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Port details
viennarna Alignment tools for the structural analysis of RNA
2.4.18_1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.4.18_1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-06-24 09:29:23
Last Update: 2021-06-16 19:31:27
Commit Hash: 63e653a
License: ViennaRNALicense
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (239 items)
Collapse this list.
  1. /usr/local/share/licenses/viennarna-2.4.18_1/catalog.mk
  2. /usr/local/share/licenses/viennarna-2.4.18_1/LICENSE
  3. /usr/local/share/licenses/viennarna-2.4.18_1/ViennaRNALicense
  4. bin/AnalyseDists
  5. bin/AnalyseSeqs
  6. bin/Kinfold
  7. bin/RNA2Dfold
  8. bin/RNALalifold
  9. bin/RNALfold
  10. bin/RNAPKplex
  11. bin/RNAaliduplex
  12. bin/RNAalifold
  13. bin/RNAcofold
  14. bin/RNAdistance
  15. bin/RNAdos
  16. bin/RNAduplex
  17. bin/RNAeval
  18. bin/RNAfold
  19. bin/RNAforester
  20. bin/RNAheat
  21. bin/RNAinverse
  22. bin/RNAlocmin
  23. bin/RNApaln
  24. bin/RNAparconv
  25. bin/RNApdist
  26. bin/RNAplex
  27. bin/RNAplfold
  28. bin/RNAplot
  29. bin/RNApvmin
  30. bin/RNAsnoop
  31. bin/RNAsubopt
  32. bin/RNAup
  33. bin/b2ct
  34. bin/ct2db
  35. bin/kinwalker
  36. bin/popt
  37. include/ViennaRNA/2Dfold.h
  38. include/ViennaRNA/2Dpfold.h
  39. include/ViennaRNA/LPfold.h
  40. include/ViennaRNA/Lfold.h
  41. include/ViennaRNA/MEA.h
  42. include/ViennaRNA/PKplex.h
  43. include/ViennaRNA/PS_dot.h
  44. include/ViennaRNA/ProfileAln.h
  45. include/ViennaRNA/RNAstruct.h
  46. include/ViennaRNA/ali_plex.h
  47. include/ViennaRNA/alifold.h
  48. include/ViennaRNA/aln_util.h
  49. include/ViennaRNA/alphabet.h
  50. include/ViennaRNA/boltzmann_sampling.h
  51. include/ViennaRNA/centroid.h
  52. include/ViennaRNA/char_stream.h
  53. include/ViennaRNA/cofold.h
  54. include/ViennaRNA/combinatorics.h
  55. include/ViennaRNA/commands.h
  56. include/ViennaRNA/concentrations.h
  57. include/ViennaRNA/constraints.h
  58. include/ViennaRNA/constraints/SHAPE.h
  59. include/ViennaRNA/constraints/basic.h
  60. include/ViennaRNA/constraints/hard.h
  61. include/ViennaRNA/constraints/ligand.h
  62. include/ViennaRNA/constraints/soft.h
  63. include/ViennaRNA/constraints_SHAPE.h
  64. include/ViennaRNA/constraints_hard.h
  65. include/ViennaRNA/constraints_ligand.h
  66. include/ViennaRNA/constraints_soft.h
  67. include/ViennaRNA/convert_epars.h
  68. include/ViennaRNA/data_structures.h
  69. include/ViennaRNA/datastructures/basic.h
  70. include/ViennaRNA/datastructures/char_stream.h
  71. include/ViennaRNA/datastructures/hash_tables.h
  72. include/ViennaRNA/datastructures/heap.h
  73. include/ViennaRNA/datastructures/lists.h
  74. include/ViennaRNA/datastructures/stream_output.h
  75. include/ViennaRNA/dist_vars.h
  76. include/ViennaRNA/dp_matrices.h
  77. include/ViennaRNA/duplex.h
  78. include/ViennaRNA/edit_cost.h
  79. include/ViennaRNA/energy_const.h
  80. include/ViennaRNA/energy_par.h
  81. include/ViennaRNA/equilibrium_probs.h
  82. include/ViennaRNA/eval.h
  83. include/ViennaRNA/exterior_loops.h
  84. include/ViennaRNA/file_formats.h
  85. include/ViennaRNA/file_formats_msa.h
  86. include/ViennaRNA/file_utils.h
  87. include/ViennaRNA/findpath.h
  88. include/ViennaRNA/fold.h
  89. include/ViennaRNA/fold_compound.h
  90. include/ViennaRNA/fold_vars.h
  91. include/ViennaRNA/gquad.h
  92. include/ViennaRNA/grammar.h
  93. include/ViennaRNA/hairpin_loops.h
  94. include/ViennaRNA/heat_capacity.h
  95. include/ViennaRNA/interior_loops.h
