non port: biology/ncbi-toolkit/Makefile |
Number of commits found: 57 |
Friday, 12 Jan 2024
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15:11 Baptiste Daroussin (bapt)
MANPREFIX: eliminate its usage
While here move manpages to share/man
d432922 |
Friday, 28 Jul 2023
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17:13 Daniel Engberg (diizzy)
*/*: Bump jpeg-turbo users treewide
New major version 3.0.0
664a2fa |
Wednesday, 26 Jul 2023
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00:48 Muhammad Moinur Rahman (bofh)
*/*: Fix build with llvm16 on 13.2-STABLE
As like as HEAD(14.0-RELEASE) llvm16 was merged in base for 13.2-STABLE
with the OSVERSION 1302507.
- Utilize USE_CXXSTD=c++14 or similar solution where applicable
- Update conditionals to addtionally check for OSVERSION greater than
1302507 and less than 1400000
Approved by: portmgr (blanket)
Sponsored by: The FreeBSD Foundation
95274bf |
Thursday, 20 Jul 2023
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17:42 Muhammad Moinur Rahman (bofh)
biology/ncbi-toolkit: Fix build with llvm16
Approved by: portmgr (blanket)
Sponsored by: The FreeBSD Foundation
1da1ae6 |
Tuesday, 6 Jun 2023
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20:45 Muhammad Moinur Rahman (bofh)
biology/ncbi-toolkit: Fix build with llvm15
Approved by: portmgr (blanket)
ed5efb1 |
Saturday, 22 Oct 2022
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09:36 Daniel Engberg (diizzy)
*/*: Bump PORTREVISION for consumers of libunistring
Reported by: jbeich
df6c65a |
Wednesday, 7 Sep 2022
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21:10 Stefan Eßer (se)
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.
This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.
There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.
The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.
Approved by: portmgr (tcberner)
b7f0544 |
Wednesday, 20 Jul 2022
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14:20 Tobias C. Berner (tcberner)
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>
* Johann Visagie <johann@egenetics.com>
* Johann Visagie <wjv@FreeBSD.org>
* Mauricio Herrera Cuadra <mauricio@arareko.net>
* Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
* Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
* Motomichi Matsuzaki <mzaki@niid.go.jp>
* Po-Chuan Hsieh <sunpoet@FreeBSD.org>
* Razi Khaja <razi@genet.sickkids.on.ca>
* Reed A. Cartwright <cartwright@asu.edu>
* Ryo MIYAMOTO
* Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
* Sangwoo Shim <sangwoos@gmail.com>
* Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
* Tassilo Philipp <tphilipp@potion-studios.com>
* Tony Maher
* Tony Maher <tonym@biolateral.com.au>
* Wen Heping <wen@FreeBSD.org>
* Wen Heping <wenheping@gmail.com>
* Yonatan <onatan@gmail.com>
* Yuri Victorovich <yuri@rawbw.com>
* ballen
* barnhart@genetics.wustl.edu
* camson@bilateral.com.au
* chuynh@biolateral.com.au
* dbader@eece.unm.edu
* frankch@waru.life.nthu.edu.tw
* h2
* lentferj
* maho@FreeBSD.org
* mzaki@biol.s.u-tokyo.ac.jp
* tonym
* wen@FreeBSD.org
With hat: portmgr
37526bb |
Wednesday, 29 Jun 2022
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14:53 Stefan Eßer (se)
Fix CONFLICTS_INSTALL in benchmarks and biology
Approved by: portmgr (implicit)
b521142 |
Sunday, 6 Feb 2022
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18:36 Stefan Eßer (se)
Update CONFLICTS definitions in categories a* to c*
Update the CONFLICTS definitions of ports in the following categories:
- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters
An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.
There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.
Approved by: portmgr (implicit)
bdd2d4a |
Tuesday, 6 Apr 2021
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14:31 Mathieu Arnold (mat)
Remove # $FreeBSD$ from Makefiles.
305f148 |
Sunday, 30 Aug 2020
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03:10 novel
Chase security/p11-kit update
After switch to meson libp11-kit.so no longer has symbols
in the LIBP11_KIT_1.0 namespace. As a workaround, bump
PORTREVISION of consumers to get those rebuilt.
