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Port details
viennarna Alignment tools for the structural analysis of RNA
2.6.4_2 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 2.6.4Version 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: 2024-03-02 20:35:56
Commit Hash: 5ebea8e
License: ViennaRNALicense
WWW:
https://www.tbi.univie.ac.at/RNA/
Description:
The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. RNA secondary structure prediction through energy minimization is the most used function in the package. We provide three kinds of dynamic programming algorithms for structure prediction: the minimum free energy algorithm of (Zuker & Stiegler 1981) which yields a single optimal structure, the partition function algorithm of (McCaskill 1990) which calculates base pair probabilities in the thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty et.al 1999) which generates all suboptimal structures within a given energy range of the optimal energy. For secondary structure comparison, the package contains several measures of distance (dissimilarities) using either string alignment or tree-editing (Shapiro & Zhang 1990). Finally, we provide an algorithm to design sequences with a predefined structure (inverse folding).
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (258 items)
Collapse this list.
  1. /usr/local/share/licenses/viennarna-2.6.4_2/catalog.mk
  2. /usr/local/share/licenses/viennarna-2.6.4_2/LICENSE
  3. /usr/local/share/licenses/viennarna-2.6.4_2/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/RNAmultifold
  24. bin/RNApaln
  25. bin/RNAparconv
  26. bin/RNApdist
  27. bin/RNAplex
  28. bin/RNAplfold
  29. bin/RNAplot
  30. bin/RNApvmin
  31. bin/RNAsnoop
  32. bin/RNAsubopt
  33. bin/RNAup
  34. bin/RNAxplorer
  35. bin/b2ct
  36. bin/ct2db
  37. bin/kinwalker
  38. bin/popt
  39. include/ViennaRNA/2Dfold.h
  40. include/ViennaRNA/2Dpfold.h
  41. include/ViennaRNA/LPfold.h
  42. include/ViennaRNA/Lfold.h
  43. include/ViennaRNA/MEA.h
  44. include/ViennaRNA/PKplex.h
  45. include/ViennaRNA/PS_dot.h
  46. include/ViennaRNA/ProfileAln.h
  47. include/ViennaRNA/RNAstruct.h
  48. include/ViennaRNA/ali_plex.h
  49. include/ViennaRNA/alifold.h
  50. include/ViennaRNA/aln_util.h
  51. include/ViennaRNA/alphabet.h
  52. include/ViennaRNA/boltzmann_sampling.h
  53. include/ViennaRNA/centroid.h
  54. include/ViennaRNA/char_stream.h
  55. include/ViennaRNA/cofold.h
  56. include/ViennaRNA/combinatorics.h
  57. include/ViennaRNA/commands.h
  58. include/ViennaRNA/concentrations.h
  59. include/ViennaRNA/constraints.h
  60. include/ViennaRNA/constraints/SHAPE.h
  61. include/ViennaRNA/constraints/basic.h
  62. include/ViennaRNA/constraints/hard.h
  63. include/ViennaRNA/constraints/ligand.h
  64. include/ViennaRNA/constraints/soft.h
  65. include/ViennaRNA/constraints/soft_special.h
  66. include/ViennaRNA/constraints_SHAPE.h
  67. include/ViennaRNA/constraints_hard.h
  68. include/ViennaRNA/constraints_ligand.h
  69. include/ViennaRNA/constraints_soft.h
  70. include/ViennaRNA/convert_epars.h
  71. include/ViennaRNA/data_structures.h
  72. include/ViennaRNA/datastructures/array.h
  73. include/ViennaRNA/datastructures/basic.h
  74. include/ViennaRNA/datastructures/char_stream.h
  75. include/ViennaRNA/datastructures/hash_tables.h
  76. include/ViennaRNA/datastructures/heap.h
  77. include/ViennaRNA/datastructures/lists.h
  78. include/ViennaRNA/datastructures/stream_output.h
  79. include/ViennaRNA/datastructures/string.h
  80. include/ViennaRNA/dist_vars.h
  81. include/ViennaRNA/dp_matrices.h
  82. include/ViennaRNA/duplex.h