  96. include/ViennaRNA/inverse.h
  97. include/ViennaRNA/io/file_formats.h
  98. include/ViennaRNA/io/file_formats_msa.h
  99. include/ViennaRNA/io/utils.h
  100. include/ViennaRNA/json.h
  101. include/ViennaRNA/landscape/findpath.h
  102. include/ViennaRNA/landscape/move.h
  103. include/ViennaRNA/landscape/neighbor.h
  104. include/ViennaRNA/landscape/paths.h
  105. include/ViennaRNA/landscape/walk.h
  106. include/ViennaRNA/loop_energies.h
  107. include/ViennaRNA/loops/all.h
  108. include/ViennaRNA/loops/external.h
  109. include/ViennaRNA/loops/hairpin.h
  110. include/ViennaRNA/loops/internal.h
  111. include/ViennaRNA/loops/multibranch.h
  112. include/ViennaRNA/mfe.h
  113. include/ViennaRNA/mfe_window.h
  114. include/ViennaRNA/mm.h
  115. include/ViennaRNA/model.h
  116. include/ViennaRNA/move_set.h
  117. include/ViennaRNA/multibranch_loops.h
  118. include/ViennaRNA/naview.h
  119. include/ViennaRNA/neighbor.h
  120. include/ViennaRNA/pair_mat.h
  121. include/ViennaRNA/params.h
  122. include/ViennaRNA/params/basic.h
  123. include/ViennaRNA/params/constants.h
  124. include/ViennaRNA/params/convert.h
  125. include/ViennaRNA/params/default.h
  126. include/ViennaRNA/params/io.h
  127. include/ViennaRNA/part_func.h
  128. include/ViennaRNA/part_func_co.h
  129. include/ViennaRNA/part_func_up.h
  130. include/ViennaRNA/part_func_window.h
  131. include/ViennaRNA/perturbation_fold.h
  132. include/ViennaRNA/pk_plex.h
  133. include/ViennaRNA/plex.h
  134. include/ViennaRNA/plot_aln.h
  135. include/ViennaRNA/plot_layouts.h
  136. include/ViennaRNA/plot_structure.h
  137. include/ViennaRNA/plot_utils.h
  138. include/ViennaRNA/plotting/RNApuzzler/RNApuzzler.h
  139. include/ViennaRNA/plotting/RNApuzzler/RNAturtle.h
  140. include/ViennaRNA/plotting/alignments.h
  141. include/ViennaRNA/plotting/layouts.h
  142. include/ViennaRNA/plotting/naview.h
  143. include/ViennaRNA/plotting/probabilities.h
  144. include/ViennaRNA/plotting/structures.h
  145. include/ViennaRNA/plotting/utils.h
  146. include/ViennaRNA/profiledist.h
  147. include/ViennaRNA/read_epars.h
  148. include/ViennaRNA/ribo.h
  149. include/ViennaRNA/search/BoyerMoore.h
  150. include/ViennaRNA/sequence.h
  151. include/ViennaRNA/snofold.h
  152. include/ViennaRNA/snoop.h
  153. include/ViennaRNA/stream_output.h
  154. include/ViennaRNA/string_utils.h
  155. include/ViennaRNA/stringdist.h
  156. include/ViennaRNA/structure_utils.h
  157. include/ViennaRNA/structured_domains.h
  158. include/ViennaRNA/subopt.h
  159. include/ViennaRNA/svm.h
  160. include/ViennaRNA/svm_utils.h
  161. include/ViennaRNA/treedist.h
  162. include/ViennaRNA/units.h
  163. include/ViennaRNA/unstructured_domains.h
  164. include/ViennaRNA/utils.h
  165. include/ViennaRNA/utils/alignments.h
  166. include/ViennaRNA/utils/basic.h
  167. include/ViennaRNA/utils/cpu.h
  168. include/ViennaRNA/utils/higher_order_functions.h
  169. include/ViennaRNA/utils/strings.h
  170. include/ViennaRNA/utils/structures.h
  171. include/ViennaRNA/utils/svm.h
  172. include/ViennaRNA/utils/units.h
  173. include/ViennaRNA/vrna_config.h
  174. include/ViennaRNA/walk.h
  175. include/ViennaRNA/zscore.h
  176. include/g2.h
  177. include/g2_FIG.h
  178. include/g2_PS.h
  179. include/g2_X11.h
  180. include/g2_gd.h
  181. lib/libRNA.a
  182. lib/libg2.a
  183. libdata/pkgconfig/RNAlib2.pc
  184. man/man1/AnalyseDists.1.gz
  185. man/man1/AnalyseSeqs.1.gz
  186. man/man1/Kinfold.1.gz
  187. man/man1/RNA2Dfold.1.gz
