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Port details
phylip Phylogeny Inference Package
3.697_1,1 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 3.697_1,1Version 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: 2000-07-10 00:25:48
Last Update: 2021-04-07 17:54:26
Commit Hash: 5980fd4
License: BSD2CLAUSE
WWW:
http://evolution.genetics.washington.edu/phylip.html
Description:
PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites, distance matrices, and 0/1 discrete characters. WWW: http://evolution.genetics.washington.edu/phylip.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 (50 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/phylip-3.697_1,1/catalog.mk
  3. /usr/local/share/licenses/phylip-3.697_1,1/LICENSE
  4. /usr/local/share/licenses/phylip-3.697_1,1/BSD2CLAUSE
  5. bin/clique
  6. bin/consense
  7. bin/contml
  8. bin/contrast
  9. bin/dnacomp
  10. bin/dnadist
  11. bin/dnainvar
  12. bin/dnaml
  13. bin/dnamlk
  14. bin/dnamove
  15. bin/dnapars
  16. bin/dnapenny
  17. bin/dollop
  18. bin/dolmove
  19. bin/dolpenny
  20. bin/drawgram
  21. bin/drawtree
  22. bin/factor
  23. bin/fitch
  24. bin/gendist
  25. bin/kitsch
  26. bin/mix
  27. bin/move
  28. bin/neighbor
  29. bin/pars
  30. bin/penny
  31. bin/proml
  32. bin/promlk
  33. bin/protdist
  34. bin/protpars
  35. bin/restdist
  36. bin/restml
  37. bin/retree
  38. bin/seqboot
  39. bin/treedist
  40. lib/libdrawgram.so
  41. lib/libdrawtree.so
  42. share/phylip/font1
  43. share/phylip/font2
  44. share/phylip/font3
  45. share/phylip/font4
  46. share/phylip/font5
  47. share/phylip/font6
  48. @owner
  49. @group
  50. @mode
Collapse this list.
Dependency lines:
  • phylip>0:biology/phylip
No installation instructions:
This port has been deleted.
PKGNAME: phylip
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1514795118 SHA256 (phylip-3.697.tar.gz) = 9a26d8b08b8afea7f708509ef41df484003101eaf4beceb5cf7851eb940510c1 SIZE (phylip-3.697.tar.gz) = 3958696

Packages (timestamps in pop-ups are UTC):
phylip
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest--3.697_1,1---3.697_1,1-
FreeBSD:13:quarterly--------
FreeBSD:14:latest--------
FreeBSD:14:quarterly--------
FreeBSD:15:latest--n/a-n/a---
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. bash : shells/bash
  2. gmake>=4.3 : devel/gmake
  3. x11.pc : x11/libX11
  4. xaw7.pc : x11-toolkits/libXaw
  5. xt.pc : x11-toolkits/libXt
Runtime dependencies:
  1. x11.pc : x11/libX11
  2. xaw7.pc : x11-toolkits/libXaw
  3. xt.pc : x11-toolkits/libXt
There are no ports dependent upon this port

Configuration Options:
===> The following configuration options are available for phylip-3.697_1,1: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings
Options name:
biology_phylip
USES:
gmake xorg
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. http://evolution.gs.washington.edu/phylip/download/
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: 50

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
3.697_1,1
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)
3.697_1,1
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.
3.697_1,1
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)
3.697,1
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
3.697,1
04 Nov 2019 21:08:20
Revision:516742Original commit files touched by this commit
zeising search for other commits by this committer
Add USES=xorg USES=gl, ports categories b

Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories
starting with 'b'.
3.697,1
01 Jan 2018 08:40:23
Revision:457755Original commit files touched by this commit
wen search for other commits by this committer
- Update to 3.697
3.696,1
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
3.696,1
28 Jul 2015 17:52:12
Revision:393084Original commit files touched by this commit
antoine search for other commits by this committer
Unbreak

Reported by:	pkg-fallout
3.696,1
25 Jul 2015 15:06:49
Revision:392887Original commit files touched by this commit
danfe search for other commits by this committer
- Fix four cases of an obvious typo: LICENSE_FILES -> LICENSE_FILE
- While here: move knobs to their expected location, remove useless check
  for ${PORT_OPTIONS:MDOCS} when installing documentation, standardize
  Makefile headers
3.696,1
02 Nov 2014 14:14:00
Revision:372070Original commit files touched by this commit
pawel search for other commits by this committer
- Update to version 3.696
- Add LICENSE, no EXAMPLES included in distfile now
- Rework pkg-descr, remove author info - it's available on homepage

