| non port: biology/emboss/Makefile |
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SVNWeb
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Number of commits found: 86 |
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Wed, 7 Sep 2022
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[ 21:10 Stefan Eßer (se)  ]    b7f0544 (Only the first 10 of 27931 ports in this commit are shown above.  )
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 )
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Wed, 20 Jul 2022
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[ 14:20 Tobias C. Berner (tcberner) ] 37526bb (Only the first 10 of 82 ports in this commit are shown above. )
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 )
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Fri, 29 Oct 2021
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[ 09:50 Stefan Eßer (se) ] 819f25b (Only the first 10 of 388 ports in this commit are shown above. )
*/*: Remove redundant '-[0-9]*' from CONFLICTS
The conflict checks compare the patterns first against the package
names without version (as reported by "pkg query "%n"), then - if
there was no match - agsinst the full package names including the
version (as reported by "pkg query "%n-%v").
Many CONFLICTS definitions used patterns like "bash-[0-9]*" to filter
for the bash package in any version. But that pattern is functionally
identical with just "bash".
Approved by: portmgr (blanket)
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Fri, 24 Sep 2021
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[ 21:34 Jason W. Bacon (jwb) ] c68b6dc
biology/emboss: Add "emboss" command in ${LOCALBASE}/bin
Standard emboss commands are installed under a special prefix because
of multiple conflicts. The emboss command turns the standard commands
into subcommands, so no special PATH is needed.
/usr/local/emboss/bin/needle [args]
can be run as
emboss needle [args]
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Mon, 6 Sep 2021
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[ 15:13 Jason W. Bacon (jwb) ] e47c577
biology/emboss: Put emboss-shell in default PATH
PREFIX is overridden by default in the port Makefile, so PREFIX/bin
is not normally in PATH. The purpose of emboss-shell is to prepend
PREFIX/bin to PATH to give access to emboss tools.
Also fix tcsh detection.
PR: 258316
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[ 14:21 Jason W. Bacon (jwb) ] fa2e0b8
biology/emboss: Add emboss-shell: Run subshell with proper PATH
Also silence portlint and stage-qa warnings
PR: 258316
Approved by: wen
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Tue, 6 Apr 2021
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[ 14:31 Mathieu Arnold (mat) ] 305f148 (Only the first 10 of 29333 ports in this commit are shown above. )
Remove # $FreeBSD$ from Makefiles.
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Mon, 4 May 2020
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[ 21:31 dinoex ]   (Only the first 10 of 72 ports in this commit are shown above. )
- update libgd to 2.3.0
- new option RAQM
- resurrect deprecated gdlib-config
- bump dependend ports
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Thu, 7 Nov 2019
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[ 20:20 zeising ] (Only the first 10 of 70 ports in this commit are shown above. )
Sprinkle more USES=xorg
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Wed, 20 Jul 2016
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[ 09:33 dinoex ] (Only the first 10 of 77 ports in this commit are shown above. )
- update libgd to 2.2.2
- new MASTER_SITES
- add security patch
PR: 210913
Submitted by: Piotr Kubaj
MFH: 2016Q3
Security: CVE-2015-8874
Security: CVE-2016-3074
Security: http://www.openwall.com/lists/oss-security/2016/07/12/4
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Fri, 1 Apr 2016
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[ 13:29 mat ] (Only the first 10 of 1009 ports in this commit are shown above. )
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
With hat: portmgr
Sponsored by: Absolight
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Wed, 18 Mar 2015
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[ 21:52 bapt ]
Fix packaging as a user (pkg already takes care of credentials)
Strip binaries
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Thu, 25 Dec 2014
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[ 20:54 bapt ] (Only the first 10 of 446 ports in this commit are shown above. )
Bump portrevision after png update
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[ 19:04 antoine ] (Only the first 10 of 332 ports in this commit are shown above. )
Change libpng15.so to libpng.so in LIB_DEPENDS to prepare the upgrade
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Mon, 9 Jun 2014
