notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Want a good monitor light? See my photosAll times are UTC
Ukraine
This referral link gives you 10% off a Fastmail.com account and gives me a discount on my Fastmail account.

Get notified when packages are built

A new feature has been added. FreshPorts already tracks package built by the FreeBSD project. This information is displayed on each port page. You can now get an email when FreshPorts notices a new package is available for something on one of your watch lists. However, you must opt into that. Click on Report Subscriptions on the right, and New Package Notification box, and click on Update.

FInally, under Watch Lists, click on ABI Package Subscriptions to select your ABI (e.g. FreeBSD:14:amd64) & package set (latest/quarterly) combinatio for a given watch list. This is what FreshPorts will look for.

Port details
t_coffee Multiple DNA or protein sequence alignment package
9.03_11 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 9.03_11Version of this port present on the latest quarterly branch.
Broken BROKEN: unfetchable
Deprecated DEPRECATED: Broken for more than 6 months
Expired This port expired on: 2020-05-05
Ignore IGNORE: is marked as broken: unfetchable
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: 2002-01-25 11:58:16
Last Update: 2020-05-05 15:38:12
SVN Revision: 534093
License: GPLv2
WWW:
http://www.tcoffee.org/
Description:
From the website: T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Related publications: - 3DCoffee: Combining Protein Sequences and Structures within Multiple Sequence Alignments. O. O'Sullivan, K Suhre, C. Abergel, D.G. Higgins, C. Notredame. Journal of Molecular Biology, Vol 340, pp385-395, 2004 - T-Coffee: A novel method for multiple sequence alignments. C.Notredame, D. Higgins, J. Heringa, Journal of Molecular Biology,Vol 302, pp205-217,2000 - COFFEE: A New Objective Function For Multiple Sequence Alignmnent. C. Notredame, L. Holme and D.G. Higgins,Bioinformatics,Vol 14 (5) 407-422,1998 WWW: http://www.tcoffee.org/
Homepage    cgit ¦ GitHub ¦ 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 (5 items)
Collapse this list.
  1. bin/TMalign
  2. bin/t_coffee
  3. /usr/local/share/licenses/t_coffee-9.03_11/catalog.mk
  4. /usr/local/share/licenses/t_coffee-9.03_11/LICENSE
  5. /usr/local/share/licenses/t_coffee-9.03_11/GPLv2
Collapse this list.
Dependency lines:
  • t_coffee>0:biology/t_coffee
No installation instructions:
This port has been deleted.
PKGNAME: t_coffee
Flavors: there is no flavor information for this port.
distinfo:
SHA256 (T-COFFEE_distribution_Version_9.03.r1318.tar.gz) = 5bb9a531a4036b741a8ff0fe19f3591a3f33bf7ac4f484e5329b1b5dd1fff43c SIZE (T-COFFEE_distribution_Version_9.03.r1318.tar.gz) = 3455629

No package information for this port in our database
Sometimes this happens. Not all ports have packages.
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gfortran9 : lang/gcc9
  2. as : devel/binutils
Runtime dependencies:
  1. clustalw : biology/clustalw
  2. gfortran9 : lang/gcc9
There are no ports dependent upon this port

Configuration Options:
===> The following configuration options are available for t_coffee-9.03_11: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings
Options name:
N/A
USES:
fortran
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. http://www.tcoffee.org/Packages/Stable/Version_9.03.r1318/
Collapse this list.

Number of commits found: 45

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
9.03_11
05 May 2020 15:38:12
Revision:534093Original commit files touched by this commit
rene search for other commits by this committer
Remove expired ports:

Adjusted for ports rescued since r534032

2020-05-05 audio/festvox-czech: Broken for more than 6 months
2020-05-05 audio/gkrellmvolume2: Broken for more than 6 months
2020-05-05 audio/mixmos: Broken for more than 6 months
2020-05-05 audio/mma: Broken for more than 6 months
2020-05-05 audio/pd-cyclone: Broken for more than 6 months
2020-05-05 audio/shorten: Broken for more than 6 months
2020-05-05 audio/taglib-sharp: Broken for more than 6 months
2020-05-05 audio/xhippo: Broken for more than 6 months
2020-05-05 biology/consed: Broken for more than 6 months
2020-05-05 biology/plinkseq: Broken for more than 6 months
2020-05-05 biology/seqtools: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above View all of this commit message)
9.03_11
04 Apr 2020 20:51:41
Revision:530719Original commit files touched by this commit Sanity Test Failure
antoine search for other commits by this committer
Deprecate ports broken for more than 6 months
9.03_11
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
9.03_11
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
9.03_10
22 Apr 2019 13:16:34
Revision:499638Original commit files touched by this commit
gerald search for other commits by this committer
Related to revision 499061 bump ports with USES=fortran to have them
benefit from the improved situation where libgcc_s is only used when
absolutely necessary.

