diff --git a/biology/viennarna/Makefile b/biology/viennarna/Makefile index 06c607940453..8ed2c240704f 100644 --- a/biology/viennarna/Makefile +++ b/biology/viennarna/Makefile @@ -1,58 +1,63 @@ PORTNAME= viennarna -DISTVERSION= 2.6.4 -PORTREVISION= 2 +DISTVERSION= 2.7.0 CATEGORIES= biology -MASTER_SITES= https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_6_x/ +MASTER_SITES= https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_7_x/ DISTNAME= ViennaRNA-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Alignment tools for the structural analysis of RNA -WWW= https://www.tbi.univie.ac.at/RNA/ +WWW= https://www.tbi.univie.ac.at/RNA/ \ + https://github.com/ViennaRNA/ViennaRNA LICENSE= ViennaRNALicense LICENSE_NAME= Vienna RNA License LICENSE_FILE= ${WRKSRC}/COPYING LICENSE_PERMS= auto-accept dist-mirror pkg-mirror #BROKEN_FreeBSD_14= fails to compile: no member named 'bind2nd' in namespace 'std' BUILD_DEPENDS= bash:shells/bash \ lapacke>0:math/lapacke \ libgd>0:graphics/gd # for the static lib BUILD_DEPENDS+= swig:devel/swig \ xxd:sysutils/xxd LIB_DEPENDS= libgmp.so:math/gmp \ libgsl.so:math/gsl \ liblapack.so:math/lapack \ libmpfr.so:math/mpfr USES= autoreconf bison compiler:c++17-lang fortran gmake \ libtool localbase perl5 pkgconfig xorg # w/out autoreconf -lstdc++ is present in configure and Makefiles and this causes link failure USE_XORG= ice x11 xext # only for build GNU_CONFIGURE= yes GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share 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 CXXFLAGS+= -Dregister= # workaround for https://github.com/ViennaRNA/ViennaRNA/issues/214 TEST_TARGET= check CONFLICTS_INSTALL= g2 # include/g2.h INFO= RNAlib DATASDIR= ${PREFIX}/share/ViennaRNA DOCSDIR= ${PREFIX}/share/doc/ViennaRNA EXAMPLESDIR= ${PREFIX}/share/examples/ViennaRNA OPTIONS_DEFINE= DOCS EXAMPLES PORTDOCS= * PORTEXAMPLES= * post-configure: # remove -lstdc++ from .pc file @${REINPLACE_CMD} -e 's| -lstdc++||' ${WRKSRC}/RNAlib2.pc +post-install: + # remove stray files + @${RM} ${STAGEDIR}/RNA/RNAconsensus.py + @${RMDIR} ${STAGEDIR}/RNA + .include diff --git a/biology/viennarna/distinfo b/biology/viennarna/distinfo index 75d1552bb0c9..df74d24eeb75 100644 --- a/biology/viennarna/distinfo +++ b/biology/viennarna/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1699041043 -SHA256 (ViennaRNA-2.6.4.tar.gz) = d1259ce5809601a12b0dc9b724ea2c55806fece80d8d83ad417ea8a2dd574982 -SIZE (ViennaRNA-2.6.4.tar.gz) = 69749819 +TIMESTAMP = 1730430067 +SHA256 (ViennaRNA-2.7.0.tar.gz) = 9a99fd68ed380894defb4d5e6a8a2871629270028cdf7f16f0a05da6e8c71473 +SIZE (ViennaRNA-2.7.0.tar.gz) = 53185587 diff --git a/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am b/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am deleted file mode 100644 index 8857bf17c682..000000000000 --- a/biology/viennarna/files/patch-RNA-Tutorial_Makefile.am +++ /dev/null @@ -1,11 +0,0 @@ ---- RNA-Tutorial/Makefile.am.orig 2020-11-23 22:41:05 UTC -+++ RNA-Tutorial/Makefile.am -@@ -90,7 +90,7 @@ 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/pkg-plist b/biology/viennarna/pkg-plist index afaa24303e60..ee361b469586 100644 --- a/biology/viennarna/pkg-plist +++ b/biology/viennarna/pkg-plist @@ -1,252 +1,315 @@ bin/AnalyseDists bin/AnalyseSeqs bin/Kinfold bin/RNA2Dfold bin/RNALalifold bin/RNALfold