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Port details
primer3 Primer3 helps to choose primers for PCR reactions
2.3.6 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 2.3.6Version of this port present on the latest quarterly branch.
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: 2002-09-17 15:31:31
Last Update: 2023-08-05 18:55:50
Commit Hash: 16f82a5
License: GPLv2
WWW:
http://www-genome.wi.mit.edu/genome_software/other/primer3.html
Description:
"Primer3 is a complete rewrite of the original PRIMER program (Primer 0.5), written by Steve Lincoln, Mark Daly, and Eric Lander. See DIFFERENCES FROM EARLIER VERSIONS for a discussion of how Primer3 differs from its predecessors, Primer 0.5 and Primer v2. Primer3 picks primers for PCR reactions, considering as criteria: o oligonucleotide melting temperature, size, GC content, and primer-dimer possibilities, o PCR product size, o positional constraints within the source sequence, and o miscellaneous other constraints. All of these criteria are user-specifiable as constraints, and some are specifiable as terms in an objective function that characterizes an optimal primer pair." - from the README file
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 (4 items)
Collapse this list.
  1. bin/primer3
  2. /usr/local/share/licenses/primer3-2.3.6/catalog.mk
  3. /usr/local/share/licenses/primer3-2.3.6/LICENSE
  4. /usr/local/share/licenses/primer3-2.3.6/GPLv2
Collapse this list.
Dependency lines:
  • primer3>0:biology/primer3
To install the port:
cd /usr/ports/biology/primer3/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/primer3
  • pkg install primer3
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: primer3
Flavors: there is no flavor information for this port.
distinfo:
SHA256 (primer3-src-2.3.6.tar.gz) = 2ff54faf957f0d7e4c79d9536fa1027b028bc5e4c6005f142df42ef85562ecd4 SIZE (primer3-src-2.3.6.tar.gz) = 1667573

Packages (timestamps in pop-ups are UTC):
primer3
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.3.62.3.62.3.62.3.62.3.6-2.3.6-
FreeBSD:13:quarterly2.3.62.3.62.3.62.3.62.3.62.3.62.3.62.3.6
FreeBSD:14:latest2.3.62.3.62.3.62.3.62.3.62.3.6-2.3.6
FreeBSD:14:quarterly2.3.62.3.6-2.3.62.3.62.3.62.3.62.3.6
FreeBSD:15:latest2.3.62.3.6n/a2.3.6n/a2.3.62.3.62.3.6
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. gmake>=4.3 : devel/gmake
This port is required by:
for Build
  1. biology/emboss

Configuration Options:
No options to configure
Options name:
biology_primer3
USES:
gmake
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (56 items)
Collapse this list.
  1. http://cfhcable.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  2. http://cytranet.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  3. http://deac-ams.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  4. http://deac-fra.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  5. http://deac-riga.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  6. http://downloads.sourceforge.net/project/primer3/primer3/2.3.6/
  7. http://excellmedia.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  8. http://freefr.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  9. http://gigenet.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  10. http://ixpeering.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  11. http://jaist.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  12. http://jztkft.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  13. http://kumisystems.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  14. http://liquidtelecom.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  15. http://nchc.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  16. http://netactuate.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  17. http://netcologne.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  18. http://netix.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  19. http://onboardcloud.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  20. http://phoenixnap.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  21. http://razaoinfo.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  22. http://sinalbr.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  23. http://sitsa.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  24. http://sonik.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  25. http://tenet.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  26. http://udomain.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  27. http://ufpr.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  28. http://versaweb.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  29. https://cfhcable.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  30. https://cytranet.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  31. https://deac-ams.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  32. https://deac-fra.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  33. https://deac-riga.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  34. https://downloads.sourceforge.net/project/primer3/primer3/2.3.6/
  35. https://excellmedia.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  36. https://freefr.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  37. https://gigenet.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  38. https://ixpeering.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  39. https://jaist.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  40. https://jztkft.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  41. https://kumisystems.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  42. https://liquidtelecom.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  43. https://nchc.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  44. https://netactuate.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  45. https://netcologne.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  46. https://netix.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  47. https://onboardcloud.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  48. https://phoenixnap.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  49. https://razaoinfo.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  50. https://sinalbr.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  51. https://sitsa.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  52. https://sonik.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  53. https://tenet.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  54. https://udomain.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  55. https://ufpr.dl.sourceforge.net/project/primer3/primer3/2.3.6/
  56. https://versaweb.dl.sourceforge.net/project/primer3/primer3/2.3.6/
Collapse this list.

Number of commits found: 33

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.3.6
05 Aug 2023 18:55:50
commit hash: 16f82a503aae4a5ccde843d9cceb014c8c8ed3cecommit hash: 16f82a503aae4a5ccde843d9cceb014c8c8ed3cecommit hash: 16f82a503aae4a5ccde843d9cceb014c8c8ed3cecommit hash: 16f82a503aae4a5ccde843d9cceb014c8c8ed3ce files touched by this commit
Muhammad Moinur Rahman (bofh) search for other commits by this committer
biology/primer3: Fix build with llvm16

Approved by:	portmgr (blanket)
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)
2.3.6
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)
2.3.6
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)
2.3.6
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.
2.3.6
25 Aug 2018 03:35:46
Revision:477995Original commit files touched by this commit
tobik search for other commits by this committer
biology/primer3: Fix build with Clang 6

thal.c:426:13: error: comparison between pointer and integer ('int' and 'const
unsigned char *')
   if ('\0' == oligo_f) {
       ~~~~ ^  ~~~~~~~
thal.c:431:13: error: comparison between pointer and integer ('int' and 'const
unsigned char *')
   if ('\0' == oligo_r) {
       ~~~~ ^  ~~~~~~~

http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/primer3-2.3.6.log
2.3.6
20 May 2014 19:32:39
Revision:354670Original commit files touched by this commit
tijl search for other commits by this committer
Quote ${CC} and similar variables in MAKE_ARGS.