  83. include/ViennaRNA/edit_cost.h
  84. include/ViennaRNA/energy_const.h
  85. include/ViennaRNA/energy_par.h
  86. include/ViennaRNA/equilibrium_probs.h
  87. include/ViennaRNA/eval.h
  88. include/ViennaRNA/exterior_loops.h
  89. include/ViennaRNA/file_formats.h
  90. include/ViennaRNA/file_formats_msa.h
  91. include/ViennaRNA/file_utils.h
  92. include/ViennaRNA/findpath.h
  93. include/ViennaRNA/fold.h
  94. include/ViennaRNA/fold_compound.h
  95. include/ViennaRNA/fold_vars.h
  96. include/ViennaRNA/gquad.h
  97. include/ViennaRNA/grammar.h
  98. include/ViennaRNA/hairpin_loops.h
  99. include/ViennaRNA/heat_capacity.h
  100. include/ViennaRNA/interior_loops.h
  101. include/ViennaRNA/inverse.h
  102. include/ViennaRNA/io/file_formats.h
  103. include/ViennaRNA/io/file_formats_msa.h
  104. include/ViennaRNA/io/utils.h
  105. include/ViennaRNA/json.h
  106. include/ViennaRNA/landscape/findpath.h
  107. include/ViennaRNA/landscape/move.h
  108. include/ViennaRNA/landscape/neighbor.h
  109. include/ViennaRNA/landscape/paths.h
  110. include/ViennaRNA/landscape/walk.h
  111. include/ViennaRNA/loop_energies.h
  112. include/ViennaRNA/loops/all.h
  113. include/ViennaRNA/loops/external.h
  114. include/ViennaRNA/loops/hairpin.h
  115. include/ViennaRNA/loops/internal.h
  116. include/ViennaRNA/loops/multibranch.h
  117. include/ViennaRNA/mconf.h
  118. include/ViennaRNA/mfe.h
  119. include/ViennaRNA/mfe_window.h
  120. include/ViennaRNA/mm.h
  121. include/ViennaRNA/model.h
  122. include/ViennaRNA/move_set.h
  123. include/ViennaRNA/multibranch_loops.h
  124. include/ViennaRNA/naview.h
  125. include/ViennaRNA/neighbor.h
  126. include/ViennaRNA/pair_mat.h
  127. include/ViennaRNA/params.h
  128. include/ViennaRNA/params/basic.h
  129. include/ViennaRNA/params/constants.h
  130. include/ViennaRNA/params/convert.h
  131. include/ViennaRNA/params/default.h
  132. include/ViennaRNA/params/io.h
  133. include/ViennaRNA/params/salt.h
  134. include/ViennaRNA/part_func.h
  135. include/ViennaRNA/part_func_co.h
  136. include/ViennaRNA/part_func_up.h
  137. include/ViennaRNA/part_func_window.h
  138. include/ViennaRNA/perturbation_fold.h
  139. include/ViennaRNA/pf_multifold.h
  140. include/ViennaRNA/pk_plex.h
  141. include/ViennaRNA/plex.h
  142. include/ViennaRNA/plot_aln.h
  143. include/ViennaRNA/plot_layouts.h
  144. include/ViennaRNA/plot_structure.h
  145. include/ViennaRNA/plot_utils.h
  146. include/ViennaRNA/plotting/RNApuzzler/RNApuzzler.h
  147. include/ViennaRNA/plotting/RNApuzzler/RNAturtle.h
  148. include/ViennaRNA/plotting/alignments.h
  149. include/ViennaRNA/plotting/layouts.h
  150. include/ViennaRNA/plotting/naview/naview.h
  151. include/ViennaRNA/plotting/probabilities.h
  152. include/ViennaRNA/plotting/structures.h
  153. include/ViennaRNA/plotting/utils.h
  154. include/ViennaRNA/profiledist.h
  155. include/ViennaRNA/read_epars.h
  156. include/ViennaRNA/ribo.h
  157. include/ViennaRNA/search/BoyerMoore.h
  158. include/ViennaRNA/sequence.h
  159. include/ViennaRNA/snofold.h
  160. include/ViennaRNA/snoop.h
  161. include/ViennaRNA/stream_output.h
  162. include/ViennaRNA/string_utils.h
  163. include/ViennaRNA/stringdist.h
  164. include/ViennaRNA/structure_utils.h
  165. include/ViennaRNA/structured_domains.h
  166. include/ViennaRNA/subopt.h
  167. include/ViennaRNA/subopt_zuker.h
  168. include/ViennaRNA/svm.h
  169. include/ViennaRNA/svm_utils.h
  170. include/ViennaRNA/treedist.h
  171. include/ViennaRNA/units.h
  172. include/ViennaRNA/unstructured_domains.h
  173. include/ViennaRNA/utils.h
  174. include/ViennaRNA/utils/alignments.h