bin/RNAPKplex bin/RNAaliduplex bin/RNAalifold bin/RNAcofold +bin/RNAconsensus bin/RNAdistance bin/RNAdos bin/RNAduplex bin/RNAeval bin/RNAfold bin/RNAforester bin/RNAheat bin/RNAinverse bin/RNAlocmin bin/RNAmultifold bin/RNApaln bin/RNAparconv bin/RNApdist bin/RNAplex bin/RNAplfold bin/RNAplot bin/RNApvmin bin/RNAsnoop bin/RNAsubopt bin/RNAup bin/RNAxplorer 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/SHAPE.h include/ViennaRNA/ali_plex.h include/ViennaRNA/alifold.h include/ViennaRNA/aln_util.h include/ViennaRNA/alphabet.h +include/ViennaRNA/backtrack/exterior.h +include/ViennaRNA/backtrack/global.h +include/ViennaRNA/backtrack/gquad.h +include/ViennaRNA/backtrack/hairpin.h +include/ViennaRNA/backtrack/internal.h +include/ViennaRNA/backtrack/multibranch.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/combinatorics/basic.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/soft_special.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/array.h include/ViennaRNA/datastructures/basic.h include/ViennaRNA/datastructures/char_stream.h +include/ViennaRNA/datastructures/dp_matrices.h include/ViennaRNA/datastructures/hash_tables.h include/ViennaRNA/datastructures/heap.h include/ViennaRNA/datastructures/lists.h +include/ViennaRNA/datastructures/sparse_mx.h include/ViennaRNA/datastructures/stream_output.h include/ViennaRNA/datastructures/string.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/eval/basic.h +include/ViennaRNA/eval/exterior.h +include/ViennaRNA/eval/gquad.h +include/ViennaRNA/eval/hairpin.h +include/ViennaRNA/eval/internal.h +include/ViennaRNA/eval/multibranch.h +include/ViennaRNA/eval/structures.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/grammar/basic.h +include/ViennaRNA/grammar/mfe.h +include/ViennaRNA/grammar/partfunc.h include/ViennaRNA/hairpin_loops.h include/ViennaRNA/heat_capacity.h include/ViennaRNA/interior_loops.h include/ViennaRNA/inverse.h +include/ViennaRNA/inverse/basic.h +include/ViennaRNA/io/commands.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/mconf.h include/ViennaRNA/mfe.h +include/ViennaRNA/mfe/exterior.h +include/ViennaRNA/mfe/global.h +include/ViennaRNA/mfe/gquad.h +include/ViennaRNA/mfe/internal.h +include/ViennaRNA/mfe/local.h +include/ViennaRNA/mfe/multibranch.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/params/ribosum.h include/ViennaRNA/params/salt.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/partfunc/exterior.h +include/ViennaRNA/partfunc/global.h +include/ViennaRNA/partfunc/gquad.h +include/ViennaRNA/partfunc/internal.h +include/ViennaRNA/partfunc/local.h +include/ViennaRNA/partfunc/multibranch.h +include/ViennaRNA/partfunc/multifold.h include/ViennaRNA/perturbation_fold.h include/ViennaRNA/pf_multifold.h include/ViennaRNA/pk_plex.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/naview.h include/ViennaRNA/plotting/probabilities.h include/ViennaRNA/plotting/structures.h include/ViennaRNA/plotting/utils.h +include/ViennaRNA/probabilities/basepairs.h +include/ViennaRNA/probabilities/structures.h +include/ViennaRNA/probing/SHAPE.h +include/ViennaRNA/probing/basic.h include/ViennaRNA/profiledist.h include/ViennaRNA/read_epars.h include/ViennaRNA/ribo.h +include/ViennaRNA/sampling/basic.h include/ViennaRNA/search/BoyerMoore.h include/ViennaRNA/sequence.h +include/ViennaRNA/sequences/alignments.h +include/ViennaRNA/sequences/alphabet.h +include/ViennaRNA/sequences/sequence.h +include/ViennaRNA/sequences/utils.