diff --git a/biology/viennarna/Makefile b/biology/viennarna/Makefile index f48bf3a3a2f2..fdc2daa5c55c 100644 --- a/biology/viennarna/Makefile +++ b/biology/viennarna/Makefile @@ -1,66 +1,74 @@ PORTNAME= viennarna -DISTVERSION= 2.7.0 -PORTREVISION= 3 +DISTVERSION= 2.7.2 CATEGORIES= biology 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/ \ https://github.com/ViennaRNA/ViennaRNA LICENSE= ViennaRNALicense LICENSE_NAME= Vienna RNA License LICENSE_FILE= ${WRKSRC}/COPYING LICENSE_PERMS= auto-accept dist-mirror pkg-mirror 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= libdlib.so:science/dlib-cpp \ 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 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+= -Wno-missing-template-arg-list-after-template-kw 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++||' ${WRKSRC}/RNAlib2.pc post-extract: # remove bundled dlib to ensure we use system version @${RM} -rf ${WRKSRC}/src/dlib-19.24 post-install: # remove stray files @${RM} ${STAGEDIR}/RNA/RNAconsensus.py @${RMDIR} ${STAGEDIR}/RNA +# tests as of 2.7.2: +# TOTAL: 83 +# PASS: 83 +# SKIP: 0 +# XFAIL: 0 +# FAIL: 0 +# XPASS: 0 +# ERROR: 0 + .include diff --git a/biology/viennarna/distinfo b/biology/viennarna/distinfo index df74d24eeb75..f76e21f9b282 100644 --- a/biology/viennarna/distinfo +++ b/biology/viennarna/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1730430067 -SHA256 (ViennaRNA-2.7.0.tar.gz) = 9a99fd68ed380894defb4d5e6a8a2871629270028cdf7f16f0a05da6e8c71473 -SIZE (ViennaRNA-2.7.0.tar.gz) = 53185587 +TIMESTAMP = 1782619651 +SHA256 (ViennaRNA-2.7.2.tar.gz) = 1ab5f4a4f76fc85a2243546088e45f5d85f2d7a56cc656e969b005cce9bfab5f +SIZE (ViennaRNA-2.7.2.tar.gz) = 67253851 diff --git a/biology/viennarna/files/patch-interfaces_Makefile.am b/biology/viennarna/files/patch-interfaces_Makefile.am new file mode 100644 index 000000000000..29f273242680 --- /dev/null +++ b/biology/viennarna/files/patch-interfaces_Makefile.am @@ -0,0 +1,10 @@ +--- interfaces/Makefile.am.orig 2026-04-14 04:48:56 UTC ++++ interfaces/Makefile.am +@@ -1,6 +1,6 @@ AM_CPPFLAGS = -I$(top_srcdir)/src + AM_CPPFLAGS = -I$(top_srcdir)/src + +-SUBDIRS = @PERL_INTERFACE@ @PYTHON_INTERFACE@ @PYTHON2_INTERFACE@ ++SUBDIRS = @PERL_INTERFACE@ @PYTHON_INTERFACE@ + + SOURCES = \ + RNA.i \ diff --git a/biology/viennarna/files/patch-m4_ac__rna__build__requirements.m4 b/biology/viennarna/files/patch-m4_ac__rna__build__requirements.m4 index 67d75c4a94c0..fc2b77cb3e08 100644 --- a/biology/viennarna/files/patch-m4_ac__rna__build__requirements.m4 +++ b/biology/viennarna/files/patch-m4_ac__rna__build__requirements.m4 @@ -1,43 +1,44 @@ # Use system dlib instead of bundled version # - Replace bundled dlib detection with pkg-config # - Use system dlib from science/dlib-cpp port # - Remove hardcoded paths to bundled dlib-19.24 ---- m4/ac_rna_build_requirements.m4.orig 2024-06-01 20:46:46 UTC +--- m4/ac_rna_build_requirements.m4.orig 2025-12-21 15:30:13 UTC +++ m4/ac_rna_build_requirements.m4 -@@ -253,28 +253,18 @@ AC_DEFUN([RNA_CHECK_DLIB], [ +@@ -358,29 +358,18 @@ AC_DEFUN([RNA_CHECK_DLIB], [ AC_DEFUN([RNA_CHECK_DLIB], [ AX_CXX_COMPILE_STDCXX(17, noext, mandatory) -- DLIB_VERSION=19.24 +- DLIB_VERSION=20.0 - DLIB_DIR="dlib-${DLIB_VERSION}" - DLIB_PATH="${srcdir}/src/${DLIB_DIR}" - DLIB_SRC_FILE="${DLIB_PATH}/dlib/all/source.cpp" - AC_RNA_TEST_FILE($DLIB_SRC_FILE,[],[ + dnl Check for system dlib using pkg-config + PKG_CHECK_MODULES([DLIB], [dlib-1 >= 19.0], [ + AC_DEFINE([HAVE_DLIB], [1], [Define if you have dlib]) + ], [ AC_MSG_ERROR([ -================================================= -Can't find dlib's source.cpp - -Make sure you've unpacked 'src/dlib-${DLIB_VERSION}.tar.bz2'! - -Usually, you only need to execute the following command: - -tar -xjf src/dlib-${DLIB_VERSION}.tar.bz2 -C src/ -================================================= -]) +dlib development library not found. Please install dlib-cpp port. + ]) ]) - AC_SUBST(DLIB_CPPFLAGS, "-I\$(top_srcdir)/src/${DLIB_DIR} -DDLIB_NO_GUI_SUPPORT") - AC_SUBST(DLIB_DIR) - AC_SUBST(DLIB_VERSION) +- + AC_SUBST(DLIB_CPPFLAGS, "${DLIB_CFLAGS} -DDLIB_NO_GUI_SUPPORT") + AC_SUBST(DLIB_LIBS, "${DLIB_LIBS}") - ]) + ## diff --git a/biology/viennarna/files/patch-m4_ac__rna__swig.m4 b/biology/viennarna/files/patch-m4_ac__rna__swig.m4 new file mode 100644 index 000000000000..ee200a37b6ce --- /dev/null +++ b/biology/viennarna/files/patch-m4_ac__rna__swig.m4 @@ -0,0 +1,65 @@ +--- m4/ac_rna_swig.m4.orig 2026-04-14 04:46:13 UTC ++++ m4/ac_rna_swig.m4 +@@ -18,7 +18,6 @@ AC_DEFUN([RNA_ENABLE_SWIG_INTERFACES],[ + + AM_CONDITIONAL(HAS_SWIG, test "x$has_swig" != "xno") + RNA_ENABLE_SWIG_PERL +- RNA_ENABLE_SWIG_PYTHON2 + RNA_ENABLE_SWIG_PYTHON + + ]) +@@ -130,54 +129,5 @@ AC_DEFUN([RNA_ENABLE_SWIG_PYTHON],[ + AC_CONFIG_FILES([interfaces/Python/Makefile interfaces/Python/version.i]) + AC_CONFIG_FILES([interfaces/Python/RNA/__init__.py]) + AC_CONFIG_FILES([setup.py setup.cfg pyproject.toml]) +- ]) +-]) +- +-AC_DEFUN([RNA_ENABLE_SWIG_PYTHON2],[ +- +- AX_REQUIRE_DEFINED([AX_PYTHON2_DEVEL]) +- +- RNA_ADD_PACKAGE([python2], +- [Python2 interface], +- [no],[],[], +- [${srcdir}/interfaces/Python2/Makefile.am]) +- +- +- ## check for python2 requirements +- AS_IF([test "x$with_python2" != "xno"],[ +- AS_IF([test "x$wants_swig" = "xno"],[ +- with_python2="no" +- ],[ +- ## if swig is not available, check whether we already have swig generated sources +- if test "x$has_swig" != "xyes" +- then +- AC_RNA_TEST_FILE([${srcdir}/interfaces/Python2/RNA_wrap.cpp],[],[ +- with_python2="no" +- ]) +- AC_RNA_TEST_FILE([${srcdir}/interfaces/Python2/RNA.py],[],[ +- with_python2="no" +- ]) +- fi +- ]) +- ]) +- +- AS_IF([test "x$with_python2" != "xno"],[ +- +- ## check for python2 config +- AX_PYTHON2_DEVEL +- +- if test "x$python2_enabled_but_failed" != "x" +- then +- with_python2="no" +- else +- AC_SUBST(PYTHON2DIR,$python2dir) +- AC_SUBST(PKGPYTHON2DIR,$pkgpython2dir) +- AC_SUBST(PYEXEC2DIR,$py2execdir) +- AC_SUBST(PKGPYEXEC2DIR,$pkgpy2execdir) +- +- AC_DEFINE([WITH_PYTHON2_INTERFACE], [1], [Create the Python 2.x interface to RNAlib]) +- AC_SUBST([PYTHON2_INTERFACE], [Python2]) +- AC_CONFIG_FILES([interfaces/Python2/Makefile interfaces/Python2/version.i]) +- fi + ]) + ]) diff --git a/biology/viennarna/pkg-plist b/biology/viennarna/pkg-plist index ee361b469586..99620f5550e6 100644 --- a/biology/viennarna/pkg-plist +++ b/biology/viennarna/pkg-plist @@ -1,315 +1,325 @@ 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/transform.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/math/functions.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/probing/strategy_deigan.h +include/ViennaRNA/probing/strategy_eddy.h +include/ViennaRNA/probing/strategy_nlogp.h +include/ViennaRNA/probing/strategy_zarringhalam.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/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/prior_probing_1M7_paired.data +share/ViennaRNA/prior_probing_1M7_unpaired.data +share/ViennaRNA/prior_probing_DMS_paired.data +share/ViennaRNA/prior_probing_DMS_unpaired.data 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