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Port details
paml Phylogenetic Analysis by Maximum Likelihood (PAML)
4.10.7 biology on this many watch lists=1 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 4.10.7Version of this port present on the latest quarterly branch.
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2000-07-10 00:21:06
Last Update: 2023-07-08 03:46:53
Commit Hash: 5fc3014
People watching this port, also watch:: tmux, font-misc-meltho, xclock, tk85, p5-Net-HTTP
License: GPLv3
WWW:
http://abacus.gene.ucl.ac.uk/software/paml.html
Description:
Phylogenetic Analysis by Maximum Likelihood (PAML) PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is not good for tree making. It may be used to estimate parameters and test hypotheses for the study the evolutionary process using trees reconstructed with programs such as PAUP*, PHYLIP, MOLPHY, PhyML, or RaxML.
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 (218 items)
Collapse this list.
  1. /usr/local/share/licenses/paml-4.10.7/catalog.mk
  2. /usr/local/share/licenses/paml-4.10.7/LICENSE
  3. /usr/local/share/licenses/paml-4.10.7/GPLv3
  4. bin/baseml
  5. bin/basemlg
  6. bin/chi2
  7. bin/codeml
  8. bin/evolver
  9. bin/evolverNSbranches
  10. bin/evolverNSbranchsites
  11. bin/evolverNSsites
  12. bin/infinitesites
  13. bin/mcmctree
  14. bin/pamp
  15. bin/yn00
  16. share/doc/paml/MCMCtree.Tutorials.pdf
  17. share/doc/paml/README.md
  18. share/doc/paml/pamlDOC.pdf
  19. share/doc/paml/pamlFAQs.pdf
  20. share/doc/paml/pamlHistory.txt
  21. share/examples/paml/3s.trees
  22. share/examples/paml/4s.trees
  23. share/examples/paml/5s.trees
  24. share/examples/paml/6s.trees
  25. share/examples/paml/9s.trees
  26. share/examples/paml/CladeModelCD/ECP_EDN_15.nuc
  27. share/examples/paml/CladeModelCD/PAMLCladeModelCDnotes.pdf
  28. share/examples/paml/CladeModelCD/codeml.CladeC.ctl
  29. share/examples/paml/CladeModelCD/codeml.CladeD.ctl
  30. share/examples/paml/CladeModelCD/tree.txt
  31. share/examples/paml/DatingSoftBound/BF.Clock23.xlsx
  32. share/examples/paml/DatingSoftBound/BFdriverDOC.pdf
  33. share/examples/paml/DatingSoftBound/FixedDsClock23.txt
  34. share/examples/paml/DatingSoftBound/README.BayesFactor.txt
  35. share/examples/paml/DatingSoftBound/README.txt
  36. share/examples/paml/DatingSoftBound/bf1/mcmctree.ctl
  37. share/examples/paml/DatingSoftBound/bf2/mcmctree.ctl
  38. share/examples/paml/DatingSoftBound/mcmctree.Infinitesites.ctl
  39. share/examples/paml/DatingSoftBound/mcmctree.ctl
  40. share/examples/paml/DatingSoftBound/mtCDNApri.trees
  41. share/examples/paml/DatingSoftBound/mtCDNApri123.txt
  42. share/examples/paml/GeneticCode.txt
  43. share/examples/paml/HIVNSsites/HIVenvSweden.trees
  44. share/examples/paml/HIVNSsites/HIVenvSweden.txt
  45. share/examples/paml/HIVNSsites/HIVenvSweden4s.trees
  46. share/examples/paml/HIVNSsites/HIVenvSweden4s.txt
  47. share/examples/paml/HIVNSsites/README.txt
  48. share/examples/paml/HIVNSsites/codeml.ctl
  49. share/examples/paml/MCaa.dat
  50. share/examples/paml/MCaa.txt
  51. share/examples/paml/MCbase.dat
  52. share/examples/paml/MCbase.txt
  53. share/examples/paml/MCbaseRandomTree.dat
  54. share/examples/paml/MCbaseRandomTree.txt
  55. share/examples/paml/MCcodon.dat
  56. share/examples/paml/MCcodon.txt
  57. share/examples/paml/MHC.Swanson2002MBE/README.txt
  58. share/examples/paml/MHC.Swanson2002MBE/bigmhc.phy
  59. share/examples/paml/MHC.Swanson2002MBE/bigmhc.trees
  60. share/examples/paml/MHC.Swanson2002MBE/codeml.ctl
  61. share/examples/paml/MouseLemurs/MouseLemurs.aa
  62. share/examples/paml/MouseLemurs/MouseLemurs.nuc
  63. share/examples/paml/MouseLemurs/MouseLemurs.trees
  64. share/examples/paml/MouseLemurs/MouseLemurs123.nuc
  65. share/examples/paml/MouseLemurs/README.txt
  66. share/examples/paml/MouseLemurs/README2.txt