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[ 11:21 olgeni ] (Only the first 10 of 120 ports in this commit are shown above. )
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)
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Thu, 5 Jun 2014
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[ 03:28 miwi ]
- Update to 6.6.0
- Stage support
PR: 190508
Submitted by: Muhammad Moinur Rahman
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Mon, 5 May 2014
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[ 09:45 bapt ] (Only the first 10 of 293 ports in this commit are shown above. )
Convert all :U to :tu and :L to :tl
Since FreeBSD 8.4 and FreeBSD 9.1 make(1) do support :tu and :tl as a
replacement for :U and :L (which has been marked as deprecated)
bmake which is the default on FreeBSD 10+ only support by default
:tu/:tl a hack has been added at the time to support :U and :L to ease
migration. This hack is now not necessary anymore
Note that this makes the ports tree incompatible with make(1) from
FreeBSD 8.3 or earlier
With hat: portmgr
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Wed, 11 Dec 2013
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[ 14:43 bapt ] (Only the first 10 of 12 ports in this commit are shown above. )
In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology
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Fri, 20 Sep 2013
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[ 15:55 bapt ] (Only the first 10 of 94 ports in this commit are shown above. )
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
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Fri, 9 Aug 2013
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[ 14:05 dinoex ] (Only the first 10 of 86 ports in this commit are shown above. )
- update libdg to 2.1.0
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Tue, 9 Jul 2013
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[ 21:49 bapt ]
Convert from USE_MOTIF to USES=motif
While here:
- trim headers
- Remove indefinite article from comment
- convert USE_GMAKE to USES=gmake
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Mon, 1 Oct 2012
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[ 14:55 wen ]
- Take maintainership
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[ 14:45 tabthorpe ] (Only the first 10 of 47 ports in this commit are shown above. )
- Reassign to the heap at maintainer's request
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Fri, 1 Jun 2012
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[ 05:26 dinoex ] (Only the first 10 of 4371 ports in this commit are shown above. )
- update png to 1.5.10
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Mon, 2 May 2011
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[ 12:44 makc ] (Only the first 10 of 195 ports in this commit are shown above. )
Bump PORTREVISION after open-mofit update
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Sat, 4 Dec 2010
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[ 07:34 ade ] (Only the first 10 of 1730 ports in this commit are shown above. )
Sync to new bsd.autotools.mk
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Wed, 7 Apr 2010
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[ 01:16 wen ]
- Update to 6.2.0
Submitted by: Wen Heping(myself)
Approved by: maintainer(via Email)
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Sun, 28 Mar 2010
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[ 06:47 dinoex ] (Only the first 10 of 4470 ports in this commit are shown above. )
- update to 1.4.1
Reviewed by: exp8 run on pointyhat
Supported by: miwi
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Fri, 5 Feb 2010
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[ 11:46 dinoex ] (Only the first 10 of 4271 ports in this commit are shown above. )
- update to jpeg-8
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Fri, 14 Aug 2009
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[ 08:33 miwi ]
- Update MASTER_SITES
PR: 137750
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
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Sun, 2 Aug 2009
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[ 19:36 mezz ] (Only the first 10 of 1514 ports in this commit are shown above. )
-Repocopy devel/libtool15 -> libtool22 and libltdl15 -> libltdl22.
-Update libtool and libltdl to 2.2.6a.
-Remove devel/libtool15 and devel/libltdl15.
-Fix ports build with libtool22/libltdl22.
-Bump ports that depend on libltdl22 due to shared library version change.
-Explain what to do update in the UPDATING.
It has been tested with GNOME2, XFCE4, KDE3, KDE4 and other many wm/desktop
and applications in the runtime.
With help: marcus and kwm
Pointyhat-exp: a few times by pav
Tested by: pgollucci, "Romain Tartière" <romain@blogreen.org>, and
a few MarcusCom CVS users. Also, I might have missed a few.
