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Port details
viennarna Alignment tools for the structural analysis of RNA
2.4.14 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 2.4.14Version 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: 2020-01-06 04:17:49
SVN Revision: 522200
License: ViennaRNALicense
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (232 items)
  1. /usr/local/share/licenses/viennarna-2.4.14/catalog.mk
  2. /usr/local/share/licenses/viennarna-2.4.14/LICENSE
  3. /usr/local/share/licenses/viennarna-2.4.14/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/interior_loops.h
  95. include/ViennaRNA/inverse.h
  96. include/ViennaRNA/io/file_formats.h
  97. include/ViennaRNA/io/file_formats_msa.h
  98. include/ViennaRNA/io/utils.h
  99. include/ViennaRNA/json.h
  100. include/ViennaRNA/landscape/findpath.h
  101. include/ViennaRNA/landscape/move.h
  102. include/ViennaRNA/landscape/neighbor.h
  103. include/ViennaRNA/landscape/paths.h
  104. include/ViennaRNA/landscape/walk.h
  105. include/ViennaRNA/loop_energies.h
  106. include/ViennaRNA/loops/all.h
  107. include/ViennaRNA/loops/external.h
  108. include/ViennaRNA/loops/hairpin.h
  109. include/ViennaRNA/loops/internal.h
  110. include/ViennaRNA/loops/multibranch.h
  111. include/ViennaRNA/mfe.h
  112. include/ViennaRNA/mfe_window.h
  113. include/ViennaRNA/mm.h
  114. include/ViennaRNA/model.h
  115. include/ViennaRNA/move_set.h
  116. include/ViennaRNA/multibranch_loops.h
  117. include/ViennaRNA/naview.h
  118. include/ViennaRNA/neighbor.h
  119. include/ViennaRNA/pair_mat.h
  120. include/ViennaRNA/params.h
  121. include/ViennaRNA/params/basic.h
  122. include/ViennaRNA/params/constants.h
  123. include/ViennaRNA/params/convert.h
  124. include/ViennaRNA/params/default.h
  125. include/ViennaRNA/params/io.h
  126. include/ViennaRNA/part_func.h
  127. include/ViennaRNA/part_func_co.h
  128. include/ViennaRNA/part_func_up.h
  129. include/ViennaRNA/part_func_window.h
  130. include/ViennaRNA/perturbation_fold.h
  131. include/ViennaRNA/plex.h
  132. include/ViennaRNA/plot_aln.h
  133. include/ViennaRNA/plot_layouts.h
  134. include/ViennaRNA/plot_structure.h
  135. include/ViennaRNA/plot_utils.h
  136. include/ViennaRNA/plotting/RNApuzzler/RNApuzzler.h
  137. include/ViennaRNA/plotting/RNApuzzler/RNAturtle.h
  138. include/ViennaRNA/plotting/alignments.h
  139. include/ViennaRNA/plotting/layouts.h
  140. include/ViennaRNA/plotting/naview.h
  141. include/ViennaRNA/plotting/probabilities.h
  142. include/ViennaRNA/plotting/structures.h
  143. include/ViennaRNA/plotting/utils.h
  144. include/ViennaRNA/profiledist.h
  145. include/ViennaRNA/read_epars.h
  146. include/ViennaRNA/ribo.h
  147. include/ViennaRNA/search/BoyerMoore.h
  148. include/ViennaRNA/sequence.h
  149. include/ViennaRNA/snofold.h
  150. include/ViennaRNA/snoop.h
  151. include/ViennaRNA/stream_output.h
  152. include/ViennaRNA/string_utils.h
  153. include/ViennaRNA/stringdist.h
  154. include/ViennaRNA/structure_utils.h
  155. include/ViennaRNA/structured_domains.h
  156. include/ViennaRNA/subopt.h
  157. include/ViennaRNA/svm.h
  158. include/ViennaRNA/svm_utils.h
  159. include/ViennaRNA/treedist.h
  160. include/ViennaRNA/units.h
  161. include/ViennaRNA/unstructured_domains.h
  162. include/ViennaRNA/utils.h
  163. include/ViennaRNA/utils/alignments.h
  164. include/ViennaRNA/utils/basic.h
  165. include/ViennaRNA/utils/cpu.h
  166. include/ViennaRNA/utils/higher_order_functions.h
  167. include/ViennaRNA/utils/strings.h