PR:		194163
Submitted by:	tkato432@yahoo.com
3.695_3,1
20 Oct 2014 07:10:48
Revision:371237Original commit files touched by this commit
bapt search for other commits by this committer
Cleanup plist
3.695_3,1
16 Apr 2014 18:28:50
Revision:351411Original commit files touched by this commit
zeising search for other commits by this committer
The FreeBSD x11@ and graphics team proudly presents
a zeising, kwm production, with help from dumbbell, bdrewery:

NEW XORG ON FREEBSD 9-STABLE AND 10-STABLE

This update switches over to use the new xorg stack by default on FreeBSD 9
and 10 stable, on osversions where vt(9) is available.
It is still possible to use the old stack by specifying WITHOUT_NEW_XORG in
/etc/make.conf .
FreeBSD 8-STABLE and released versions of FreeBSD still use
the old version.
A package repository with binary packages for new xorg will
be available soon.

This patch also contains updates of libxcb and related ports, pixman, as well
(Only the first 15 lines of the commit message are shown above View all of this commit message)
3.695_2,1
23 Mar 2014 21:52:54
Revision:348893Original commit files touched by this commit
pawel search for other commits by this committer
- Add staging support
- Strip libraries
3.695_1,1
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
3.695_1,1
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)
3.695_1
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)
3.695_1,1
24 Jun 2013 18:09:53
Revision:321697Original commit files touched by this commit
rakuco search for other commits by this committer
Fix some screw ups introduced in r319847.

I'm not sure if the submitter of ports/179224 didn't even test his patch or
if the distfile was re-rolled in a bizarre way.

Anyway, fix distfile and also cd into the correct directories to actually
build the port.

PR:		ports/179790
3.695_1,1
19 Jun 2013 15:43:56
Revision:321283Original commit files touched by this commit
bsam search for other commits by this committer
. pet portlint: add USE_LDCONFIG;
. bump PORTREVISION.
3.695,1
04 Jun 2013 10:02:30
Revision:319847Original commit files touched by this commit
miwi search for other commits by this committer
- Update to 3.6.9.5

PR:		179224
Submitted by:	Ports Fury
3.69,1
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
3.69,1
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.
3.69,1
16 Sep 2009 14:27:00
Original commit files touched by this commit
miwi search for other commits by this committer
-Update to 3.69

PR:             138813
Submitted by:   Ports Fury
Feature safe:   yes
3.68_1,1
23 Jan 2009 16:28:36
Original commit files touched by this commit
flz search for other commits by this committer
- Update X.org ports to 7.4+ (few ports are more recent than the katamari).
- Bump PORTREVISION for all ports depending on libglut since the shlib
version number went from 4 to 3.
- Bump PORTREVISION for all ports depending on libXaw as libXaw.so.8 isn't
installed anymore.
- Couple of ports fixes (mostly missing xorg components added to USE_XORG).
3.68,1
27 Aug 2008 16:21:06
Original commit files touched by this commit
gahr search for other commits by this committer
- Fix build

Reported by:    QA Tindie
3.68,1
27 Aug 2008 15:19:32
Original commit files touched by this commit
gahr search for other commits by this committer
- Update to 3.68
3.67_1,1
09 Jun 2008 13:01:30
Original commit files touched by this commit
gahr search for other commits by this committer
- Fix build depends
- Bump port revision

Reported by:    pointyhat via pav
3.67,1
03 Jun 2008 23:31:14
Original commit files touched by this commit
gahr search for other commits by this committer
- Update to 3.67
- Sanitize Makefile a little bit
3.66_2
19 Apr 2008 17:56:05
Original commit files touched by this commit Sanity Test Failure
miwi search for other commits by this committer
- Remove unneeded dependency from gtk12/gtk20 [1]
- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Remove X11BASE support in favor of LOCALBASE or PREFIX
- Use USE_LDCONFIG instead of INSTALLS_SHLIB
- Remove unneeded USE_GCC 3.4+

Thanks to all Helpers:
        Dmitry Marakasov, Chess Griffin, beech@, dinoex, rafan, gahr,
        ehaupt, nox, itetcu, flz, pav

PR:             116263
Tested on:      pointyhat
Approved by:    portmgr (pav)
3.66_1,1
19 May 2007 20:32:57
Original commit files touched by this commit
flz search for other commits by this committer
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
3.66,1
27 Jan 2007 21:23:52
Original commit files touched by this commit
itetcu search for other commits by this committer
Update to 3.66

PR:             ports/108434
Submitted by:   Marcelo Araujo
3.65,1
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
3.65,1
02 Dec 2006 20:34:11
Original commit files touched by this commit
rafan search for other commits by this committer
- Respect X11BASE

Approved by:    maintainer (implicit)
3.65,1
09 Feb 2006 01:17:59
Original commit files touched by this commit
lawrance search for other commits by this committer
Put PORTEPOCH back.