  188. man/man1/RNALalifold.1.gz
  189. man/man1/RNALfold.1.gz
  190. man/man1/RNAPKplex.1.gz
  191. man/man1/RNAaliduplex.1.gz
  192. man/man1/RNAalifold.1.gz
  193. man/man1/RNAcofold.1.gz
  194. man/man1/RNAdistance.1.gz
  195. man/man1/RNAdos.1.gz
  196. man/man1/RNAduplex.1.gz
  197. man/man1/RNAeval.1.gz
  198. man/man1/RNAfold.1.gz
  199. man/man1/RNAforester.1.gz
  200. man/man1/RNAheat.1.gz
  201. man/man1/RNAinverse.1.gz
  202. man/man1/RNAlocmin.1.gz
  203. man/man1/RNApaln.1.gz
  204. man/man1/RNAparconv.1.gz
  205. man/man1/RNApdist.1.gz
  206. man/man1/RNAplex.1.gz
  207. man/man1/RNAplfold.1.gz
  208. man/man1/RNAplot.1.gz
  209. man/man1/RNApvmin.1.gz
  210. man/man1/RNAsnoop.1.gz
  211. man/man1/RNAsubopt.1.gz
  212. man/man1/RNAup.1.gz
  213. man/man1/ct2db.1.gz
  214. man/man1/kinwalker.1.gz
  215. share/ViennaRNA/2Dlandscape.R
  216. share/ViennaRNA/2Dlandscape_mfe.gri
  217. share/ViennaRNA/2Dlandscape_pf.gri
  218. share/ViennaRNA/DoxygenLayout.xml
  219. share/ViennaRNA/bin/RNAdesign.pl
  220. share/ViennaRNA/bin/b2mt.pl
  221. share/ViennaRNA/bin/cmount.pl
  222. share/ViennaRNA/bin/coloraln.pl
  223. share/ViennaRNA/bin/dpzoom.pl
  224. share/ViennaRNA/bin/mountain.pl
  225. share/ViennaRNA/bin/refold.pl
  226. share/ViennaRNA/bin/relplot.pl
  227. share/ViennaRNA/bin/rotate_ss.pl
  228. share/ViennaRNA/bin/switch.pl
  229. share/ViennaRNA/dna_mathews1999.par
  230. share/ViennaRNA/dna_mathews2004.par
  231. share/ViennaRNA/rna_andronescu2007.par
  232. share/ViennaRNA/rna_langdon2018.par
  233. share/ViennaRNA/rna_misc_special_hairpins.par
  234. share/ViennaRNA/rna_turner1999.par
  235. share/ViennaRNA/rna_turner2004.par
  236. share/ViennaRNA/viennarna.bib
  237. @owner
  238. @group
  239. @mode
Collapse this list.
Dependency lines:
  • viennarna>0:biology/viennarna
To install the port: cd /usr/ports/biology/viennarna/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/viennarna
  • pkg install viennarna
PKGNAME: viennarna
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
viennarna
ABIlatestquarterly
FreeBSD:11:aarch64-2.4.14_1
FreeBSD:11:amd642.4.18_12.4.18_1
FreeBSD:11:armv6-2.4.14_1
FreeBSD:11:i3862.4.18_12.4.18_1
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-2.4.18_1
FreeBSD:12:amd642.4.18_12.4.18_1
FreeBSD:12:armv6-2.4.15
FreeBSD:12:armv7-2.4.15
FreeBSD:12:i3862.4.18_12.4.18_1
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64-2.4.17
FreeBSD:13:aarch642.4.172.4.18_1
FreeBSD:13:amd642.4.18_12.4.18_1
FreeBSD:13:armv62.4.172.4.17
FreeBSD:13:armv72.4.172.4.17
FreeBSD:13:i3862.4.18_12.4.18_1
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc642.4.172.4.18_1
FreeBSD:14:aarch642.4.18_1-
FreeBSD:14:amd642.4.18_1-
FreeBSD:14:armv62.4.17-
FreeBSD:14:armv72.4.17-
FreeBSD:14:i3862.4.18_1-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc642.4.17-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. bash : shells/bash
  2. libgd>0 : graphics/gd
  3. gmake>=4.3 : devel/gmake
  4. pkgconf>=1.3.0_1 : devel/pkgconf
  5. autoconf>=2.69 : devel/autoconf
  6. automake>=1.16.1 : devel/automake
  7. libtoolize : devel/libtool
  8. perl5>=5.32.r0<5.33 : lang/perl5.32
  9. x11.pc : x11/libX11
  10. xext.pc : x11/libXext
Runtime dependencies:
  1. perl5>=5.32.r0<5.33 : lang/perl5.32
  2. x11.pc : x11/libX11
  3. xext.pc : x11/libXext
  4. indexinfo : print/indexinfo
Library dependencies:
  1. libgmp.so : math/gmp
  2. libgsl.so : math/gsl
  3. libmpfr.so : math/mpfr
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/
Collapse this list.

