/stream_output.h +include/ViennaRNA/dist_vars.h +include/ViennaRNA/dp_matrices.h +include/ViennaRNA/duplex.h +include/ViennaRNA/edit_cost.h +include/ViennaRNA/energy_const.h +include/ViennaRNA/energy_par.h +include/ViennaRNA/equilibrium_probs.h +include/ViennaRNA/eval.h +include/ViennaRNA/exterior_loops.h +include/ViennaRNA/file_formats.h +include/ViennaRNA/file_formats_msa.h +include/ViennaRNA/file_utils.h +include/ViennaRNA/findpath.h +include/ViennaRNA/fold.h +include/ViennaRNA/fold_compound.h +include/ViennaRNA/fold_vars.h +include/ViennaRNA/gquad.h +include/ViennaRNA/grammar.h +include/ViennaRNA/hairpin_loops.h +include/ViennaRNA/interior_loops.h +include/ViennaRNA/inverse.h +include/ViennaRNA/io/file_formats.h +include/ViennaRNA/io/file_formats_msa.h +include/ViennaRNA/io/utils.h +include/ViennaRNA/json.h +include/ViennaRNA/landscape/findpath.h +include/ViennaRNA/landscape/move.h +include/ViennaRNA/landscape/neighbor.h +include/ViennaRNA/landscape/paths.h +include/ViennaRNA/landscape/walk.h +include/ViennaRNA/loop_energies.h +include/ViennaRNA/loops/all.h +include/ViennaRNA/loops/external.h +include/ViennaRNA/loops/hairpin.h +include/ViennaRNA/loops/internal.h +include/ViennaRNA/loops/multibranch.h +include/ViennaRNA/mfe.h +include/ViennaRNA/mfe_window.h +include/ViennaRNA/mm.h +include/ViennaRNA/model.h +include/ViennaRNA/move_set.h +include/ViennaRNA/multibranch_loops.h +include/ViennaRNA/naview.h +include/ViennaRNA/neighbor.h +include/ViennaRNA/pair_mat.h +include/ViennaRNA/params.h +include/ViennaRNA/params/basic.h +include/ViennaRNA/params/constants.h +include/ViennaRNA/params/convert.h +include/ViennaRNA/params/default.h +include/ViennaRNA/params/io.h +include/ViennaRNA/part_func.h +include/ViennaRNA/part_func_co.h +include/ViennaRNA/part_func_up.h +include/ViennaRNA/part_func_window.h +include/ViennaRNA/perturbation_fold.h +include/ViennaRNA/plex.h +include/ViennaRNA/plot_aln.h +include/ViennaRNA/plot_layouts.h +include/ViennaRNA/plot_structure.h +include/ViennaRNA/plot_utils.h +include/ViennaRNA/plotting/RNApuzzler/RNApuzzler.h +include/ViennaRNA/plotting/RNApuzzler/RNAturtle.h +include/ViennaRNA/plotting/alignments.h +include/ViennaRNA/plotting/layouts.h +include/ViennaRNA/plotting/naview.h +include/ViennaRNA/plotting/probabilities.h +include/ViennaRNA/plotting/structures.h +include/ViennaRNA/plotting/utils.h +include/ViennaRNA/profiledist.h +include/ViennaRNA/read_epars.h +include/ViennaRNA/ribo.h +include/ViennaRNA/search/BoyerMoore.h +include/ViennaRNA/sequence.h +include/ViennaRNA/snofold.h +include/ViennaRNA/snoop.h +include/ViennaRNA/stream_output.h +include/ViennaRNA/string_utils.h +include/ViennaRNA/stringdist.h +include/ViennaRNA/structure_utils.h +include/ViennaRNA/structured_domains.h +include/ViennaRNA/subopt.h +include/ViennaRNA/svm.h +include/ViennaRNA/svm_utils.h +include/ViennaRNA/treedist.h +include/ViennaRNA/units.h +include/ViennaRNA/unstructured_domains.h +include/ViennaRNA/utils.h +include/ViennaRNA/utils/alignments.h +include/ViennaRNA/utils/basic.h +include/ViennaRNA/utils/cpu.h +include/ViennaRNA/utils/higher_order_functions.h +include/ViennaRNA/utils/strings.h +include/ViennaRNA/utils/structures.h +include/ViennaRNA/utils/svm.h +include/ViennaRNA/vrna_config.h +include/ViennaRNA/walk.h +include/g2.h +include/g2_FIG.h +include/g2_PS.h +include/g2_X11.h +include/g2_gd.h +lib/libRNA.a +lib/libg2.a +libdata/pkgconfig/RNAlib2.pc +man/man1/AnalyseDists.1.gz +man/man1/AnalyseSeqs.1.gz +man/man1/Kinfold.1.gz +man/man1/RNA2Dfold.1.gz +man/man1/RNALalifold.1.gz +man/man1/RNALfold.1.gz +man/man1/RNAPKplex.1.gz +man/man1/RNAaliduplex.1.gz +man/man1/RNAalifold.1.gz +man/man1/RNAcofold.1.gz +man/man1/RNAdistance.1.gz +man/man1/RNAduplex.1.gz +man/man1/RNAeval.1.gz +man/man1/RNAfold.1.gz +man/man1/RNAforester.1.gz +man/man1/RNAheat.1.gz +man/man1/RNAinverse.1.gz +man/man1/RNAlocmin.1.gz +man/man1/RNApaln.1.gz +man/man1/RNAparconv.1.gz +man/man1/RNApdist.1.gz +man/man1/RNAplex.1.gz +man/man1/RNAplfold.1.gz +man/man1/RNAplot.1.gz +man/man1/RNApvmin.1.gz +man/man1/RNAsnoop.1.gz +man/man1/RNAsubopt.1.gz +man/man1/RNAup.1.gz +man/man1/ct2db.1.gz +man/man1/kinwalker.1.gz +share/ViennaRNA/2Dlandscape_mfe.gri +share/ViennaRNA/2Dlandscape_pf.gri +share/ViennaRNA/DoxygenLayout.xml +share/ViennaRNA/bin/RNAdesign.pl +share/ViennaRNA/bin/b2mt.pl +share/ViennaRNA/bin/cmount.pl +share/ViennaRNA/bin/coloraln.pl +share/ViennaRNA/bin/dpzoom.pl +share/ViennaRNA/bin/mountain.pl +share/ViennaRNA/bin/refold.pl +share/ViennaRNA/bin/relplot.pl +share/ViennaRNA/bin/rotate_ss.pl +share/ViennaRNA/bin/switch.pl +share/ViennaRNA/dna_mathews1999.par +share/ViennaRNA/dna_mathews2004.par +share/ViennaRNA/rna_andronescu2007.par +share/ViennaRNA/rna_langdon2018.par +share/ViennaRNA/rna_turner1999.par +share/ViennaRNA/rna_turner2004.par +share/ViennaRNA/viennarna.bib