  67. share/examples/paml/MouseLemurs/aaml.ctl
  68. share/examples/paml/MouseLemurs/aaml2.ctl
  69. share/examples/paml/MouseLemurs/baseml.ctl
  70. share/examples/paml/MouseLemurs/baseml2.ctl
  71. share/examples/paml/MouseLemurs/codeml.ctl
  72. share/examples/paml/MouseLemurs/codonml.ctl
  73. share/examples/paml/MouseLemurs/codonml2.ctl
  74. share/examples/paml/MouseLemurs/mtmam.dat
  75. share/examples/paml/README.txt
  76. share/examples/paml/Technical/Pt/eigenQREV.pdf
  77. share/examples/paml/Technical/Pt/testPMat.c
  78. share/examples/paml/Technical/Simulation/Codon/MCcodonNSbranches.dat
  79. share/examples/paml/Technical/Simulation/Codon/MCcodonNSbranchsites.dat
  80. share/examples/paml/Technical/Simulation/Codon/MCcodonNSclade.dat
  81. share/examples/paml/Technical/Simulation/Codon/MCcodonNSsites.dat
  82. share/examples/paml/Technical/Simulation/Codon/PositiveSites.c
  83. share/examples/paml/Technical/Simulation/Codon/README.txt
  84. share/examples/paml/Technical/Simulation/Codon/codeml.ctl
  85. share/examples/paml/Technical/Simulation/multiruns.c
  86. share/examples/paml/Technical/Simulation/multiruns.txt
  87. share/examples/paml/TipDate.FluH1/H1.Beast.Nulldata.xml
  88. share/examples/paml/TipDate.FluH1/H1.Beast.xml
  89. share/examples/paml/TipDate.FluH1/H1.NodeNumbers.tre
  90. share/examples/paml/TipDate.FluH1/H1.nexus
  91. share/examples/paml/TipDate.FluH1/H1.tre
  92. share/examples/paml/TipDate.FluH1/H1.txt
  93. share/examples/paml/TipDate.FluH1/baseml.ctl
  94. share/examples/paml/TipDate.FluH1/commands.txt
  95. share/examples/paml/TipDate.FluH1/in.BV.HKYG5
  96. share/examples/paml/TipDate.FluH1/mcmctreeClock1.ctl
  97. share/examples/paml/TipDate.FluH1/mcmctreeClock2.ctl
  98. share/examples/paml/TipDate.FluH1/mcmctreeClock3.ctl
  99. share/examples/paml/TipDate.HIV2/HIV2ge.tre
  100. share/examples/paml/TipDate.HIV2/HIV2ge.txt
  101. share/examples/paml/TipDate.HIV2/README.txt
  102. share/examples/paml/TipDate.HIV2/baseml.ctl
  103. share/examples/paml/TipDate.HIV2/in.BV.HKYG5
  104. share/examples/paml/TipDate.HIV2/mcmctree.ExactlnL.ctl
  105. share/examples/paml/TipDate.HIV2/mcmctree.ctl
  106. share/examples/paml/YN00abglobin.result.txt
  107. share/examples/paml/aaml.ctl
  108. share/examples/paml/abglobin.aa
  109. share/examples/paml/abglobin.nuc
  110. share/examples/paml/abglobin.trees
  111. share/examples/paml/baseml.ctl
  112. share/examples/paml/brown.nuc
  113. share/examples/paml/brown.rooted.trees
  114. share/examples/paml/brown.trees
  115. share/examples/paml/codeml.ctl
  116. share/examples/paml/codonml.ctl
  117. share/examples/paml/dNdSGene1.nuc
  118. share/examples/paml/dat/MtZoa.dat
  119. share/examples/paml/dat/cpREV10.dat
  120. share/examples/paml/dat/cpREV64.dat
  121. share/examples/paml/dat/dayhoff-dcmut.dat
  122. share/examples/paml/dat/dayhoff.dat
  123. share/examples/paml/dat/g1974a.dat
  124. share/examples/paml/dat/g1974c.dat
  125. share/examples/paml/dat/g1974p.dat
  126. share/examples/paml/dat/g1974v.dat
  127. share/examples/paml/dat/grantham.dat
  128. share/examples/paml/dat/jones-dcmut.dat
  129. share/examples/paml/dat/jones.dat
  130. share/examples/paml/dat/lg.dat
  131. share/examples/paml/dat/miyata.dat
  132. share/examples/paml/dat/mtArt.dat
  133. share/examples/paml/dat/mtREV24.dat
  134. share/examples/paml/dat/mtmam.dat
  135. share/examples/paml/dat/wag.dat
  136. share/examples/paml/dating-cross-bracing/6s-bracing.trees
  137. share/examples/paml/dating-cross-bracing/6s.trees
  138. share/examples/paml/dating-cross-bracing/MCbase-6s.txt
  139. share/examples/paml/dating-cross-bracing/mc.txt
  140. share/examples/paml/dating-cross-bracing/mcmctree-bracing.ctl
  141. share/examples/paml/dating-cross-bracing/mcmctree.ctl
  142. share/examples/paml/horai.nuc
  143. share/examples/paml/horai.trees
  144. share/examples/paml/lysin/README.txt
  145. share/examples/paml/lysin/RasMol.txt