Number of commits found: 14

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
16 Jun 2021 19:31:27
 files touched by this commit commit hash:63e653adaa7493aa98f17f9fbc834c0aed7e096e  2.4.18_1
tcberner search for other commits by this committer
math/gsl: update to 2.7

From [1]

* What is new in gsl-2.7:
	* fixed doc bug for gsl_histogram_min_bin (lhcsky at 163.com)
	* fixed bug #60335 (spmatrix test failure, J. Lamb)
	* fixed bug #36577
	* clarified documentation on interpolation accelerators (V. Krishnan)
	* fixed bug #45521 (erroneous GSL_ERROR_NULL in ode-initval2, thanks to M.
Sitte)
	* fixed doc bug #59758
	* fixed bug #58202 (rstat median for n=5)
	* added support for native C complex number types in gsl_complex
	   when using a C11 compiler
	* upgraded to autoconf 2.71, automake 1.16.3, libtool 2.4.6
(Only the first 15 lines of the commit message are shown above View all of this commit message)
24 Apr 2021 01:57:38
 files touched by this commit commit hash:874e67eb5c6bf27198b1cd8fcf0ea02f3d2176e0  2.4.18
yuri search for other commits by this committer
biology/viennarna: Update 2.4.17 -> 2.4.18
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  2.4.17
mat search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  2.4.17
mat search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
06 Dec 2020 20:14:53
Original commit files touched by this commit Revision:557171  2.4.17
yuri search for other commits by this committer
biology/viennarna: Update 2.4.16 -> 2.4.17
11 Nov 2020 23:27:39
Original commit files touched by this commit Revision:554920  2.4.16
yuri search for other commits by this committer
biology/viennarna: Update 2.4.15 -> 2.4.16
07 Sep 2020 21:49:08
Original commit files touched by this commit Revision:547949  2.4.15
yuri search for other commits by this committer
biology/viennarna: Update 2.4.14 -> 2.4.15
04 May 2020 21:31:39
Original commit files touched by this commit Revision:533989  2.4.14_1
dinoex search for other commits by this committer
- update libgd to 2.3.0
- new option RAQM
- resurrect deprecated gdlib-config
- bump dependend ports
06 Jan 2020 04:17:49
Original commit files touched by this commit Revision:522200  2.4.14
yuri search for other commits by this committer
biology/viennarna: Update 2.4.13 -> 2.4.14

Reported by:	repology
04 Nov 2019 21:08:20
Original commit files touched by this commit Revision:516742  2.4.13_2
zeising search for other commits by this committer
Add USES=xorg USES=gl, ports categories b

Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories
starting with 'b'.
25 Oct 2019 23:41:34
Original commit files touched by this commit Revision:515671  2.4.13_2
tcberner search for other commits by this committer
math/gsl: update to 2.6

- math/p5-Math-GSL does not seem to have any upstream activity to make it work
with this version -> mark it broken
  - this also breaks the two consumers of this port

- biology/gemma: has a conflict with cblas, and is makred broken.

PR:		241363
Exp-run by:	antoine
26 Jul 2019 20:46:57
Original commit files touched by this commit Revision:507372  2.4.13_1
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
24 Jun 2019 19:30:15
Original commit files touched by this commit Revision:505049  2.4.13
yuri search for other commits by this committer
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.
24 Jun 2019 09:29:05
Original commit files touched by this commit Revision:505017  2.4.13
yuri search for other commits by this committer
New port: biology/viennarna: Alignment tools for the structural analysis of RNA

Number of commits found: 14