Suggested by:	tijl
9.03_9
12 Dec 2018 01:35:36
Revision:487272Original 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
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

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, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
9.03_8
29 Jul 2018 22:18:46
Revision:475857Original 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
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542
9.03_7
10 Mar 2018 17:46:06
Revision:464084Original commit files touched by this commit
gerald search for other commits by this committer
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
9.03_6
10 Sep 2017 20:55:39
Revision:449591Original 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
(via Mk/bsd.default-versions.mk and lang/gcc) which has moved from
GCC 5.4 to GCC 6.4 under most circumstances.

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, c++11-lib, c++11-lang,
   c++14-lang, c++0x, c11, or gcc-c++11-lib.

PR:		219275
9.03_5
01 Apr 2017 15:23:32
Revision:437439Original commit files touched by this commit
gerald search for other commits by this committer
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using using Mk/bsd.octave.mk which in turn has USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
   c++11-lang, c++0x, c11, or gcc-c++11-lib.

PR:		216707
9.03_4
07 Dec 2016 13:24:57
Revision:428057Original commit files touched by this commit
gerald search for other commits by this committer
Bump PORTREVISIONS for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms), part II.

The first part covered  ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.

This adds ports with USES=fortran and ports using Mk/bsd.octave.mk
which in turn has USES=fortran.

PR:		214965
Reported by:	thierry
9.03_3
01 Apr 2016 13:29:17
Revision:412344Original commit files touched by this commit
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
9.03_3
14 May 2015 10:15:09
Revision:386312Original commit files touched by this commit
mat search for other commits by this committer
MASTER_SITES cleanup.

- Replace ${MASTER_SITE_FOO} with FOO.
- Merge MASTER_SITE_SUBDIR into MASTER_SITES when possible. (This means 99.9%
  of the time.)
- Remove occurrences of MASTER_SITE_LOCAL when no subdirectory was present and
  no hint of what it should be was present.
- Fix some logic.
- And generally, make things more simple and easy to understand.

While there, add magic values to the FESTIVAL, GENTOO, GIMP, GNUPG, QT and
SAMBA macros.

Also, replace some EXTRACT_SUFX occurences with USES=tar:*.

Checked by:	make fetch-urlall-list
With hat:	portmgr
Sponsored by:	Absolight
9.03_3
02 Mar 2015 23:09:43
Revision:380301Original commit files touched by this commit
bapt search for other commits by this committer
Remove Authors from pkg-descr
9.03_3
10 Sep 2014 20:50:37
Revision:367888Original commit files touched by this commit
gerald search for other commits by this committer
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)
9.03_2
09 Jun 2014 11:21:53
Revision:357139Original commit files touched by this commit
olgeni search for other commits by this committer
Remove indefinite articles and trailing periods from COMMENT, plus
minor COMMENT typos and surrounding whitespace fixes. Categories A-C.

CR:		D196
Approved by:	portmgr (bapt)
9.03_2
10 Mar 2014 20:55:22
Revision:347809Original commit files touched by this commit
gerald search for other commits by this committer
Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)
9.03_1
18 Dec 2013 17:24:51
Revision:336851Original commit files touched by this commit
tijl search for other commits by this committer
USES=fortran, staging.
9.03_1
26 Oct 2013 00:52:36
Revision:331644Original commit files touched by this commit
gerald search for other commits by this committer
Update to libmpc version 1.0.1 which brings the following fixes:

 - Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui
(Only the first 15 lines of the commit message are shown above View all of this commit message)
9.03
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)
9.03
14 Aug 2013 22:35:54
Revision:324744Original commit files touched by this commit Sanity Test Failure
ak search for other commits by this committer
- Remove MAKE_JOBS_SAFE variable

Approved by:	portmgr (bdrewery)
9.03
14 Jan 2013 08:04:38
Revision:310361Original commit files touched by this commit
araujo search for other commits by this committer
- Update to 9.03.