Reported by:	Dominic Fandrey <kamikaze@bsdforen.de>
2.3.6
06 Apr 2014 03:56:03
Revision:350288Original commit files touched by this commit
wen search for other commits by this committer
- Update to 2.3.6
- Reset maintainer to ports@
2.3.5
14 Mar 2014 12:35:03
Revision:348218Original commit files touched by this commit
ehaupt search for other commits by this committer
Support staging
2.3.5
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)
2.3.5
28 Aug 2013 06:04:51
Revision:325508Original commit files touched by this commit
bapt search for other commits by this committer
Make sure to respect CC and CXX, this fixes the build on head without gcc
2.3.5
20 Aug 2013 14:11:56
Revision:325050Original commit files touched by this commit
wen search for other commits by this committer
- Update to 2.3.5
- Add LICENSE
- Remove pkg-message since license changed upstream
- Do not install test files as example
1.1.4
01 Oct 2012 14:55:55
Revision:305131Original commit files touched by this commit
wen search for other commits by this committer
- Take maintainership
1.1.4
01 Oct 2012 14:45:17
Revision:305130Original commit files touched by this commit
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
1.1.4
27 Jan 2012 17:41:00
Original commit files touched by this commit
miwi search for other commits by this committer
- Respect CC

PR:             163172
Submitted by:   Jan Beich <jbeich@tormail.net>
Approved by:    maintainer timeout
1.1.4
22 Oct 2011 23:50:23
Original commit files touched by this commit
eadler search for other commits by this committer
- remove maintainer tags from pkg-descr

Approved by:    portmgr
Approved by:    bapt (mentor)
1.1.4
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
1.1.4
29 Dec 2010 20:04:42
Original commit files touched by this commit
pgollucci search for other commits by this committer
- DISTNAME= ${PORTNAME}-${PORTVERSION} is the default and not needed.

PR:             ports/153292
Submitted by:   myself (pgollucci)
Tested by:      -exp run by pav
Approved by:    portmgr (pav)
1.1.4
18 Dec 2009 02:55:57
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 1.1.4

Submitted by:   Wen Heping (myself)
Approved by:    maintainer (via Email)
1.1.3
04 Apr 2008 20:46:36
Original commit files touched by this commit
pav search for other commits by this committer
- Update to 1.1.3

PR:             ports/122374
Submitted by:   Wen heping <wenheping@gmail.com>
Patch revised:  Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
1.0.1
29 Dec 2006 23:40:53
Original commit files touched by this commit
miwi search for other commits by this committer
- Update to 1.0.1
- Update MASTER_SITES
- Pass maintainership to submitter

PR:             ports/107246
Submitted by:   Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
1.0.0
26 Dec 2006 12:46:34
Original commit files touched by this commit
linimon search for other commits by this committer
Reset tonymaher@optusnet.com.au due to maintainer-timeouts and no response
to email.

Hat:            portmgr
1.0.0
03 May 2006 23:26:35
Original commit files touched by this commit
edwin search for other commits by this committer
Remove USE_REINPLACE from all categories starting with B
1.0.0
22 Jan 2006 08:20:34
Original commit files touched by this commit
edwin search for other commits by this committer
SHA256ify

Approved by:    krion@
1.0.0
09 Jan 2006 03:25:03
Original commit files touched by this commit
edwin search for other commits by this committer
Fix maintainer address

    From: Tony Maher <anthony.maher@uts.edu.au>
    To: Edwin Groothuis <edwin@FreeBSD.org>
    Subject: Re: ports/91537: maths/xgobi - download site moved/maintainer
addressupdate

    Actually I need  modify all my ports to use OptusNet rather than
    Biolateral.  Is there an easy way to do this or should I submit a
    separate 1-line patch and PR for each port?

    biology/crimap
    biology/dna-qc
    biology/flip
    biology/primer3
    biology/seqio
    biology/wise
    math/xgobi
    net/generic-nqs

Submitted by:   Tony Maher <anthony.maher@uts.edu.au>
1.0.0
13 Jun 2005 04:31:34
Original commit files touched by this commit
pat search for other commits by this committer
- Update to 1.0.0
- Make DATADIR/EXAMPLESDIR/DOCSDIR safe
- Don't hardcode ${CPIO}

PR:             ports/82154
Submitted by:   George Hartzell <hartzell@alerce.com>
Approved by:    maintainer
0.9
31 Mar 2004 03:12:58
Original commit files touched by this commit
trevor search for other commits by this committer
SIZEify (maintainer timeout)
0.9
27 Feb 2004 22:20:43
Original commit files touched by this commit
krion search for other commits by this committer
- Fix MASTER_SITES

PR:             ports/63469
Submitted by:   maintainer
0.9
20 Dec 2003 12:20:49
Original commit files touched by this commit
krion search for other commits by this committer
- Fix MASTER_SITES

PR:             60417
Submitted by:   maintainer
0.9
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
0.9
21 Feb 2003 11:01:38
Original commit files touched by this commit
knu search for other commits by this committer
De-pkg-comment.
0.9
07 Nov 2002 13:45:17
Original commit files touched by this commit
edwin search for other commits by this committer
Updated to fix problems as stated in PR ports/42915

PR:             ports/42915
Submitted by:   Tony Maher <tonym@biolateral.com.au>
0.9
17 Sep 2002 15:31:10
Original commit files touched by this commit
ijliao search for other commits by this committer
add primer3 0.9
Primer3 helps to choose primers for PCR reactions

PR:             35298
Submitted by:   Tony Maher <tonym@biolateral.com.au>

Number of commits found: 33