See more details in the comments of the linked PR.
PR: 248819
Reported by: John Hein
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Saturday, 16 May 2020
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10:51 sunpoet
Bump PORTREVISION for security/nettle shlib change
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Saturday, 28 Sep 2019
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10:52 zeising
biologi/ncbi-toolkit: Remove dependency on libXp
Remove the dependency on libXp from ncbi-toolkit, since libXp is deprecated
and it isn't needed.
Remove deprecation from ncbi-toolkit.
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Friday, 27 Sep 2019
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16:18 zeising
Deprecate x11/libXp, it is deprecated upstream
Deprecate x11/libXp, since it is about to be deprecated upstream. Do *not*
yet set a removal date for x11/libXp, this will be decided later, once most
dependencies are fixed.
Deprecate all ports depending on x11/libXp.
* astro/xephem
* audio/xmcd
* audio/xmmix
* biology/ncbi-toolkit
* deskutils/xmdiary
* ftp/llnlxdir
* ftp/llnlxftp
* graphics/SciPlot
* misc/xtar
* multimedia/mpeg2play
* science/afni
* textproc/mgdiff
Sprinkle USES=xorg as needed.
Discussed with: bapt
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Tuesday, 9 Jul 2019
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17:13 sunpoet
Update security/nettle to 3.5.1
- Bump PORTREVISION of dependent ports for shlib change
- Fix build of devel/pijul [1]
Changes: https://git.lysator.liu.se/nettle/nettle/blob/master/NEWS
PR: 238991
Exp-run by: antoine
Thanks to: tobik [1]
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Saturday, 9 Feb 2019
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23:25 sunpoet
Update dns/libidn2 to 2.1.1
- Bump PORTREVISION of dependent ports for shlib change
Changes: https://gitlab.com/libidn/libidn2/blob/master/NEWS
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Sunday, 6 Jan 2019
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20:39 sunpoet
Update dns/libidn2 to 2.1.0
- Bump PORTREVISION of dependent ports for shlib change
Changes: https://gitlab.com/libidn/libidn2/blob/master/NEWS
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Sunday, 7 Oct 2018
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18:29 yuri
biology/ncbi-toolkit: Update 2012.06.20 -> 2017.01.06
Port changes:
* Take maintainership
* Add to LIB_DEPENDS and USExx
* Remove lists of executables and manpages, use file listing instead (*)
* Update WWW
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Thursday, 8 Dec 2016
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16:39 tijl
Remove libjpeg.so.11 compatibility link that was added in r374303 to
prevent massive PORTREVISION bumps. Bump dependent ports that have not
been bumped since.
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Wednesday, 2 Nov 2016
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22:45 mat
Cleanup no longer needed CHMOD usage after r424898.
PR: 213743
Submitted by: mat
Exp-run by: antoine
Sponsored by: Absolight
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Friday, 24 Jun 2016
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09:04 amdmi3
- Add missing dependency, fixing build
- Switch to options helpers
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Sunday, 23 Mar 2014
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20:50 pawel
Add staging support
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Friday, 20 Sep 2013
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15:55 bapt
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
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Wednesday, 4 Sep 2013
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18:06 madpilot
- Make ports use the libc provided iconv implementation on 10-CURRENT
after r254273
- Fix a bunch of ports to properly work after this
- Mark converters/libiconv as IGNORE for systems with iconv in libc
Reviewed by: bapt
Approved by: portmgr (bapt)
Discussed with: bapt, bsam (who both contributed ideas and code)
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Tuesday, 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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Thursday, 14 Mar 2013
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05:27 miwi
- Update to 2012.06.20
PR: 176544
Submitted by: Ports Fury
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Monday, 1 Oct 2012
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14:45 tabthorpe
- Reassign to the heap at maintainer's request
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Monday, 2 May 2011
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12:41 makc
Fix build with open-motif-2.3.3
PR: ports/154044
Submitted by: Mikhail Tsatsenko <m.tsatsenko at gmail.com>
Exp-runs by: pav
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Sunday, 31 Jan 2010
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03:42 pgollucci
- use $SUB_FILES to dynamically adjust pkg-message
PR: ports/142408
Submitted by: Sevan Janiyan <venture37@geeklan.co.uk>
Approved by: fernan@iib.unsam.edu.ar (maintainer)
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Saturday, 28 Mar 2009
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16:59 miwi
- Update to 2009.03.01
PR: 133099
Submitted by: Fernan Aguero <fernan.aguero@gmail.com>
Approved by: maintainer
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Saturday, 19 Apr 2008
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17:56 miwi
- 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)
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Saturday, 19 May 2007
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20:32 flz
- 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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Saturday, 9 Dec 2006
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07:48 rafan
- Respect X11BASE
Approved by: portmgr (linimon)
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Tuesday, 6 Jun 2006
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12:05 itetcu
Update biology/ncbi-toolkit to the latest release.