  146. share/examples/paml/lysin/SiteNumbering.txt
  147. share/examples/paml/lysin/codeml.ctl
  148. share/examples/paml/lysin/codemlYangSwanson2002.ctl
  149. share/examples/paml/lysin/lysin.nuc
  150. share/examples/paml/lysin/lysin.trees
  151. share/examples/paml/lysin/lysinYangSwanson2002.nuc
  152. share/examples/paml/lysozyme/README.txt
  153. share/examples/paml/lysozyme/codeml.ctl
  154. share/examples/paml/lysozyme/lysozymeLarge.ctl
  155. share/examples/paml/lysozyme/lysozymeLarge.nuc
  156. share/examples/paml/lysozyme/lysozymeLarge.trees
  157. share/examples/paml/lysozyme/lysozymeSmall.ctl
  158. share/examples/paml/lysozyme/lysozymeSmall.nuc
  159. share/examples/paml/lysozyme/lysozymeSmall.trees
  160. share/examples/paml/lysozyme/lysozymeSmall.txt
  161. share/examples/paml/mcmctree.ctl
  162. share/examples/paml/mtCDNA/AAcodon.result.txt
  163. share/examples/paml/mtCDNA/README.txt
  164. share/examples/paml/mtCDNA/codeml.AAcodon.ctl
  165. share/examples/paml/mtCDNA/codeml.ctl
  166. share/examples/paml/mtCDNA/miyata.dat
  167. share/examples/paml/mtCDNA/mtCDNAmam.nuc
  168. share/examples/paml/mtCDNA/mtCDNAmam.trees
  169. share/examples/paml/mtCDNA/mtCDNApri.aa
  170. share/examples/paml/mtCDNA/mtCDNApri.nuc
  171. share/examples/paml/mtCDNA/mtCDNApri.trees
  172. share/examples/paml/mtCDNAape/2s.trees
  173. share/examples/paml/mtCDNAape/OmegaAA.dat
  174. share/examples/paml/mtCDNAape/README.txt
  175. share/examples/paml/mtCDNAape/codeml.HC.ctl
  176. share/examples/paml/mtCDNAape/codeml.ctl
  177. share/examples/paml/mtCDNAape/mtCDNA.HC.txt
  178. share/examples/paml/mtCDNAape/mtCDNAape.trees
  179. share/examples/paml/mtCDNAape/mtCDNAape.txt
  180. share/examples/paml/mtprim9.nuc
  181. share/examples/paml/myxo/codeml-M0.ctl
  182. share/examples/paml/myxo/myxovirus.aln
  183. share/examples/paml/myxo/myxovirus.tree
  184. share/examples/paml/ndata/4s-ndata-maintree.trees
  185. share/examples/paml/ndata/4s-ndata.trees
  186. share/examples/paml/ndata/4s-ndata.txt
  187. share/examples/paml/ndata/4s.trees
  188. share/examples/paml/ndata/5s-mc.trees
  189. share/examples/paml/ndata/MCbase.txt
  190. share/examples/paml/ndata/README.txt
  191. share/examples/paml/ndata/baseml-ndata-maintree-ml.ctl
  192. share/examples/paml/ndata/baseml-ndata-maintree.ctl
  193. share/examples/paml/ndata/baseml-ndata.ctl
  194. share/examples/paml/ndata/baseml.ctl
  195. share/examples/paml/ndata/codeml-ndata-maintree-ml.ctl
  196. share/examples/paml/ndata/codeml-ndata-maintree.ctl
  197. share/examples/paml/ndata/codeml-ndata.ctl
  198. share/examples/paml/ndata/mc.txt
  199. share/examples/paml/nhomo/README.txt
  200. share/examples/paml/nhomo/baseml-nhomo4.ctl
  201. share/examples/paml/nhomo/baseml-nhomo5.ctl
  202. share/examples/paml/nhomo/data-MCU0.95-rep1.txt
  203. share/examples/paml/nhomo/mlb-nhomo4.txt
  204. share/examples/paml/nhomo/mlb-nhomo5.txt
  205. share/examples/paml/nhomo/rst-nhomo4.txt
  206. share/examples/paml/nhomo/rst-nhomo5.txt
  207. share/examples/paml/nhomo/tree-nhomo4.txt
  208. share/examples/paml/nhomo/tree-nhomo5.txt
  209. share/examples/paml/pamp.ctl
  210. share/examples/paml/paupblock
  211. share/examples/paml/paupend
  212. share/examples/paml/paupstart
  213. share/examples/paml/stewart.aa
  214. share/examples/paml/stewart.trees
  215. share/examples/paml/yn00.ctl
  216. @owner
  217. @group
  218. @mode
Collapse this list.
Dependency lines:
  • paml>0:biology/paml
To install the port:
cd /usr/ports/biology/paml/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/paml
  • pkg install paml
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: paml
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1688759942 SHA256 (abacus-gene-paml-4.10.7_GH0.tar.gz) = 0f29e768b3797b69eadc6332c3d046d8727702052d56c3b729883626c0a5a4e3 SIZE (abacus-gene-paml-4.10.7_GH0.tar.gz) = 5250841