  175. include/ViennaRNA/utils/basic.h
  176. include/ViennaRNA/utils/cpu.h
  177. include/ViennaRNA/utils/higher_order_functions.h
  178. include/ViennaRNA/utils/strings.h
  179. include/ViennaRNA/utils/structures.h
  180. include/ViennaRNA/utils/svm.h
  181. include/ViennaRNA/utils/units.h
  182. include/ViennaRNA/vrna_config.h
  183. include/ViennaRNA/walk.h
  184. include/ViennaRNA/wrap_dlib.h
  185. include/ViennaRNA/zscore.h
  186. include/g2.h
  187. include/g2_FIG.h
  188. include/g2_PS.h
  189. include/g2_X11.h
  190. include/g2_gd.h
  191. lib/libRNA.a
  192. lib/libg2.a
  193. libdata/pkgconfig/RNAlib2.pc
  194. share/man/man1/AnalyseDists.1.gz
  195. share/man/man1/AnalyseSeqs.1.gz
  196. share/man/man1/Kinfold.1.gz
  197. share/man/man1/RNA2Dfold.1.gz
  198. share/man/man1/RNALalifold.1.gz
  199. share/man/man1/RNALfold.1.gz
  200. share/man/man1/RNAPKplex.1.gz
  201. share/man/man1/RNAaliduplex.1.gz
  202. share/man/man1/RNAalifold.1.gz
  203. share/man/man1/RNAcofold.1.gz
  204. share/man/man1/RNAdistance.1.gz
  205. share/man/man1/RNAdos.1.gz
  206. share/man/man1/RNAduplex.1.gz
  207. share/man/man1/RNAeval.1.gz
  208. share/man/man1/RNAfold.1.gz
  209. share/man/man1/RNAforester.1.gz
  210. share/man/man1/RNAheat.1.gz
  211. share/man/man1/RNAinverse.1.gz
  212. share/man/man1/RNAlocmin.1.gz
  213. share/man/man1/RNAmultifold.1.gz
  214. share/man/man1/RNApaln.1.gz
  215. share/man/man1/RNAparconv.1.gz
  216. share/man/man1/RNApdist.1.gz
  217. share/man/man1/RNAplex.1.gz
  218. share/man/man1/RNAplfold.1.gz
  219. share/man/man1/RNAplot.1.gz
  220. share/man/man1/RNApvmin.1.gz
  221. share/man/man1/RNAsnoop.1.gz
  222. share/man/man1/RNAsubopt.1.gz
  223. share/man/man1/RNAup.1.gz
  224. share/man/man1/RNAxplorer.1.gz
  225. share/man/man1/ct2db.1.gz
  226. share/man/man1/kinwalker.1.gz
  227. share/ViennaRNA/2Dlandscape.R
  228. share/ViennaRNA/2Dlandscape_mfe.gri
  229. share/ViennaRNA/2Dlandscape_pf.gri
  230. share/ViennaRNA/DoxygenLayout.xml
  231. share/ViennaRNA/bin/RNAdesign.pl
  232. share/ViennaRNA/bin/b2mt.pl
  233. share/ViennaRNA/bin/cmount.pl
  234. share/ViennaRNA/bin/coloraln.pl
  235. share/ViennaRNA/bin/dpzoom.pl
  236. share/ViennaRNA/bin/mountain.pl
  237. share/ViennaRNA/bin/refold.pl
  238. share/ViennaRNA/bin/relplot.pl
  239. share/ViennaRNA/bin/rotate_ss.pl
  240. share/ViennaRNA/bin/switch.pl
  241. share/ViennaRNA/dna_mathews1999.par
  242. share/ViennaRNA/dna_mathews2004.par
  243. share/ViennaRNA/rna_andronescu2007.par
  244. share/ViennaRNA/rna_langdon2018.par
  245. share/ViennaRNA/rna_misc_special_hairpins.par
  246. share/ViennaRNA/rna_mod_7DA_parameters.json
  247. share/ViennaRNA/rna_mod_dihydrouridine_parameters.json
  248. share/ViennaRNA/rna_mod_inosine_parameters.json
  249. share/ViennaRNA/rna_mod_m6A_parameters.json
  250. share/ViennaRNA/rna_mod_pseudouridine_parameters.json
  251. share/ViennaRNA/rna_mod_purine_parameters.json
  252. share/ViennaRNA/rna_mod_template_parameters.json
  253. share/ViennaRNA/rna_turner1999.par
  254. share/ViennaRNA/rna_turner2004.par
  255. share/ViennaRNA/viennarna.bib
  256. @owner
  257. @group
  258. @mode
Collapse this list.
Dependency lines:
  • viennarna>0:biology/viennarna
Conflicts:
CONFLICTS_INSTALL:
  • g2
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
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
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: viennarna
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1699041043 SHA256 (ViennaRNA-2.6.4.tar.gz) = d1259ce5809601a12b0dc9b724ea2c55806fece80d8d83ad417ea8a2dd574982 SIZE (ViennaRNA-2.6.4.tar.gz) = 69749819