Quoting from www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml
Major changes include:
blastall now uses the new engine by default, resulting
in significant performance improvements and enabling
query concatenation for all program types.
PR: ports/98570
Submitted by: maintainer
Approved by: lawrance (mentor, implict)
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Saturday, 14 Jan 2006
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19:34 pav
- Update to 2005.12.06
PR: ports/91714
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
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Tuesday, 11 Oct 2005
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22:33 sem
- Update to 20050605
PR: ports/87266
Submitted by: maintainer
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Wednesday, 14 Sep 2005
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09:24 vs
Don't strip static libraries on installation ;)
(Unbreaks e.g. biology/nclever)
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Sunday, 20 Mar 2005
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11:47 pav
- Fix man page damage I did last night
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
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Saturday, 19 Mar 2005
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21:32 pav
- Update to 2.2.10 from 20041020
- Transfer maintainership
PR: ports/67735
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Approved by: old maintainer indirectly in
http://lists.freebsd.org/pipermail/freebsd-ports-bugs/2004-June/035351.html
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Monday, 1 Nov 2004
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22:21 pav
- Update to 2004.06.16
Inspired by: ports/72726
Approved by: maintainer timeout (2 weeks)
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Thursday, 13 Nov 2003
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14:45 trevor
Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.
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Monday, 5 May 2003
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12:24 arved
Update to 2003.04.21
PR: 51709
Submitted by: Tony Maher <tonymaher@optushome.com.au>
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Friday, 21 Feb 2003
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11:01 knu
De-pkg-comment.
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Saturday, 21 Sep 2002
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14:56 ijliao
add forgotten "USE_REINPLACE=yes"
Submitted by: maintainer
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06:59 ijliao
upgrade to 20020426
PR: 39357
Submitted by: maintainer
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Saturday, 8 Jun 2002
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00:40 petef
Correct MASTER_SITES.
PR: 39016
Submitted by: maintainer
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Friday, 22 Feb 2002
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07:57 pat
Update to 2001.12.20
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Wednesday, 19 Sep 2001
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14:03 wjv
- Add installation of include files - Bump PORTREVISION
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Monday, 6 Aug 2001
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11:50 wjv
Update maintainer's email address.
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Tuesday, 10 Jul 2001
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17:35 fenner
Update Tony Maher's email address.
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Wednesday, 20 Jun 2001
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15:25 wjv
Update to version 2001.04.03; add installation of some documentation.
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Wednesday, 15 Nov 2000
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00:54 jeh
They made changes to the "blast" program.
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Tuesday, 7 Nov 2000
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23:28 asami
Change motif to a normal dependency. REQUIRES_MOTIF is now called USE_MOTIF
and generates a LIB_DEPENDS to x11-toolkits/open-motif. As before, it implies
USE_XPM (and therefore USE_XLIB). Motif-dummy is removed from
PKG_IGNORE_DEPENDS, whose sole resident is now XFree86-3.
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Friday, 3 Nov 2000
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13:23 jeh
Yes. They did re-roll this version, it is legit. They donot version the dist,
but store them in versioned dir. Update Makefile to handle that. Update
CHECKSUM
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Thursday, 2 Nov 2000
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11:25 jeh
Updated to new version. That is the pits, the day after it becomes a port
they release a new version. This is a new version, w/o a number.
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Sunday, 29 Oct 2000
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13:56 jeh
New Port: biology/ncbi-toolkit National Center for Biotechnology Information
(NCBI) Development Toolkit.
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Number of commits found: 57 |