Packages (timestamps in pop-ups are UTC):
paml
ABIlatestquarterly
FreeBSD:13:aarch644.10.74.10.7
FreeBSD:13:amd644.10.74.10.7
FreeBSD:13:armv64.9j4.10.6
FreeBSD:13:armv74.10.74.10.7
FreeBSD:13:i3864.10.74.10.7
FreeBSD:13:powerpc-4.10.7
FreeBSD:13:powerpc644.9j4.10.7
FreeBSD:13:powerpc64le-4.10.7
FreeBSD:14:aarch644.10.74.10.7
FreeBSD:14:amd644.10.74.10.7
FreeBSD:14:armv64.10.6-
FreeBSD:14:armv74.10.74.10.7
FreeBSD:14:i3864.10.74.10.7
FreeBSD:14:powerpc4.10.64.10.7
FreeBSD:14:powerpc64-4.10.7
FreeBSD:14:powerpc64le4.10.64.10.7
FreeBSD:15:aarch644.10.7-
FreeBSD:15:amd644.10.7-
FreeBSD:15:armv74.10.7-
FreeBSD:15:powerpc4.10.7-
FreeBSD:15:powerpc644.10.7-
FreeBSD:15:powerpc64le4.10.7-
 
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
There are no ports dependent upon this port

Configuration Options:
===> The following configuration options are available for paml-4.10.7: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings
Options name:
biology_paml
USES:
dos2unix gmake
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/abacus-gene/paml/tar.gz/4.10.7?dummy=/
Collapse this list.

