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Port details
grappa Genome Rearrangements Analysis and Phylogeny Software
2.0_1 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 2.0_1Version of this port present on the latest quarterly branch.
Deprecated DEPRECATED: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
Expired This port expired on: 2021-04-01
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: 2001-07-04 05:39:40
Last Update: 2021-04-07 17:54:26
Commit Hash: 5980fd4
License: GPLv2
WWW:
http://www.cs.unm.edu/~moret/GRAPPA/
Description:
GRAPPA: Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms This suite of programs implements the approach to phylogeny reconstruction from gene orders described in the paper Moret, B.M.E., Wyman, S., Bader, D.A., Warnow, T., and Yan, M., ``A detailed study of breakpoint analysis,'' Proc. 6th Pacific Symp. Biocomputing PSB 2001, Hawaii (2001). In its current state, "grappa" allows one to explore either the space of all possible trees on n labelled leaves or the space of all such trees that obey (are refinements of) a particular constraint tree. "invdist" takes the first two genomes in the input file and returns their inversion distance. "distmat" prints the inversion and breakpoint distance matrices. WWW: http://www.cs.unm.edu/~moret/GRAPPA/
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 (6 items)
Collapse this list.
  1. bin/grappa
  2. bin/invdist
  3. bin/distmat
  4. /usr/local/share/licenses/grappa-2.0_1/catalog.mk
  5. /usr/local/share/licenses/grappa-2.0_1/LICENSE
  6. /usr/local/share/licenses/grappa-2.0_1/GPLv2
Collapse this list.
Dependency lines:
  • grappa>0:biology/grappa
No installation instructions:
This port has been deleted.
PKGNAME: grappa
Flavors: there is no flavor information for this port.
distinfo:
SHA256 (GRAPPA20.tar.gz) = 19b3c5ab21c845eaf4fcf56fcf09a15db84597d8438155bb463d8f3e1bb51103 SIZE (GRAPPA20.tar.gz) = 172261

Packages (timestamps in pop-ups are UTC):
grappa
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest--2.0_1---2.0_1-
FreeBSD:13:quarterly--------
FreeBSD:14:latest--------
FreeBSD:14:quarterly--------
FreeBSD:15:latest--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
There are no ports dependent upon this port

Configuration Options:
No options to configure
Options name:
biology_grappa
USES:
gmake
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. http://www.cs.unm.edu/~moret/GRAPPA/
Collapse this list.
Port Moves
  • port deleted on 2021-04-07
    REASON: Has expired: Unmaintained and dead upstream, does not build with -fno-common (llvm 11)

Number of commits found: 22

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.0_1
07 Apr 2021 17:54:26
commit hash: 5980fd40bc59f3f872f57f75b3a31fb986c1b06ecommit hash: 5980fd40bc59f3f872f57f75b3a31fb986c1b06ecommit hash: 5980fd40bc59f3f872f57f75b3a31fb986c1b06ecommit hash: 5980fd40bc59f3f872f57f75b3a31fb986c1b06e files touched by this commit
Rene Ladan (rene) search for other commits by this committer
Remove expired ports:

2021-04-01 ftp/wzdftpd: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 astro/roadmap: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/cosmo: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/bomberinstinct: Unmaintained and dead upstream, does not build
with -fno-common (llvm 11)
2021-04-01 games/drm: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/bygfoot: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/cre: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 irc/hybserv: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 irc/xaric: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 mail/elmo: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 misc/cave: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 security/bugs: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 security/dmitry: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.0_1
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.
2.0_1
30 Aug 2020 09:47:50
Revision:547044Original commit files touched by this commit
zeising search for other commits by this committer
Extend expiration of ports broken with -fno-common

Extend the expiration of unmaintained leaf ports that are broken with
-fno-common and previously had a short expiration date.  The new date is set
to 2021-04-01, meaning the ports will be in the 2021Q2 branch, giving people
until 2021-06-30 (10 months from now) to fix issues.
Improve the wording of the deprecation message, mentioning both llvm 11 and
-fno-common.
Bump portrevision to force reinstall.  This way the warning message about
deprecation will be displayed to users installing or reinstalling the
software.

MFH:		2020Q3 (maybe)
2.0
29 Aug 2020 08:34:52
Revision:546885Original commit files touched by this commit
tcberner search for other commits by this committer
biology/: Fix build with clang11 and deprecate ports@ ports
2.0
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
2.0
25 Sep 2015 18:55:08
Revision:397864Original commit files touched by this commit
rm search for other commits by this committer
biology/grappa: define license (GPLv2)

As per the web site, the license for GRAPPA is GPLv2
https://www.cs.unm.edu/~moret/GRAPPA/

PR:		202426
Submitted by:	George <george@nycbug.org>
2.0
20 Dec 2013 13:27:13
Revision:337010Original commit files touched by this commit
pawel search for other commits by this committer
- Respect CC/CFLAGS

PR:		ports/184857
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
2.0
10 Dec 2013 17:25:39
Revision:336071Original commit files touched by this commit
bapt search for other commits by this committer
Support stage
USE_GMAKE -> USES=gmake
Respect CC
2.0
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)
2.0
11 Apr 2011 19:54:35
Original commit files touched by this commit
ade search for other commits by this committer
Update to GNU make 3.82 after numerous -exp runs.
2.0
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
2.0
13 Dec 2006 13:20:20
Original commit files touched by this commit
linimon search for other commits by this committer
Reset dbader@ece.unm.edu due to timeouts and no response to email.

Hat:            portmgr
2.0
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
2.0
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@
2.0
15 Apr 2005 18:48:57
Original commit files touched by this commit
leeym search for other commits by this committer
- update grappa to 2.0
- utilize PLIST_FILES
- unbreak it on 4.x
- update maintainer's email

PR:             79241
Submitted by:   David A. Bader <dbader@ece.unm.edu>
1.0.3_1
17 Aug 2004 10:29:40
Original commit files touched by this commit
kris search for other commits by this committer
This is now buildable on 5.x, remove BROKEN.
1.0.3_1
31 Mar 2004 03:12:58
Original commit files touched by this commit
trevor search for other commits by this committer
SIZEify (maintainer timeout)
1.0.3_1
04 Feb 2004 05:21:48
Original commit files touched by this commit
marcus search for other commits by this committer
Bump PORTREVISION on all ports that depend on gettext to aid with upgrading.

(Part 2)
1.0.3
19 Dec 2003 10:22:05
Original commit files touched by this commit
linimon search for other commits by this committer
Mark as broken on 5.x due to the usual gcc terminating-character hassles.
Notified mainatainer.
1.0.3
21 Feb 2003 11:01:38
Original commit files touched by this commit
knu search for other commits by this committer
De-pkg-comment.
29 Aug 2001 12:53:29
commit hash: fp1.18071@dev.null.freshports.orgcommit hash: fp1.18071@dev.null.freshports.orgcommit hash: fp1.18071@dev.null.freshports.orgcommit hash: fp1.18071@dev.null.freshports.org files touched by this commit
wjv search for other commits by this committer
- Update to version 1.0.3    
04 Jul 2001 09:39:40
commit hash: fp1.15790@dev.null.freshports.orgcommit hash: fp1.15790@dev.null.freshports.orgcommit hash: fp1.15790@dev.null.freshports.orgcommit hash: fp1.15790@dev.null.freshports.org files touched by this commit
wjv search for other commits by this committer
Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogeny   Software.    

Number of commits found: 22