PR:		ports/172499
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
5.68
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
5.68
10 Jun 2012 18:42:48
Original commit files touched by this commit
swills search for other commits by this committer
- Convert all remaining instances of BUILD_DEPENDS=${RUN_DEPENDS} or
  RUN_DEPENDS=${BUILD_DEPENDS} to use := which portlint has warned
  about for a while.

PR:             ports/168208
Approved by:    portmgr (miwi)
5.68
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)
5.68
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
5.68
09 Sep 2008 13:43:15
Original commit files touched by this commit
gahr search for other commits by this committer
- Respect PORTDOCS/PORTEXAMPLES

Reported by:    QA Tindie
Approved by:    portmgr
5.68
05 Apr 2008 10:47:12
Original commit files touched by this commit
rafan search for other commits by this committer
- Update to 5.68
- Remove gcc version restriction

PR:             ports/122435
Submitted by:   Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
4.96
02 May 2007 07:15:46
Original commit files touched by this commit
edwin search for other commits by this committer
[patch] cleanup non-supported FreeBSD versions

PR:             ports/111728
Submitted by:   Edwin Groothuis <edwin@mavetju.org>
Approved by:    maintainer timeout
4.96
09 Mar 2007 11:26:16
Original commit files touched by this commit
miwi search for other commits by this committer
- Update to 4.96

PR:             110080
Submitted by:   Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
3.27
22 Jan 2007 23:22:53
Original commit files touched by this commit
rafan search for other commits by this committer
- Project moves to a new home. Change MASTER_SITES and WWW

PR:             ports/108214
Submitted by:   Thomas Abthorpe <thomas at goodking.ca>
Approved by:    Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
3.27
10 Feb 2006 09:45:28
Original commit files touched by this commit
lawrance search for other commits by this committer
Update to 3.27.
Use GCC 3.3 on systems with 3.4, due to an internal compiler error.

PR:             ports/93050
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
3.18
22 Jan 2006 01:25:24
Original commit files touched by this commit
edwin search for other commits by this committer
Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtry

Approved by:    krion@
PR:             ports/88711 (related)
3.18
06 Dec 2005 15:10:08
Original commit files touched by this commit
tdb search for other commits by this committer
- Update to 3.18 to make fetchable again
- Mark broken on 6.x upwards

PR:             89977
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Approved by:    clement (mentor)
3.14
28 Oct 2005 06:32:18
Original commit files touched by this commit
kris search for other commits by this committer
BROKEN: Unfetchable
3.14
11 Oct 2005 20:47:02
Original commit files touched by this commit
sem search for other commits by this committer
Forced commit to note the port was updated to 3.14 not 3.13
3.14
11 Oct 2005 20:44:38
Original commit files touched by this commit
sem search for other commits by this committer
- Update to 3.13. It fixes fetching.

PR:             ports/87264
Submitted by:   maintainer
2.03
25 Nov 2004 23:03:54
Original commit files touched by this commit
sem search for other commits by this committer
- Update to 2.03
- Pass maintainership to submitter

PR:             ports/74332
Submitted by:   Fernan Aguero <fernan(at)iib.unsam.edu.ar>
1.37
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.
1.37
31 Mar 2004 03:12:58
Original commit files touched by this commit
trevor search for other commits by this committer
SIZEify (maintainer timeout)
1.37
22 Jan 2004 12:18:43
Original commit files touched by this commit
trevor search for other commits by this committer
Use the CPIO macro defined in bsd.port.mk.
1.37
13 Nov 2003 14:45:08
Original commit files touched by this commit
trevor search for other commits by this committer
Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.
1.37
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
1.37
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.
25 Jan 2002 14:58:16
commit hash: fp1.23898@dev.null.freshports.orgcommit hash: fp1.23898@dev.null.freshports.orgcommit hash: fp1.23898@dev.null.freshports.orgcommit hash: fp1.23898@dev.null.freshports.org files touched by this commit
wjv search for other commits by this committer
Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.    

Number of commits found: 45