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non port: biology/ncbi-toolkit/Makefile

Number of commits found: 57

Friday, 12 Jan 2024
15:11 Baptiste Daroussin (bapt) search for other commits by this committer
MANPREFIX: eliminate its usage

While here move manpages to share/man
commit hash: d4329229fbe8ad0a96a1b9ec796d17cf512455d1 commit hash: d4329229fbe8ad0a96a1b9ec796d17cf512455d1 commit hash: d4329229fbe8ad0a96a1b9ec796d17cf512455d1 commit hash: d4329229fbe8ad0a96a1b9ec796d17cf512455d1 d432922
Friday, 28 Jul 2023
17:13 Daniel Engberg (diizzy) search for other commits by this committer
*/*: Bump jpeg-turbo users treewide

New major version 3.0.0
commit hash: 664a2fa1e56e670a356f54c94389bdb47d868f3f commit hash: 664a2fa1e56e670a356f54c94389bdb47d868f3f commit hash: 664a2fa1e56e670a356f54c94389bdb47d868f3f commit hash: 664a2fa1e56e670a356f54c94389bdb47d868f3f 664a2fa
Wednesday, 26 Jul 2023
00:48 Muhammad Moinur Rahman (bofh) search for other commits by this committer
*/*: 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
commit hash: 95274bf4f99c71fc056013d966aec239161dfd74 commit hash: 95274bf4f99c71fc056013d966aec239161dfd74 commit hash: 95274bf4f99c71fc056013d966aec239161dfd74 commit hash: 95274bf4f99c71fc056013d966aec239161dfd74 95274bf
Thursday, 20 Jul 2023
17:42 Muhammad Moinur Rahman (bofh) search for other commits by this committer
biology/ncbi-toolkit: Fix build with llvm16

Approved by:	portmgr (blanket)
Sponsored by:	The FreeBSD Foundation
commit hash: 1da1ae626f93ca16ce1874ee5ffdf77540fa2817 commit hash: 1da1ae626f93ca16ce1874ee5ffdf77540fa2817 commit hash: 1da1ae626f93ca16ce1874ee5ffdf77540fa2817 commit hash: 1da1ae626f93ca16ce1874ee5ffdf77540fa2817 1da1ae6
Tuesday, 6 Jun 2023
20:45 Muhammad Moinur Rahman (bofh) search for other commits by this committer
biology/ncbi-toolkit: Fix build with llvm15

Approved by:	portmgr (blanket)
commit hash: ed5efb16c468d45308d1909e75c8c5c19cfcd708 commit hash: ed5efb16c468d45308d1909e75c8c5c19cfcd708 commit hash: ed5efb16c468d45308d1909e75c8c5c19cfcd708 commit hash: ed5efb16c468d45308d1909e75c8c5c19cfcd708 ed5efb1
Saturday, 22 Oct 2022
09:36 Daniel Engberg (diizzy) search for other commits by this committer
*/*: Bump PORTREVISION for consumers of libunistring

Reported by:	jbeich
commit hash: df6c65a0267a323b1adfc7dca649e9f7b649cc7c commit hash: df6c65a0267a323b1adfc7dca649e9f7b649cc7c commit hash: df6c65a0267a323b1adfc7dca649e9f7b649cc7c commit hash: df6c65a0267a323b1adfc7dca649e9f7b649cc7c df6c65a
Wednesday, 7 Sep 2022
21:10 Stefan Eßer (se) search for other commits by this committer
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)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Wednesday, 20 Jul 2022
14:20 Tobias C. Berner (tcberner) search for other commits by this committer
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
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 37526bb
Wednesday, 29 Jun 2022
14:53 Stefan Eßer (se) search for other commits by this committer
Fix CONFLICTS_INSTALL in benchmarks and biology

Approved by:	portmgr (implicit)
commit hash: b52114270fb74b73a57ab9e58cfb84f4ac0271a3 commit hash: b52114270fb74b73a57ab9e58cfb84f4ac0271a3 commit hash: b52114270fb74b73a57ab9e58cfb84f4ac0271a3 commit hash: b52114270fb74b73a57ab9e58cfb84f4ac0271a3 b521142
Sunday, 6 Feb 2022
18:36 Stefan Eßer (se) search for other commits by this committer
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)
commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e bdd2d4a
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Sunday, 30 Aug 2020
03:10 novel search for other commits by this committer
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
Original commitRevision:546967 
Saturday, 16 May 2020
10:51 sunpoet search for other commits by this committer
Bump PORTREVISION for security/nettle shlib change
Original commitRevision:535391 
Saturday, 28 Sep 2019
10:52 zeising search for other commits by this committer
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.
Original commitRevision:513114 
Friday, 27 Sep 2019
16:18 zeising search for other commits by this committer
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
Original commitRevision:513046 
Tuesday, 9 Jul 2019
17:13 sunpoet search for other commits by this committer
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]
Original commitRevision:506289 
Saturday, 9 Feb 2019
23:25 sunpoet search for other commits by this committer
Update dns/libidn2 to 2.1.1

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://gitlab.com/libidn/libidn2/blob/master/NEWS
Original commitRevision:492534 
Sunday, 6 Jan 2019
20:39 sunpoet search for other commits by this committer
Update dns/libidn2 to 2.1.0

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://gitlab.com/libidn/libidn2/blob/master/NEWS
Original commitRevision:489529 
Sunday, 7 Oct 2018
18:29 yuri search for other commits by this committer
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
Original commitRevision:481472 
Thursday, 8 Dec 2016
16:39 tijl search for other commits by this committer
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.
Original commitRevision:428135 
Wednesday, 2 Nov 2016
22:45 mat search for other commits by this committer
Cleanup no longer needed CHMOD usage after r424898.