Repocopy by: marcus
Approved by: portmgr
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Fri, 31 Jul 2009
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[ 13:57 dinoex ] (Only the first 10 of 3009 ports in this commit are shown above. )
- bump all port that indirectly depends on libjpeg and have not yet been bumped
or updated
Requested by: edwin
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Sat, 14 Mar 2009
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[ 15:16 miwi ]
- Force commit to correct the entry
- Update to 6.0.1
PR: 132504
Submitted by: Wen Heping <wenheping@gmail.com>
Approved by: maintainer
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[ 15:14 miwi ]
- Update to 0.1.24
PR: 132527
Submitted by: Wen Heping <wenheping@gmail.com>
Approved by: maintainer
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Thu, 17 Apr 2008
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[ 17:06 pav ]
- Replace SF with second working master site
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
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[ 01:31 rafan ]
- It seems that upstream removes their distfiles from sourceforge, so add
the download site pointed by their webpage as first choice.
Noticed by: pointyhat via pav
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Sun, 13 Apr 2008
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[ 07:22 rafan ] (Only the first 10 of 14 ports in this commit are shown above. )
- Update to 5.0.0
PR: ports/122437
Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
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Sun, 23 Mar 2008
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[ 16:44 miwi ] (Only the first 10 of 104 ports in this commit are shown above. )
- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Bump PORTREVISION
Approved by: portmgr (xorg cleanup)
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Sat, 19 May 2007
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[ 20:32 flz ] (Only the first 10 of 7868 ports in this commit are shown above. )
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
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Fri, 31 Mar 2006
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[ 09:43 thierry ] (Only the first 10 of 23 ports in this commit are shown above. )
For EMBOSS:
This patch brings EMBOSS up to date with the current version.
i. The patches included in files/ are bugfixes for files in
EMBOSS-3.0.0 that appeared after the release. They are
documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README
This is just 'for the record' so that we remember to remove these
patches in the next update.
ii. EMBOSS is now installed by default in LOCALBASE/emboss
This is to avoid CONFLICTS with other ports that install files
with the same names. Installing EMBOSS to another PREFIX is also
possible.(Only the first 15 lines of the commit message are shown above )
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Thu, 23 Feb 2006
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[ 10:40 ade ] (Only the first 10 of 2514 ports in this commit are shown above. )
Conversion to a single libtool environment.
Approved by: portmgr (kris)
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Thu, 2 Feb 2006
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[ 23:12 marcus ]
Remove CONFLICTS with nss.
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Tue, 15 Nov 2005
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[ 06:52 ade ] (Only the first 10 of 1438 ports in this commit are shown above. )
Mass-conversion to the USE_AUTOTOOLS New World Order. The code present
in bsd.autotools.mk essentially makes this a no-op given that all the
old variables set a USE_AUTOTOOLS_COMPAT variable, which is parsed in
exactly the same way as USE_AUTOTOOLS itself.
Moreover, USE_AUTOTOOLS has already been extensively tested by the GNOME
team -- all GNOME 2.12.x ports use it.
Preliminary documentation can be found at:
http://people.FreeBSD.org/~ade/autotools.txt
which is in the process of being SGMLized before introduction into the
Porters Handbook.
Light blue touch-paper. Run.
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Sun, 29 May 2005
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[ 18:26 pav ]
- Update to 2.10.0
PR: ports/81579
Submitted by: "Choe, Cheng-Dae" <whitekid@gmail.com>
Approved by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
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Fri, 11 Feb 2005
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[ 21:11 sem ]
- Add (or fix) CONFLICTS line. The ports install bin/digest.
Approved by: portmgr (krion)
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Fri, 26 Nov 2004
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[ 01:11 sem ]
- Update to 2.9.0
- Pass maintainership to submitter
PR: ports/74333
Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar>
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Sat, 20 Nov 2004
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[ 07:40 linimon ]
With portmgr hat on, reset inactive maintainer.