Packages (timestamps in pop-ups are UTC):
viennarna
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.6.4_22.6.4_22.4.172.6.4_22.6.4_2-2.4.17-
FreeBSD:13:quarterly2.6.4_12.6.4_12.5.12.6.4_12.6.4_1-2.6.4_12.6.4_1
FreeBSD:14:latest2.6.4_22.6.4_22.5.12.6.4_22.6.4_22.5.1-2.5.1
FreeBSD:14:quarterly2.6.4_12.6.4_1-2.6.4_12.6.4_1-2.6.4_12.6.4_1
FreeBSD:15:latest2.6.4_22.6.4_2n/a2.6.4_1n/a-2.6.4_12.6.4_1
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. bash : shells/bash
  2. lapacke>0 : math/lapacke
  3. libgd>0 : graphics/gd
  4. swig : devel/swig
  5. xxd : sysutils/xxd
  6. bison : devel/bison
  7. gfortran13 : lang/gcc13
  8. gmake>=4.3 : devel/gmake
  9. pkgconf>=1.3.0_1 : devel/pkgconf
  10. as : devel/binutils
  11. autoconf>=2.71 : devel/autoconf
  12. automake>=1.16.5 : devel/automake
  13. libtoolize : devel/libtool
  14. perl5>=5.36<5.37 : lang/perl5.36
  15. ice.pc : x11/libICE
  16. x11.pc : x11/libX11
  17. xext.pc : x11/libXext
Runtime dependencies:
  1. gfortran13 : lang/gcc13
  2. perl5>=5.36<5.37 : lang/perl5.36
  3. ice.pc : x11/libICE
  4. x11.pc : x11/libX11
  5. xext.pc : x11/libXext
  6. indexinfo : print/indexinfo
Library dependencies:
  1. libgmp.so : math/gmp
  2. libgsl.so : math/gsl
  3. liblapack.so : math/lapack
  4. libmpfr.so : math/mpfr
This port is required by:
for Build
  1. biology/locarna