Number of commits found: 52

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
4.10.7
08 Jul 2023 03:46:53
commit hash: 5fc301443c77a4952c42153f12a7520f913f60a3commit hash: 5fc301443c77a4952c42153f12a7520f913f60a3commit hash: 5fc301443c77a4952c42153f12a7520f913f60a3commit hash: 5fc301443c77a4952c42153f12a7520f913f60a3 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/paml: Update to 4.10.7

Remove -Wmemset-elt-size from CFLAGS.  The warning is only applicable to
gcc and is already enabled with -Wall.

Changes:	https://github.com/abacus-gene/paml/releases/tag/4.10.7
Sponsored by:	The FreeBSD Foundation
4.10.6
13 Nov 2022 02:35:29
commit hash: a875dde83e05c32752b096808e6b3ca50088a8a3commit hash: a875dde83e05c32752b096808e6b3ca50088a8a3commit hash: a875dde83e05c32752b096808e6b3ca50088a8a3commit hash: a875dde83e05c32752b096808e6b3ca50088a8a3 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/paml: Update to 4.10.6

https://github.com/abacus-gene/paml/releases/tag/v4.10.6

Sponsored by:	The FreeBSD Foundation
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)
4.10.5
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)
4.10.5
26 Aug 2022 04:22:46
commit hash: 5aec6e4a190d0d6a6f78ce9c5674fd5bf6b4b5d0commit hash: 5aec6e4a190d0d6a6f78ce9c5674fd5bf6b4b5d0commit hash: 5aec6e4a190d0d6a6f78ce9c5674fd5bf6b4b5d0commit hash: 5aec6e4a190d0d6a6f78ce9c5674fd5bf6b4b5d0 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/paml: Update to 4.10.5

https://github.com/abacus-gene/paml/releases/tag/v4.10.0
https://github.com/abacus-gene/paml/releases/tag/untagged-a5659203e8ec0ddb58b8
https://github.com/abacus-gene/paml/releases/tag/v4.10.5

Sponsored by:	The FreeBSD Foundation
4.9j
20 Jul 2022 14:20:57
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
4.9j
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.
4.9j
20 Aug 2020 17:07:04
Revision:545542Original commit files touched by this commit
kevans search for other commits by this committer
biology/paml: fix the build with LLVM 11

LLVM 11 switched from -fcommon to -fno-common by default. This revealed a
slight misposition of names in paml.h, which caused one symbol per enum
that's not used anywhere.

The fix just moves the names back so that the enums are named that, rather
than creating new unused symbols.

Reviewed by:	zeising
Approved by:	jrm (maintainer)
MFH:		2020Q3
4.9j
22 Nov 2019 15:32:40
Revision:518150Original commit files touched by this commit
jrm search for other commits by this committer
biology/paml: Update to version 4.9j

- Remove BROKEN=. Version 4.9i became unfetchable when the author pulled
  the tarball to prevent users from downloading a version with new, serious
  bugs.