  168. include/ViennaRNA/utils/structures.h
  169. include/ViennaRNA/utils/svm.h
  170. include/ViennaRNA/vrna_config.h
  171. include/ViennaRNA/walk.h
  172. include/g2.h
  173. include/g2_FIG.h
  174. include/g2_PS.h
  175. include/g2_X11.h
  176. include/g2_gd.h
  177. lib/libRNA.a
  178. lib/libg2.a
  179. libdata/pkgconfig/RNAlib2.pc
  180. man/man1/AnalyseDists.1.gz
  181. man/man1/AnalyseSeqs.1.gz
  182. man/man1/Kinfold.1.gz
  183. man/man1/RNA2Dfold.1.gz
  184. man/man1/RNALalifold.1.gz
  185. man/man1/RNALfold.1.gz
  186. man/man1/RNAPKplex.1.gz
  187. man/man1/RNAaliduplex.1.gz
  188. man/man1/RNAalifold.1.gz
  189. man/man1/RNAcofold.1.gz
  190. man/man1/RNAdistance.1.gz
  191. man/man1/RNAdos.1.gz
  192. man/man1/RNAduplex.1.gz
  193. man/man1/RNAeval.1.gz
  194. man/man1/RNAfold.1.gz
  195. man/man1/RNAforester.1.gz
  196. man/man1/RNAheat.1.gz
  197. man/man1/RNAinverse.1.gz
  198. man/man1/RNAlocmin.1.gz
  199. man/man1/RNApaln.1.gz
  200. man/man1/RNAparconv.1.gz
  201. man/man1/RNApdist.1.gz
  202. man/man1/RNAplex.1.gz
  203. man/man1/RNAplfold.1.gz
  204. man/man1/RNAplot.1.gz
  205. man/man1/RNApvmin.1.gz
  206. man/man1/RNAsnoop.1.gz
  207. man/man1/RNAsubopt.1.gz
  208. man/man1/RNAup.1.gz
  209. man/man1/ct2db.1.gz
  210. man/man1/kinwalker.1.gz
  211. share/ViennaRNA/2Dlandscape.R
  212. share/ViennaRNA/2Dlandscape_mfe.gri
  213. share/ViennaRNA/2Dlandscape_pf.gri
  214. share/ViennaRNA/DoxygenLayout.xml
  215. share/ViennaRNA/bin/RNAdesign.pl
  216. share/ViennaRNA/bin/b2mt.pl
  217. share/ViennaRNA/bin/cmount.pl
  218. share/ViennaRNA/bin/coloraln.pl
  219. share/ViennaRNA/bin/dpzoom.pl
  220. share/ViennaRNA/bin/mountain.pl
  221. share/ViennaRNA/bin/refold.pl
  222. share/ViennaRNA/bin/relplot.pl
  223. share/ViennaRNA/bin/rotate_ss.pl
  224. share/ViennaRNA/bin/switch.pl
  225. share/ViennaRNA/dna_mathews1999.par
  226. share/ViennaRNA/dna_mathews2004.par
  227. share/ViennaRNA/rna_andronescu2007.par
  228. share/ViennaRNA/rna_langdon2018.par
  229. share/ViennaRNA/rna_misc_special_hairpins.par
  230. share/ViennaRNA/rna_turner1999.par
  231. share/ViennaRNA/rna_turner2004.par
  232. share/ViennaRNA/viennarna.bib
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: pkg install viennarna
PKGNAME: viennarna
Flavors: there is no flavor information for this port.
distinfo:

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 : 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>=5.30.r1<5.31 : lang/perl5.30
  9. x11.pc : x11/libX11
  10. xext.pc : x11/libXext
Runtime dependencies:
  1. perl5>=5.30.r1<5.31 : lang/perl5.30
  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

USES:

Master Sites:
  1. https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/

Number of commits found: 6

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
06 Jan 2020 04:17:49
Original commit files touched by this commit  2.4.14
Revision:522200
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  2.4.13_2
Revision:516742
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  2.4.13_2
Revision:515671
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  2.4.13_1
Revision:507372
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  2.4.13
Revision:505049
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  2.4.13
Revision:505017
yuri search for other commits by this committer
New port: biology/viennarna: Alignment tools for the structural analysis of RNA

Number of commits found: 6

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