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Wed, 23 Jun 2004
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[ 08:20 vs ]
Fix MASTER_SITES:
- add trailing slash
- ftp.ebi.ac.uk only has 2.8.0
PR: ports/67427
Submitted by: Roman Neuhauser
Approved by: maintainer timeout
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Wed, 4 Feb 2004
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[ 05:21 marcus ] (Only the first 10 of 1588 ports in this commit are shown above. )
Bump PORTREVISION on all ports that depend on gettext to aid with upgrading.
(Part 2)
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Thu, 20 Nov 2003
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[ 15:06 trevor ] (Only the first 10 of 111 ports in this commit are shown above. )
Define USE_PERL5_BUILD, not erroneous USE_PERL.
Submitted by: Oliver Eikemeier
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[ 13:51 trevor ] (Only the first 10 of 111 ports in this commit are shown above. )
Define USE_PERL to make Perl available for (mostly deprecated)
"perl -pi -e" construction.
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Mon, 18 Aug 2003
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[ 16:15 nork ] (Only the first 10 of 85 ports in this commit are shown above. )
o Main modification
graphics/gd(based on 1.8.4) -> graphics/gd1
graphics/gd2(based on 2.0.15) -> graphics/gd
graphics/p5-GD(based on 1.41) -> graphics/p5-GD1
graphics/p5-GD2(based on 2.07) -> graphics/p5-GD
japanese/gd -> japanese/gd1
japanese/gd2 -> japanese/gd
o Include some feature
WITH_XPM(w/, w/o WITHOUT_X11)
o Chase this modification
o Fix build error [1]
PR: ports/54540
Submitted by: Ports Fury
Approved by: maintainer (blanket)
Reported by: bento via kris [1]
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Fri, 8 Aug 2003
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[ 04:40 kris ] (Only the first 10 of 70 ports in this commit are shown above. )
This port is scheduled for removal on Nov 7 2003 if it is still broken at
that time and no PRs have been submitted to fix it. If you are interested
in saving this port, please send your patches to the maintainer. If the
maintainer is unresponsive or the port has no maintainer, then please
submit them via send-pr.
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Thu, 7 Aug 2003
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[ 09:29 kris ]
BROKEN: Checksum mismatch
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Fri, 11 Jul 2003
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[ 18:16 nork ] (Only the first 10 of 33 ports in this commit are shown above. )
o Change library name from libgd to libgd1.
o Do not install everything except headers and libraries
(to avoid conflicting with graphics/gd2)
o Fix dependency on new libgd1(for many ports).
PR: ports/54100
Submitted by: Ports Fury
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Fri, 7 Mar 2003
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[ 05:56 ade ] (Only the first 10 of 28 ports in this commit are shown above. )
Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.
E Nomini Patri, E Fili, E Spiritu Sancti.
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Fri, 27 Sep 2002
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[ 08:58 wjv ]
- Unbreak fetching of distfiles. (Needs update as soon as freeze is over.)
Submitted by: kris, bento
Approved by: Implicitly by first rule of ports freeze, I hope!
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Fri, 20 Sep 2002
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[ 20:45 kris ]
BROKEN: Does not fetch
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Fri, 5 Jul 2002
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[ 10:09 wjv ]
- Update to version 2.4.1
- Unmark BROKEN
- Start adding support for Jemboss Java-based GUI (not active yet)
PR: 40198 ; many private requests
Submitted by: Tilman Linneweh <tilman@arved.de> (2.4.1 update)
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Fri, 17 May 2002
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[ 09:24 kris ]
BROKEN: incorrect checksums
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Mon, 25 Mar 2002
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[ 09:19 sobomax ] (Only the first 10 of 24 ports in this commit are shown above. )
Add USE_SUBMAKE, where it might be necessary.