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/structures/benchmark.h +include/ViennaRNA/structures/centroid.h +include/ViennaRNA/structures/dotbracket.h +include/ViennaRNA/structures/helix.h +include/ViennaRNA/structures/mea.h +include/ViennaRNA/structures/metrics.h +include/ViennaRNA/structures/pairtable.h +include/ViennaRNA/structures/problist.h +include/ViennaRNA/structures/shapes.h +include/ViennaRNA/structures/tree.h +include/ViennaRNA/structures/utils.h include/ViennaRNA/subopt.h +include/ViennaRNA/subopt/basic.h +include/ViennaRNA/subopt/gquad.h +include/ViennaRNA/subopt/wuchty.h +include/ViennaRNA/subopt/zuker.h include/ViennaRNA/subopt_zuker.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/log.h include/ViennaRNA/utils/strings.h include/ViennaRNA/utils/structures.h include/ViennaRNA/utils/svm.h include/ViennaRNA/utils/units.h include/ViennaRNA/vrna_config.h include/ViennaRNA/walk.h include/ViennaRNA/wrap_dlib.h -include/ViennaRNA/zscore.h +include/ViennaRNA/zscore/basic.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 +share/ViennaRNA/2Dlandscape.R +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_misc_special_hairpins.par +share/ViennaRNA/rna_mod_7DA_parameters.json +share/ViennaRNA/rna_mod_dihydrouridine_parameters.json +share/ViennaRNA/rna_mod_inosine_parameters.json +share/ViennaRNA/rna_mod_m5C_parameters.json +share/ViennaRNA/rna_mod_m6A_parameters.json +share/ViennaRNA/rna_mod_pseudouridine_parameters.json +share/ViennaRNA/rna_mod_purine_parameters.json +share/ViennaRNA/rna_mod_template_parameters.json +share/ViennaRNA/rna_turner1999.par +share/ViennaRNA/rna_turner2004.par +share/ViennaRNA/viennarna.bib share/man/man1/AnalyseDists.1.gz share/man/man1/AnalyseSeqs.1.gz share/man/man1/Kinfold.1.gz share/man/man1/RNA2Dfold.1.gz share/man/man1/RNALalifold.1.gz share/man/man1/RNALfold.1.gz share/man/man1/RNAPKplex.1.gz share/man/man1/RNAaliduplex.1.gz share/man/man1/RNAalifold.1.gz share/man/man1/RNAcofold.1.gz share/man/man1/RNAdistance.1.gz share/man/man1/RNAdos.1.gz share/man/man1/RNAduplex.1.gz share/man/man1/RNAeval.1.gz share/man/man1/RNAfold.1.gz share/man/man1/RNAforester.1.gz share/man/man1/RNAheat.1.gz share/man/man1/RNAinverse.1.gz share/man/man1/RNAlocmin.1.gz share/man/man1/RNAmultifold.1.gz share/man/man1/RNApaln.1.gz share/man/man1/RNAparconv.1.gz share/man/man1/RNApdist.1.gz share/man/man1/RNAplex.1.gz share/man/man1/RNAplfold.1.gz share/man/man1/RNAplot.1.gz share/man/man1/RNApvmin.1.gz share/man/man1/RNAsnoop.1.gz share/man/man1/RNAsubopt.1.gz share/man/man1/RNAup.1.gz share/man/man1/RNAxplorer.1.gz share/man/man1/ct2db.1.gz share/man/man1/kinwalker.1.gz -share/ViennaRNA/2Dlandscape.R -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_misc_special_hairpins.par -share/ViennaRNA/rna_mod_7DA_parameters.json -share/ViennaRNA/rna_mod_dihydrouridine_parameters.json -share/ViennaRNA/rna_mod_inosine_parameters.json -share/ViennaRNA/rna_mod_m6A_parameters.json -share/ViennaRNA/rna_mod_pseudouridine_parameters.json -share/ViennaRNA/rna_mod_purine_parameters.json -share/ViennaRNA/rna_mod_template_parameters.json -share/ViennaRNA/rna_turner1999.par -share/ViennaRNA/rna_turner2004.par -share/ViennaRNA/viennarna.bib