Upstream changes described by the author:

  - mcmctree: Initial values have ages that are too old, exceeding max
    bounds.  In theory bounds in mcmctree are always soft so that the node
    ages will move to the area of posterior mode when burnin is long enough.
    In practice the poor starting values are problematic and requires long
    burn-in.  I have rewritten the code for generating initial values to
    respect the min and max bounds specified in the fossil calibrations.

  - codeml: A bug introduced in 4.9i caused the clade labels ($) to be
    ignored.  This affects the branch, branch-site and clade models.  If
    your tree has branch labels (#) only and no clade models, everything
    will be fine.  If you have used the clade label ($) in the tree with or
    without the branch label (#), either the program will abort or the
    results will be incorrect.  The clade label ($) is supposed to label
    all branches in the clade as well as the branch itself, but all clade
    labels in the tree are ignored in 4.9i.  Earlier versions are correct.
4.9i
06 Nov 2019 12:48:32
Revision:516880Original commit files touched by this commit Sanity Test Failure
antoine search for other commits by this committer
Mark a few ports BROKEN, unfetchable
4.9i
26 Feb 2019 15:12:43
Revision:493971Original commit files touched by this commit
jrm search for other commits by this committer
biology/paml: Update to version 4.9i

Upstream changes as described by the author:

- mcmctree: I have added an option (duplication = 1) for dating a tree with
both speciations and gene duplications, so that some nodes on the tree
share divergence times. Nodes sharing ages are identified using labels in
the tree file: #1, #2, .... I have yet to update the document about
specification of the model.

- mcmctree: The TipDate option was written for one locus or partition and
never worked for more than two loci/partitions. I have edited the code so
that it works for multiple partitions, some of which may be molecular and
the others morphological.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
4.9h
26 Apr 2018 15:36:31
Revision:468355Original commit files touched by this commit
jrm search for other commits by this committer
biology/paml: Set PORTVERSION directly

Setting DISTVERSION= 4.9h in the last commit caused PORTVERSION to be translated
to 4.9.h, which was not correct.

Pointy-hat: jrm
4.9.h
25 Apr 2018 20:36:39
Revision:468297Original commit files touched by this commit
jrm search for other commits by this committer
biology/paml: Update to version 4.9h

Port Changes:
- Add EXAMPLES option and install most files under EXAMPLESDIR
- Add USES=dos2unix to fix DOS line endings

Upstream Changes:
Version 4.9h, March 2018

(*) mcmctree: gamma-Dirichlet versus conditional i.i.d. priors for
rates for loci.  Since 4.9d, the program and the documentation are
inconsistent about the two priors, and which value (0 or 1) means
which prior.  I have now checked the program and the documentation to
make sure that they are consistent:
(Only the first 15 lines of the commit message are shown above View all of this commit message)
4.9c_1
02 Nov 2016 22:45:14
Revision:425174Original commit files touched by this commit
mat search for other commits by this committer
Cleanup no longer needed CHMOD usage after r424898.

PR:		213743
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
4.9c_1
29 Sep 2016 21:12:50
Revision:422950Original commit files touched by this commit
jrm search for other commits by this committer
Update PORTREVISION and dinstinfo due to upstream tarball change

Reviewed by:	swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8083
4.9c
28 Sep 2016 02:30:29
Revision:422846Original commit files touched by this commit
jrm search for other commits by this committer
biology/paml: update to version 4.9c and various improvements

- Update to version 4.9c
- Set LICENSE=GPLv3
- Use the variable PORTDOCS to automate the generation of the DOCS plist (as
  suggested by mat@).
- Install dat/ examples/ and Technical/ directories as well as files in the root
  directory of the distribution tarball.
- Fix broken permissions.
- Delete Windows executables.
- Build and install useful binaries not built by upstream's Makefile.
- Update pkg-descr.