Configuration Options:
===> The following configuration options are available for viennarna-2.6.4_2: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings
Options name:
biology_viennarna
USES:
autoreconf bison compiler:c++17-lang fortran gmake libtool localbase perl5 pkgconfig xorg
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_6_x/
Collapse this list.

Number of commits found: 27

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.6.4_2
02 Mar 2024 20:35:56
commit hash: 5ebea8ee63694705561188cea0516d42ee214df9commit hash: 5ebea8ee63694705561188cea0516d42ee214df9commit hash: 5ebea8ee63694705561188cea0516d42ee214df9commit hash: 5ebea8ee63694705561188cea0516d42ee214df9 files touched by this commit
Nuno Teixeira (eduardo) search for other commits by this committer
biology/viennarna: Move man pages to share/man

Approved by:	portmgr (blanket)
2.6.4_1
01 Jan 2024 11:49:51
commit hash: f2489ab0c721f5ec60a9f8074e904cfbe5d21dfdcommit hash: f2489ab0c721f5ec60a9f8074e904cfbe5d21dfdcommit hash: f2489ab0c721f5ec60a9f8074e904cfbe5d21dfdcommit hash: f2489ab0c721f5ec60a9f8074e904cfbe5d21dfd files touched by this commit
Thierry Thomas (thierry) search for other commits by this committer
*/*: chase the upgrade of BLAS / LAPACK to 3.12.0

PR:		275860
2.6.4
03 Nov 2023 22:02:11
commit hash: 3a75bcff89efbcf7a3ddfc734543b7645ae3fcf6commit hash: 3a75bcff89efbcf7a3ddfc734543b7645ae3fcf6commit hash: 3a75bcff89efbcf7a3ddfc734543b7645ae3fcf6commit hash: 3a75bcff89efbcf7a3ddfc734543b7645ae3fcf6 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/viennarna: update 2.6.3 → 2.6.4
2.6.3
18 Aug 2023 06:57:13
commit hash: 4b87c88e29a4bc388f2abb490e14c9497ee13226commit hash: 4b87c88e29a4bc388f2abb490e14c9497ee13226commit hash: 4b87c88e29a4bc388f2abb490e14c9497ee13226commit hash: 4b87c88e29a4bc388f2abb490e14c9497ee13226 files touched by this commit
Muhammad Moinur Rahman (bofh) search for other commits by this committer
biology/viennarna: Mark BROKEN on 14

Fails to compile with:
error: no member named 'bind2nd' in namespace 'std'

Approved by:	portmgr (blanket)
Sponsored by:	The FreeBSD Foundation
2.6.3
22 Jul 2023 08:55:02
commit hash: c8adede0fca784c2d1ca3affc161b4c6a8af8514commit hash: c8adede0fca784c2d1ca3affc161b4c6a8af8514commit hash: c8adede0fca784c2d1ca3affc161b4c6a8af8514commit hash: c8adede0fca784c2d1ca3affc161b4c6a8af8514 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/viennarna: Update 2.6.2 → 2.6.3
2.6.2_1
16 Jul 2023 21:38:39
commit hash: 3e4f91e805a3663672f9efdae1d4bb5b44d0c81acommit hash: 3e4f91e805a3663672f9efdae1d4bb5b44d0c81acommit hash: 3e4f91e805a3663672f9efdae1d4bb5b44d0c81acommit hash: 3e4f91e805a3663672f9efdae1d4bb5b44d0c81a files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/viennarna: Remove unnecessary library from .pc file; Correct pkg-descr
2.6.2
16 Jul 2023 20:50:49
commit hash: bb900f7c9a847717df9ed78f5e8ad47261a2921acommit hash: bb900f7c9a847717df9ed78f5e8ad47261a2921acommit hash: bb900f7c9a847717df9ed78f5e8ad47261a2921acommit hash: bb900f7c9a847717df9ed78f5e8ad47261a2921a files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/viennarna: Update 2.5.1 → 2.6.2
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
2.5.1
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.5.1
31 Jul 2022 08:12:49
commit hash: c7b296877cf88cf00873673bcdcb5109ab9f3f93commit hash: c7b296877cf88cf00873673bcdcb5109ab9f3f93commit hash: c7b296877cf88cf00873673bcdcb5109ab9f3f93commit hash: c7b296877cf88cf00873673bcdcb5109ab9f3f93 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/viennarna: Update 2.5.0 -> 2.5.1

Also add test target.
2.5.0
06 Feb 2022 18:36:07
commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Update CONFLICTS definitions in categories a* to c*

Update the CONFLICTS definitions of ports in the following categories:

- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters

An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.

