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Port details
recombine Program to fit population models across sites
1.41_2 biology Deleted 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 1.41_2Version of this port present on the latest quarterly branch.
Deprecated DEPRECATED: Upstream advises to use biology/lamarc
Expired This port expired on: 2024-01-17
There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2001-08-06 11:49:53
Last Update: 2024-01-18 21:23:16
Commit Hash: 2f8680e
License: not specified in port
WWW:
https://lamarcweb.github.io/lamarcweb/recombine/
Description:
Recombine fits a model which has a single population of constant size with a single recombination rate across all sites. It can accomodate either plain DNA or RNA data or SNP (single nucleotide polymorphism) data. Recombine forms part of the Lamarc (Likelihood Analysis with Metropolis Algorithm using Random Coalescence) suite. See: http://evolution.genetics.washington.edu/lamarc.html
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (2 items)
Collapse this list.
  1. bin/filetran
  2. bin/recombine
Collapse this list.
Dependency lines:
  • recombine>0:biology/recombine
No installation instructions:
This port has been deleted.
PKGNAME: recombine
Flavors: there is no flavor information for this port.
distinfo:
SHA256 (recombine1.41.src.doc.tar.gz) = e247810ef31414f500f9c118b6462b549c761562140519f7c57f305fcb284643 SIZE (recombine1.41.src.doc.tar.gz) = 149129

Packages (timestamps in pop-ups are UTC):
recombine
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest--1.41_21.41_2--1.41_2-
FreeBSD:13:quarterly1.41_21.41_21.41_21.41_21.41_21.41_21.41_21.41_2
FreeBSD:14:latest--1.41_2--1.41_2-1.41_2
FreeBSD:14:quarterly1.41_21.41_2-1.41_21.41_21.41_21.41_21.41_2
FreeBSD:15:latest--n/a-n/a--1.41_2
FreeBSD:15:quarterly--n/a-n/a---
This port has no dependencies.
There are no ports dependent upon this port

Configuration Options:
===> The following configuration options are available for recombine-1.41_2: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings
Options name:
biology_recombine
USES:
shebangfix
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://lamarcweb.github.io/lamarcweb/recombine/
Collapse this list.
Port Moves
  • port moved to biology/lamarc on 2024-01-18
    REASON: Has expired: Upstream advises to use biology/lamarc

Number of commits found: 22

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.41_2
18 Jan 2024 21:23:16
commit hash: 2f8680e1b80827df5127b2d653f4dcf8433a1fb5commit hash: 2f8680e1b80827df5127b2d653f4dcf8433a1fb5commit hash: 2f8680e1b80827df5127b2d653f4dcf8433a1fb5commit hash: 2f8680e1b80827df5127b2d653f4dcf8433a1fb5 files touched by this commit
Rene Ladan (rene) search for other commits by this committer
biology/recombine: Remove expired port

2024-01-17 biology/recombine: Upstream advises to use biology/lamarc
1.41_2
17 Dec 2023 13:11:36
commit hash: 62d0176addaaec87f96ae4d2a504af69606c0c93commit hash: 62d0176addaaec87f96ae4d2a504af69606c0c93commit hash: 62d0176addaaec87f96ae4d2a504af69606c0c93commit hash: 62d0176addaaec87f96ae4d2a504af69606c0c93 files touched by this commit
Muhammad Moinur Rahman (bofh) search for other commits by this committer
biology/recombine: Mark DEPRECATED

- Upstream last release was in 2002
- Upstream advises to use bioloby/lamarc
- Set EXPIRATION_DATE 2024-01-17
- Pet portclippy
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)
1.41_2
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)
1.41_2
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)
1.41_2
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.
1.41_2
02 Sep 2019 05:00:43
Revision:510754Original commit files touched by this commit
cy search for other commits by this committer
Fix after gets(3) retirement using gets_s(3).

Bump PORTREVISION as this is a security issue too.

PR:		222796
MFH:		2019Q3
1.41_1
01 Sep 2019 16:40:06
Revision:510707Original commit files touched by this commit
lwhsu search for other commits by this committer
Add a patch to remove use of gets(3)

PR:		238685
Submitted by:	Walter Schwarzenfeld <w.schwarzenfeld@utanet.at>
Reported by:	emaste
Sponsored by:	The FreeBSD Foundation
1.41
19 Jul 2016 11:04:14
Revision:418767Original commit files touched by this commit
mat search for other commits by this committer
When there is a do-install target, do not use a post-install target, do
everything at once.  Sometime, rename post-install into a options helper
target.

I did not fix ports that were such a mess that I could not figure out
what they really wanted to do.  I also did not change ports that had
some version of an auto-plist code in post-install, for the same reason.

With hat:	portmgr
Sponsored by:	Absolight
1.41
16 Feb 2014 11:39:42
Revision:344537Original commit files touched by this commit
ehaupt search for other commits by this committer
- Support staging
- Use shebangfix
1.41
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)
1.41
19 Jun 2013 19:15:14
Revision:321313Original commit files touched by this commit
bsam search for other commits by this committer
. NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. mute mkdir;
. use PLIST_FILES and PORTDOCS at Makefile;
. remove pkg-plist;
. trim Makefile headers;
. remove article from COMMENT;
. pet portlint -- use opne space after WWW: at pkg-descr.
1.41
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
1.41
21 Dec 2009 02:19:12
Original commit files touched by this commit
dougb search for other commits by this committer
For ports maintained by ports@FreeBSD.org, remove names and/or
e-mail addresses from the pkg-descr file that could reasonably
be mistaken for maintainer contact information in order to avoid
confusion on the part of users looking for support. As a pleasant
side effect this also avoids confusion and/or frustration for people
who are no longer maintaining those ports.
1.41
25 Jan 2007 12:22:50
Original commit files touched by this commit
vd search for other commits by this committer
Fix master sites, un-deprecate and update biology/recombine to 1.41.
1.40
10 Dec 2006 12:36:15
Original commit files touched by this commit
gabor search for other commits by this committer
- Deprecate
- Set EXPIRATION_DATE

Approved by:    erwin (mentor)
1.40
24 Nov 2005 00:04:00
Original commit files touched by this commit
pav search for other commits by this committer
- Add SHA256
1.40
20 Nov 2004 08:09:49
Original commit files touched by this commit
linimon search for other commits by this committer
With portmgr hat on, reset inactive maintainer.  These ports are now up
for adoption.
1.40
31 Mar 2004 03:12:58
Original commit files touched by this commit
trevor search for other commits by this committer
SIZEify (maintainer timeout)
1.40
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
1.40
07 Mar 2003 05:56:43
Original commit files touched by this commit
ade search for other commits by this committer
Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.
06 Aug 2001 15:49:53
commit hash: fp1.16898@dev.null.freshports.orgcommit hash: fp1.16898@dev.null.freshports.orgcommit hash: fp1.16898@dev.null.freshports.orgcommit hash: fp1.16898@dev.null.freshports.org files touched by this commit
wjv search for other commits by this committer
Add recombine 1.40, a program to fit population models across sites.    

Number of commits found: 22