Reviewed by:	swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8040
4.9a
23 Sep 2016 21:42:02
Revision:422697Original commit files touched by this commit
jrm search for other commits by this committer
Update email address to jrm@FreeBSD.org for ports that I maintain

Reviewed by:	mat, swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D7995
4.9a
19 May 2016 10:21:25
Revision:415498Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket
4.9a
16 May 2016 16:10:36
Revision:415338Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Update to 4.9a
- While here, simplify WRKSRC and use options helpers

PR:		209535
Submitted by:	jrm@ftfl.ca (maintainer)
4.8a
10 Apr 2015 15:39:01
Revision:383736Original commit files touched by this commit
brd search for other commits by this committer
Update biology/paml to 4.8a and unbreak.

PR:		199264
Submitted by:	Joseph Mingrone <jrm@ftfl.ca>
Approved by:	bdrewery (mentor)
4.8
05 Apr 2015 17:55:36
Revision:383309Original commit files touched by this commit
bapt search for other commits by this committer
Mark as broken unfetchable ports
4.8
19 Jan 2015 12:11:26
Revision:377397Original commit files touched by this commit
wen search for other commits by this committer
- Pass maintainership to submitter

PR:		196859
Submitted by:	Joseph Mingrone<jrm@ftfl.ca>
4.8
20 Oct 2014 07:10:48
Revision:371237Original commit files touched by this commit
bapt search for other commits by this committer
Cleanup plist
4.8
29 Jul 2014 19:11:53
Revision:363374Original commit files touched by this commit
adamw search for other commits by this committer
Convert a bunch of EXTRACT_SUFX=... into USES=tar:...

Approved by:	portmgr (not really, but touches unstaged ports)
4.8
05 Apr 2014 10:56:52
Revision:350214Original commit files touched by this commit
wen search for other commits by this committer
- Update to 4.8
- Reset maintainer to ports@
4.4c
14 Mar 2014 12:59:34
Revision:348221Original commit files touched by this commit
ehaupt search for other commits by this committer
Support staging
4.4c
13 Mar 2014 07:41:34
Revision:348042Original commit files touched by this commit
miwi search for other commits by this committer
- Convert USE_GMAKE to USES
4.4c
21 Feb 2014 13:35:26
Revision:345397Original commit files touched by this commit
ehaupt search for other commits by this committer
Remove trailing whitespaces from category biology
4.4c
10 Feb 2014 13:54:28
Revision:343634Original commit files touched by this commit
ehaupt search for other commits by this committer
According to the Porter's Handbook (5.12.2.3.) default options must be added to
OPTIONS_DEFINE. This policy has been implemented only recently that's why we
have many ports violating this policy.

This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.

Approved by:    portmgr (bapt)
4.4c
21 Jan 2014 23:18:05
Revision:340671Original commit files touched by this commit
bapt search for other commits by this committer
Fix properties on pkg-plist
4.4c
03 Jan 2014 15:46:52
Revision:338550Original commit files touched by this commit
adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
4.4c
20 Sep 2013 15:55:44
Revision:327709Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
4.4c
01 Jun 2013 14:22:36
Revision:319570Original commit files touched by this commit
wen search for other commits by this committer
- Trim Makefile headers
4.4c
19 Mar 2011 12:38:54
Original commit files touched by this commit
miwi search for other commits by this committer
- Get Rid MD5 support
4.4c
08 Sep 2010 00:16:45
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 4.4c
4.4a
20 Apr 2010 08:42:05
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 4.4a
- Update my mail address to FreeBSD
4.3
13 Aug 2009 17:00:04
Original commit files touched by this commit
miwi search for other commits by this committer
- Update to 4.3

PR:             137625
Submitted by:   Wen Heping <wenheping@gmail.com> (maintainer)
4.2b
02 Mar 2009 19:02:49
Original commit files touched by this commit
miwi search for other commits by this committer
- Update to 4.2b

PR:             132249
Submitted by:   Wen Heping <wenheping@gmail.com>
4.2
25 Dec 2008 19:56:07
Original commit files touched by this commit
miwi search for other commits by this committer
- Update to 4.2

PR:             129895
Submitted by:   Wen Heping <wenheping@gmail.com> (maintainer)
4.1
30 Sep 2008 08:54:55
Original commit files touched by this commit
miwi search for other commits by this committer
- Update to 4.1
- Pass maintainership to submitter

PR:             127683
Submitted by:   Wen heping <wenheping@gmail.com>
3.15
11 Mar 2007 03:21:18
Original commit files touched by this commit
linimon search for other commits by this committer
Reset dbader@eece.unm.edu due to maintainer-timeouts.