There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.

Approved by:	portmgr (implicit)
2.5.0
25 Jan 2022 05:44:21
commit hash: 8615039c0cddc4eb7cc313105ad85ca7e1e0b0ffcommit hash: 8615039c0cddc4eb7cc313105ad85ca7e1e0b0ffcommit hash: 8615039c0cddc4eb7cc313105ad85ca7e1e0b0ffcommit hash: 8615039c0cddc4eb7cc313105ad85ca7e1e0b0ff files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/viennarna: Update 2.4.18 -> 2.5.0
2.4.18_2
12 Jan 2022 19:41:22
commit hash: 654acd81409d31495f8b1b11db61e1afbf640981commit hash: 654acd81409d31495f8b1b11db61e1afbf640981commit hash: 654acd81409d31495f8b1b11db61e1afbf640981commit hash: 654acd81409d31495f8b1b11db61e1afbf640981 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
math/gsl: bump portrevision of consumers after update to 2.7.1

PR:		260201
2.4.18_1
16 Jun 2021 19:31:27
commit hash: 63e653adaa7493aa98f17f9fbc834c0aed7e096ecommit hash: 63e653adaa7493aa98f17f9fbc834c0aed7e096ecommit hash: 63e653adaa7493aa98f17f9fbc834c0aed7e096ecommit hash: 63e653adaa7493aa98f17f9fbc834c0aed7e096e files touched by this commit
Tobias C. Berner (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)
2.4.18
24 Apr 2021 01:57:38
commit hash: 874e67eb5c6bf27198b1cd8fcf0ea02f3d2176e0commit hash: 874e67eb5c6bf27198b1cd8fcf0ea02f3d2176e0commit hash: 874e67eb5c6bf27198b1cd8fcf0ea02f3d2176e0commit hash: 874e67eb5c6bf27198b1cd8fcf0ea02f3d2176e0 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/viennarna: Update 2.4.17 -> 2.4.18
2.4.17
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
2.4.17
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
2.4.17
06 Dec 2020 20:14:53
Revision:557171Original commit files touched by this commit
yuri search for other commits by this committer
biology/viennarna: Update 2.4.16 -> 2.4.17
2.4.16
11 Nov 2020 23:27:39
Revision:554920Original commit files touched by this commit
yuri search for other commits by this committer
biology/viennarna: Update 2.4.15 -> 2.4.16
2.4.15
07 Sep 2020 21:49:08
Revision:547949Original commit files touched by this commit
yuri search for other commits by this committer
biology/viennarna: Update 2.4.14 -> 2.4.15
2.4.14_1
04 May 2020 21:31:39
Revision:533989Original commit files touched by this commit
dinoex search for other commits by this committer
- update libgd to 2.3.0
- new option RAQM
- resurrect deprecated gdlib-config
- bump dependend ports
2.4.14
06 Jan 2020 04:17:49
Revision:522200Original commit files touched by this commit
yuri search for other commits by this committer
biology/viennarna: Update 2.4.13 -> 2.4.14

Reported by:	repology
2.4.13_2
04 Nov 2019 21:08:20
Revision:516742Original commit files touched by this commit
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'.
2.4.13_2
25 Oct 2019 23:41:34
Revision:515671Original commit files touched by this commit
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
2.4.13_1
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit
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
2.4.13
24 Jun 2019 19:30:15
Revision:505049Original commit files touched by this commit
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.
2.4.13
24 Jun 2019 09:29:05
Revision:505017Original commit files touched by this commit
yuri search for other commits by this committer
New port: biology/viennarna: Alignment tools for the structural analysis of RNA

Number of commits found: 27