22:53 Muhammad Moinur Rahman (bofh) 

biology/emboss: Optionize mysql support

The port builds fine without mysql and as MySQL57 is reaching end of
life so optionize MYSQL so that other flavors can be used and still
there is an available pkg for this port.

Approved by:	portmgr (blanket)

    23253ea

10:39 Muhammad Moinur Rahman (bofh) 

biology/emboss: Ignore with mysql 8.0

PR:		269203
Reported by:	exp-run

    6db7a8c

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

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

09:50 Stefan Eßer (se) 

*/*: 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)

    819f25b

21:34 Jason W. Bacon (jwb) 

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]

    c68b6dc

15:13 Jason W. Bacon (jwb) 

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

    e47c577

14:21 Jason W. Bacon (jwb) 

biology/emboss: Add emboss-shell: Run subshell with proper PATH

Also silence portlint and stage-qa warnings

PR:             258316
Approved by:    wen

    fa2e0b8

14:31 Mathieu Arnold (mat) 

Remove # $FreeBSD$ from Makefiles.

    305f148

21:31 dinoex 

- update libgd to 2.3.0
- new option RAQM
- resurrect deprecated gdlib-config
- bump dependend ports

 

20:20 zeising 

Sprinkle more USES=xorg

 

09:33 dinoex 

- 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

 

13:29 mat 

Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight

 

21:52 bapt 

Fix packaging as a user (pkg already takes care of credentials)
Strip binaries

 

20:54 bapt 

Bump portrevision after png update

 

19:04 antoine 

Change libpng15.so to libpng.so in LIB_DEPENDS to prepare the upgrade

 

11:21 olgeni 

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)

 

03:28 miwi 

- Update to 6.6.0
- Stage support

PR:		190508
Submitted by:	Muhammad Moinur Rahman

 

09:45 bapt 

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

 

14:43 bapt 

In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology

 

15:55 bapt 

Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)

 

14:05 dinoex 

- update libdg to 2.1.0

 

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

 

14:55 wen 

- Take maintainership

 

14:45 tabthorpe 

- Reassign to the heap at maintainer's request

 

05:26 dinoex 

- update png to 1.5.10

12:44 makc 

Bump PORTREVISION after open-mofit update

07:34 ade 

Sync to new bsd.autotools.mk

01:16 wen 

- Update to 6.2.0

Submitted by:   Wen Heping(myself)
Approved by:    maintainer(via Email)

06:47 dinoex 

- update to 1.4.1
Reviewed by:    exp8 run on pointyhat
Supported by:   miwi

11:46 dinoex 

- update to jpeg-8

08:33 miwi 

- Update MASTER_SITES

PR:             137750
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

19:36 mezz 

-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

13:57 dinoex 

- bump all port that indirectly depends on libjpeg and have not yet been bumped
or updated
Requested by:   edwin

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

15:14 miwi 

- Update to 0.1.24

PR:             132527
Submitted by:   Wen Heping <wenheping@gmail.com>
Approved by:    maintainer

17:06 pav 

- Replace SF with second working master site

Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

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

07:22 rafan 

- Update to 5.0.0

PR:             ports/122437
Submitted by:   Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)

16:44 miwi 

- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Bump PORTREVISION

Approved by:    portmgr (xorg cleanup)

20:32 flz 

- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.

09:43 thierry 

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.

        iii. now EMBASSY and EMBOSS both store their distfiles in the same
             DIST_SUBDIR

        iv.  use built-in PKGMESSAGE and SUB_FILES instead of doing it the old
             (manual) way

        For EMBASSY:

        This update brings embassy in sync with the update of EMBOSS to 3.0.0.

        Things that changed from previous version of the port:

        i.  embassy now installs by default in $LOCALBASE/emboss (the
            new default PREFIX for emboss as well).

        ii. changed DIST_SUBDIR so that all the distfiles are put together with
            emboss. This makes sense(TM)

        iii. incorporated new EMBASSY apps (this accounts for the changes in
             OPTIONS and pkg-plist)

        iv.  removed obsoleted patches

        Finally, I included a sample text that could go in UPDATING.

PR:             93053
Submitted by:   Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)

10:40 ade 

Conversion to a single libtool environment.

Approved by:    portmgr (kris)

23:12 marcus 

Remove CONFLICTS with nss.

06:52 ade 

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.

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)

21:11 sem 

- Add (or fix) CONFLICTS line. The ports install bin/digest.

Approved by:    portmgr (krion)

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>

07:40 linimon 

With portmgr hat on, reset inactive maintainer.

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

05:21 marcus 

Bump PORTREVISION on all ports that depend on gettext to aid with upgrading.

(Part 2)

15:06 trevor 

Define USE_PERL5_BUILD, not erroneous USE_PERL.

Submitted by:   Oliver Eikemeier

13:51 trevor 

Define USE_PERL to make Perl available for (mostly deprecated)
"perl -pi -e" construction.

16:15 nork 

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]

04:40 kris 

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.

09:29 kris 

BROKEN: Checksum mismatch

18:16 nork 

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

05:56 ade 

Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.

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!

20:45 kris 

BROKEN: Does not fetch

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)

09:24 kris 

BROKEN: incorrect checksums

09:19 sobomax 

Add USE_SUBMAKE, where it might be necessary.

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    

12:32 wjv 

- Update port to version 2.0.1   - Add two new EMBASSY applications, MEME and
HMMER.    

11:15 wjv 

Updating my email address in my remaining ports.    

13:11 wjv 

Update to 1.13.3; remove bogus file.    

15:34 kevlo 

Update to version 1.13.1    

13:18 jeh 

Update the EMBOSS suite (biology/emboss) to version 1.12.0    

10:33 nbm 

Update the EMBOSS suite to v1.11.0    

15:58 kevlo 

Update to version 1.10.1    

15:51 kevlo 

Update to version 1.10.0    

10:01 knu 

Chase graphics/gd's shlib version bump.    

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  
 

11:36 kevlo 

Upgrade to version 1.9.0    

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.    

01:43 jeh 

- Update port biology/emboss from 1.7.0 to 1.8.0    

03:06 jeh 

Make nolonger support :U.  Fix to compensate for that.    

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.    

11:54 jeh 

Make portlint happy, remove a space    

11:49 jeh 

Update to version 1.7.0    

05:54 kevlo 

- Update to 1.6.0   - Reorder packing list    

11:24 kris 

Add USE_XLIB    

11:07 nbm 

Upgrade to 1.5.0    

15:02 nbm 

Update to emboss 1.4.0.    

11:07 sobomax 

USE_LIBTOOL implies GNU_CONFIGURE, so remove redundant GNU_CONFIGURE lines.    

17:15 nbm 

Update to emboss 1.1.0, fixing some style bugs too.    

20:13 nbm 

Add emboss, the European Molecular Biology Open Software Suite