Hat:            portmgr
3.15
20 May 2006 18:52:19
Original commit files touched by this commit
sem search for other commits by this committer
- Update to 3.15

PR:             ports/96941
Submitted by:   Paul Schmehl <pauls@utdallas.edu>
Approved by:    maintainer timeout
3.14b
10 Nov 2005 01:21:42
Original commit files touched by this commit
mnag search for other commits by this committer
Update to 3.14b
Update MASTER_SITES
Add SHA256
Remove extra TABS

PR:             88007
Submitted by:   Jean Milanez Melo <jmelo@freebsdbrasil.com.br>
Approved by:    maintainer timeout, 14 days
3.14
06 Nov 2004 03:55:37
Original commit files touched by this commit
kevlo search for other commits by this committer
Update to 3.14

PR: ports/72422
Submitted by: Choe, Cheng-Dae <whitekid@gmail.com>
3.13
31 Mar 2004 03:12:58
Original commit files touched by this commit
trevor search for other commits by this committer
SIZEify (maintainer timeout)
3.13
22 Oct 2003 09:29:55
Original commit files touched by this commit
osa search for other commits by this committer
Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:   Oleg Karachevtsev <ok@etrust.ru>
A part of PR:   57992
3.13
14 Feb 2003 23:21:23
Original commit files touched by this commit
naddy search for other commits by this committer
* Update to 3.13.

PR:             48255
Submitted by:   David A. Bader <dbader@eece.unm.edu>

* Also honor CC/CFLAGS.
29 Aug 2001 13:00:08
commit hash: fp1.18073@dev.null.freshports.orgcommit hash: fp1.18073@dev.null.freshports.orgcommit hash: fp1.18073@dev.null.freshports.orgcommit hash: fp1.18073@dev.null.freshports.org files touched by this commit
wjv search for other commits by this committer
- Update to version 3.1    
03 Jul 2001 09:17:14
commit hash: fp1.15735@dev.null.freshports.orgcommit hash: fp1.15735@dev.null.freshports.orgcommit hash: fp1.15735@dev.null.freshports.orgcommit hash: fp1.15735@dev.null.freshports.org files touched by this commit
wjv search for other commits by this committer
Update to version 3.04    
02 Apr 2001 06:16:27
commit hash: fp1.11913@dev.null.freshports.orgcommit hash: fp1.11913@dev.null.freshports.orgcommit hash: fp1.11913@dev.null.freshports.orgcommit hash: fp1.11913@dev.null.freshports.org files touched by this commit
mharo search for other commits by this committer
update to 3.03    
08 Oct 2000 00:23:30
commit hash: fp1.4706@dev.null.freshports.orgcommit hash: fp1.4706@dev.null.freshports.orgcommit hash: fp1.4706@dev.null.freshports.orgcommit hash: fp1.4706@dev.null.freshports.org files touched by this commit
asami search for other commits by this committer
Convert category biology to new layout.  
10 Jul 2000 04:21:06
commit hash: fp1.1755@dev.null.freshports.orgcommit hash: fp1.1755@dev.null.freshports.orgcommit hash: fp1.1755@dev.null.freshports.orgcommit hash: fp1.1755@dev.null.freshports.org files touched by this commit
steve search for other commits by this committer
Add paml version 3.01.   A set of utilities for performing Phylogenetic Analysis
by Maximum   Likelihood (PAML).    

Number of commits found: 52