*/*: Refactor with IGNORE_WITH_MYSQL

- There are multiple ports which has MYSQL options and are non-DEFAULT.
  Most of the time committers actually forget to check with the OPTION
  enabled and in some cases they are BROKEN with newr versions of mysql.
  So test with different versions of mysql and mark IGNOPRE_WITH_MYSQL
  appropriately. Due to the EOL of 5.7 this has not been checked.
- Unbreak sysutils/cfengine* with MySQL 8.0 and later
- The primary purpose of running this check is having statistics of the
  MySQL usability over MariaDB to explore the future possibility of
  shifting to MariaDB as the default as major ports upstream have moved
  their codebase to support MariaDB over MySQL.
- The following actions will also be taken after the sunset of MySQL 5.7
  If a port is broken on all instances of MySQL/MariaDB:
  - If a port has the option of multiple DB backends and MySQL is the
    default then the DEFAULT will be changed to PGSQL/SQLITE before
    2024Q1. And the OPTION will be removed before 2024Q2. If a
    MAINTAINER is aware about such cases and want to prefer PGSQL over
    SQLITE or vice versa please do so at your own accord. Otherwise
    PGSQL will be preferred over SQLITE.
  - If a port has the option of multiple DB backends and MySQL is not
    the default then the the OPTION will be removed before 2024Q1.

Approved by:	portmgr (blanket)

biology/emboss: fix build on powerpc*

ajfileio.c:271:7: warning: call to undeclared function 'ajSysFuncFgets'; ISO C99
and later do not support implicit function declarations
[-Wimplicit-function-declaration]
        cp = ajSysFuncFgets(&buff[ipos], isize, file->fp);
             ^
ajfileio.c:271:5: error: incompatible integer to pointer conversion assigning to
'const char *' from 'int' [-Wint-conversion]
        cp = ajSysFuncFgets(&buff[ipos], isize, file->fp);
           ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 warning and 1 error generated.

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)

biology/emboss: Ignore with mysql 8.0

PR:		269203
Reported by:	exp-run

Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)

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.

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>

*/*: 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)

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]

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

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

Also silence portlint and stage-qa warnings

PR:             258316
Approved by:    wen

Remove # $FreeBSD$ from Makefiles.

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

Sprinkle more USES=xorg

Convert to UCL & cleanup pkg-message (categories a-c)

- 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

- Fix trailing whitespace in pkg-messages

Approved by:	portmgr blanket

- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket

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

With hat:	portmgr
Sponsored by:	Absolight

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

Bump portrevision after png update

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

Cleanup plist

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)

- Update to 6.6.0
- Stage support

PR:		190508
Submitted by:	Muhammad Moinur Rahman

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

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

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

- update libdg to 2.1.0

Convert from USE_MOTIF to USES=motif
While here:
- trim headers
- Remove indefinite article from comment
- convert USE_GMAKE to USES=gmake

- Take maintainership

- Reassign to the heap at maintainer's request

- update png to 1.5.10

- remove maintainer tags from pkg-descr

Approved by:    portmgr
Approved by:    bapt (mentor)

- kick MD5

Bump PORTREVISION after open-mofit update

Sync to new bsd.autotools.mk

- Update to 6.2.0

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

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

- update to jpeg-8

- Update MASTER_SITES

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

-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

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

- Force commit to correct the entry
- Update to 6.0.1

PR:             132504
Submitted by:   Wen Heping <wenheping@gmail.com>
Approved by:    maintainer

- Update to 0.1.24

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

- Replace SF with second working master site

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

- 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

- Update to 5.0.0

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

- Sort pkg-plist before updating to 5.0.0

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

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

Approved by:    portmgr (xorg cleanup)

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

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.

Conversion to a single libtool environment.

Approved by:    portmgr (kris)

Remove CONFLICTS with nss.

SHA256ify

Approved by:    krion@

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.

- 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)

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

Approved by:    portmgr (krion)

- Update to 2.9.0
- Pass maintainership to submitter

PR:             ports/74333
Submitted by:   Fernan Aguero <fernan(at)iib.unsam.edu.ar>

Add missing files

With portmgr hat on, reset inactive maintainer.

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

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

(Part 2)

Define USE_PERL5_BUILD, not erroneous USE_PERL.

Submitted by:   Oliver Eikemeier

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

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]

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.

BROKEN: Checksum mismatch

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

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

E Nomini Patri, E Fili, E Spiritu Sancti.

- 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!

BROKEN: Does not fetch

- 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)

BROKEN: incorrect checksums

Add USE_SUBMAKE, where it might be necessary.

- 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    

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

Remove obsolete pointer to online documentation.    

Update package's URL; my email address.    

Updating my email address in my remaining ports.    

Update to 1.13.3; remove bogus file.    

Update to version 1.13.1    

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

Update the EMBOSS suite to v1.11.0    

Update to version 1.10.1    

Update to version 1.10.0    

Chase graphics/gd's shlib version bump.    

- 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  
 

Upgrade to version 1.9.0    

Update distfiles' checksums after the distfiles have been rerolled yet   again
without changing names or versions.  Also add a new MASTER_SITE.    

Distfile tarballs were rerolled without notice due to a minor bug.    

- Update port biology/emboss from 1.7.0 to 1.8.0    

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

- 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    

- 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.    

Make portlint happy, remove a space    

Update to version 1.7.0    

- Update to 1.6.0   - Reorder packing list    

Convert category biology to new layout.  

Add USE_XLIB