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Fri, 18 Jan 2002
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[ 14:04 wjv ]
- Update to version 2.2.0 - Update included EMBASSY package EMNU - Fix a
long-standing bug in Makefile that would preclude PKGMESSAGE from being
generated properly - Consider this an interim update merely to track the
latest version - more work is required to activate the newly included
"Jemboss" Java GUI interface
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Fri, 3 Aug 2001
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[ 12:32 wjv ]
- Update port to version 2.0.1 - Add two new EMBASSY applications, MEME and
HMMER.
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Wed, 27 Jun 2001
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[ 11:15 wjv ] (Only the first 10 of 17 ports in this commit are shown above. )
Updating my email address in my remaining ports.
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Fri, 15 Jun 2001
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[ 13:11 wjv ]
Update to 1.13.3; remove bogus file.
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Wed, 30 May 2001
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[ 15:34 kevlo ]
Update to version 1.13.1
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Mon, 7 May 2001
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[ 13:18 jeh ]
Update the EMBOSS suite (biology/emboss) to version 1.12.0
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Mon, 12 Mar 2001
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[ 10:33 nbm ]
Update the EMBOSS suite to v1.11.0
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Wed, 28 Feb 2001
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[ 15:58 kevlo ]
Update to version 1.10.1
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Tue, 20 Feb 2001
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[ 15:51 kevlo ]
Update to version 1.10.0
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Mon, 12 Feb 2001
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[ 10:01 knu ] (Only the first 10 of 18 ports in this commit are shown above. )
Chase graphics/gd's shlib version bump.
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Mon, 29 Jan 2001
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[ 15:48 kevlo ]
- Update EMBOSS (biology/emboss) from 1.9.0 to 1.9.1 - Update the EMBASSY
package EMNU from 1.0.2 to 1.0.3 - Merged the four pkg-plist* files into one
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Wed, 24 Jan 2001
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[ 11:36 kevlo ]
Upgrade to version 1.9.0
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Mon, 4 Dec 2000
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[ 13:00 roam ]
Update distfiles' checksums after the distfiles have been rerolled yet again
without changing names or versions. Also add a new MASTER_SITE.
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Tue, 28 Nov 2000
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[ 01:43 jeh ]
- Update port biology/emboss from 1.7.0 to 1.8.0
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Sun, 19 Nov 2000
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[ 03:06 jeh ]
Make nolonger support :U. Fix to compensate for that.
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Mon, 13 Nov 2000
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[ 13:48 jeh ]
- This is a fairly extensive rework of this port. - "EMBASSY" applications are
third party tools which have been adapted to function as part of EMBOSS, but
which are not included with the base EMBOSS distribution for licensing or
other reasons. This new version of the EMBOSS port now contains the three
current EMBASSY applications as well, and during installation the user is
presented with a dialog(1) menu to choose which of these should be
isntalled.
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Wed, 1 Nov 2000
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[ 11:54 jeh ]
Make portlint happy, remove a space
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[ 11:49 jeh ]
Update to version 1.7.0
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Tue, 10 Oct 2000
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[ 05:54 kevlo ]
- Update to 1.6.0 - Reorder packing list
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Fri, 22 Sep 2000
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[ 11:24 kris ]
Add USE_XLIB
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Fri, 8 Sep 2000
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[ 11:07 nbm ]
Upgrade to 1.5.0
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Thu, 7 Sep 2000
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[ 15:02 nbm ]
Update to emboss 1.4.0.
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Mon, 21 Aug 2000
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[ 11:07 sobomax ] (Only the first 10 of 29 ports in this commit are shown above. )
USE_LIBTOOL implies GNU_CONFIGURE, so remove redundant GNU_CONFIGURE lines.
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Sat, 12 Aug 2000
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[ 17:15 nbm ]
Update to emboss 1.1.0, fixing some style bugs too.
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Mon, 31 Jul 2000
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[ 20:13 nbm ]
Add emboss, the European Molecular Biology Open Software Suite
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Number of commits found: 86 |
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