Reported by:    chkversion
3.65
08 Feb 2006 14:45:45
Original commit files touched by this commit
lawrance search for other commits by this committer
Update to 3.65.

PR:             ports/92182
Submitted by:   "Choe, Cheng-Dae" <whitekid@gmail.com>
Approved by:    dbader@ece.unm.edu (maintainer, timeout 14 days)
3.6,1
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@
3.6,1
22 Apr 2005 12:08:12
Original commit files touched by this commit
arved search for other commits by this committer
Bump PORTEPOCH. 3.6 < 3.62

Pointyhat to:   arved
3.6
21 Apr 2005 13:45:15
Original commit files touched by this commit
arved search for other commits by this committer
Upgrade to 3.62

PR:             79234
Submitted by:   David A. Bader <dbader@ece.unm.edu>
3.62
09 Dec 2004 13:33:55
Original commit files touched by this commit
pav search for other commits by this committer
- Add some sites I found with Google, as old master site don't have this
  version anymore

Reported by:    pointyhat via krion
3.62
11 Oct 2004 22:26:34
Original commit files touched by this commit
pav search for other commits by this committer
- Update to 3.62
- Install font files

PR:             ports/72212
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by:    David A. Bader <dbader@ece.unm.edu> (maintainer)
3.6.b
31 Mar 2004 03:12:58
Original commit files touched by this commit
trevor search for other commits by this committer
SIZEify (maintainer timeout)
3.6.b
31 Jan 2004 16:06:24
Original commit files touched by this commit
pav search for other commits by this committer
- Update to 3.6.b

PR:             ports/62142
Submitted by:   David A. Bader <dbader@ece.unm.edu> (maintainer)
3.6.a3
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
3.6.a3
21 Feb 2003 11:01:38
Original commit files touched by this commit
knu search for other commits by this committer
De-pkg-comment.
3.6.a3
13 Aug 2002 16:07:45
Original commit files touched by this commit
naddy search for other commits by this committer
Update to version 3.6.a3.

PR:             41412
Submitted by:   David A. Bader <dbader@eece.unm.edu>

Additional clean-up:
* Respect CC, CFLAGS, X11BASE.
* Use versioned DIST_SUBDIR.

Approved by:    maintainer
22 Aug 2001 11:02:27
commit hash: fp1.17622@dev.null.freshports.orgcommit hash: fp1.17622@dev.null.freshports.orgcommit hash: fp1.17622@dev.null.freshports.orgcommit hash: fp1.17622@dev.null.freshports.org files touched by this commit
wjv search for other commits by this committer
- Update to version 3.6.a2.1 - since the distribution tarball hadn't been    
renamed between versions, this port failed checksum.   - Apply some whitespace
edits and cut pkg-descr down to size to placate     portlint.    
03 Jul 2001 14:15:40
commit hash: fp1.15760@dev.null.freshports.orgcommit hash: fp1.15760@dev.null.freshports.orgcommit hash: fp1.15760@dev.null.freshports.orgcommit hash: fp1.15760@dev.null.freshports.org files touched by this commit
wjv search for other commits by this committer
Add support for %%PORTDOCS%%.    
11 Apr 2001 04:51:35
commit hash: fp1.12443@dev.null.freshports.orgcommit hash: fp1.12443@dev.null.freshports.orgcommit hash: fp1.12443@dev.null.freshports.orgcommit hash: fp1.12443@dev.null.freshports.org files touched by this commit
steve search for other commits by this committer
This port require X libraries to build/run.    
02 Apr 2001 06:10:15
commit hash: fp1.11912@dev.null.freshports.orgcommit hash: fp1.11912@dev.null.freshports.orgcommit hash: fp1.11912@dev.null.freshports.orgcommit hash: fp1.11912@dev.null.freshports.org files touched by this commit
mharo search for other commits by this committer
updated port biology/phylip from vers 3.5 to 3.6    
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 04:25:48
commit hash: fp1.1756@dev.null.freshports.orgcommit hash: fp1.1756@dev.null.freshports.orgcommit hash: fp1.1756@dev.null.freshports.orgcommit hash: fp1.1756@dev.null.freshports.org files touched by this commit
steve search for other commits by this committer
Adding phylip version 3.5.    

Number of commits found: 50