PR:		213743
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
Original commitRevision:425174 
Friday, 24 Jun 2016
09:04 amdmi3 search for other commits by this committer
- Add missing dependency, fixing build
- Switch to options helpers
Original commitRevision:417414 
Sunday, 23 Mar 2014
20:50 pawel search for other commits by this committer
Add staging support
Original commitRevision:348888 
Friday, 20 Sep 2013
15:55 bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
Original commitRevision:327709 
Wednesday, 4 Sep 2013
18:06 madpilot search for other commits by this committer
- 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)
Original commitRevision:326307 
Tuesday, 9 Jul 2013
21:49 bapt search for other commits by this committer
Convert from USE_MOTIF to USES=motif
While here:
- trim headers
- Remove indefinite article from comment
- convert USE_GMAKE to USES=gmake
Original commitRevision:322587 
Thursday, 14 Mar 2013
05:27 miwi search for other commits by this committer
- Update to 2012.06.20

PR:		176544
Submitted by:	Ports Fury
Original commitRevision:314129 
Monday, 1 Oct 2012
14:45 tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
Original commitRevision:305130 
Monday, 2 May 2011
12:41 makc search for other commits by this committer
Fix build with open-motif-2.3.3

PR:             ports/154044
Submitted by:   Mikhail Tsatsenko <m.tsatsenko at gmail.com>
Exp-runs by:    pav
Original commit
Sunday, 31 Jan 2010
03:42 pgollucci search for other commits by this committer
- 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)
Original commit
Saturday, 28 Mar 2009
16:59 miwi search for other commits by this committer
- Update to 2009.03.01

PR:             133099
Submitted by:   Fernan Aguero <fernan.aguero@gmail.com>
Approved by:    maintainer
Original commit
Saturday, 19 Apr 2008
17:56 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)
Original commit
Saturday, 19 May 2007
20:32 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}.
Original commit
Saturday, 9 Dec 2006
07:48 rafan search for other commits by this committer
- Respect X11BASE

Approved by:    portmgr (linimon)
Original commit
Tuesday, 6 Jun 2006
12:05 itetcu search for other commits by this committer
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)
Original commit
Saturday, 14 Jan 2006
19:34 pav search for other commits by this committer
- Update to 2005.12.06

PR:             ports/91714
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Original commit
Tuesday, 11 Oct 2005
22:33 sem search for other commits by this committer
- Update to 20050605

PR:             ports/87266
Submitted by:   maintainer
Original commit
Wednesday, 14 Sep 2005
09:24 vs search for other commits by this committer
Don't strip static libraries on installation ;)
(Unbreaks e.g. biology/nclever)
Original commit
Sunday, 20 Mar 2005
11:47 pav search for other commits by this committer
- Fix man page damage I did last night

Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Original commit
Saturday, 19 Mar 2005
21:32 pav search for other commits by this committer
- 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
Original commit
Monday, 1 Nov 2004
22:21 pav search for other commits by this committer
- Update to 2004.06.16

Inspired by:    ports/72726
Approved by:    maintainer timeout (2 weeks)
Original commit
Thursday, 13 Nov 2003
14:45 trevor search for other commits by this committer
Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.
Original commit
Monday, 5 May 2003
12:24 arved search for other commits by this committer
Update to 2003.04.21

PR:             51709
Submitted by:   Tony Maher <tonymaher@optushome.com.au>
Original commit
Friday, 21 Feb 2003
11:01 knu search for other commits by this committer
De-pkg-comment.
Original commit
Saturday, 21 Sep 2002
14:56 ijliao search for other commits by this committer
add forgotten "USE_REINPLACE=yes"

Submitted by:   maintainer
Original commit
06:59 ijliao search for other commits by this committer
upgrade to 20020426

PR:             39357
Submitted by:   maintainer
Original commit
Saturday, 8 Jun 2002
00:40 petef search for other commits by this committer
Correct MASTER_SITES.

PR:             39016
Submitted by:   maintainer
Original commit
Friday, 22 Feb 2002
07:57 pat search for other commits by this committer
Update to 2001.12.20    
Original commit
Wednesday, 19 Sep 2001
14:03 wjv search for other commits by this committer
- Add installation of include files   - Bump PORTREVISION    
Original commit
Monday, 6 Aug 2001
11:50 wjv search for other commits by this committer
Update maintainer's email address.    
Original commit
Tuesday, 10 Jul 2001
17:35 fenner search for other commits by this committer
Update Tony Maher's email address.    
Original commit
Wednesday, 20 Jun 2001
15:25 wjv search for other commits by this committer
Update to version 2001.04.03; add installation of some documentation.    
Original commit
Wednesday, 15 Nov 2000
00:54 jeh search for other commits by this committer
They made changes to the "blast" program.    
Original commit
Tuesday, 7 Nov 2000
23:28 asami search for other commits by this committer
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.    
Original commit
Friday, 3 Nov 2000
13:23 jeh search for other commits by this committer
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    
Original commit
Thursday, 2 Nov 2000
11:25 jeh search for other commits by this committer
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.    
Original commit
Sunday, 29 Oct 2000
13:56 jeh search for other commits by this committer
New Port: biology/ncbi-toolkit   National Center for Biotechnology Information
(NCBI) Development Toolkit.    
Original commit

Number of commits found: 57