Remove non staged ports without pending PR from b*

Reset maintainership for ports not staged with no pending PR

With hat:	portmgr

- Mark BROKEN

Approved by:	portmgr@(implicit)

Use MAKE_CMD instead of GMAKE

With hat:	portmgr

biology/embassy: specify post-extraction with ${TAR}

It's possible that EXTRACT_CMD won't be predefined in the near future
in order to support distfiles in multiple formats.  We know the post-
extraction tool needs to be tar, so let's specify it directly.

This port needs staging. It doesn't like like a quick job so I'm leaving
that to the listed maintainer.

Approved by:	infrastructure improvements blanket
Approved by:	portmgr (implicit) (to skip stage check)

Reduce over inclusion of bsd.port.mk

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)

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

- Convert USE_ICONV=yes to USES=iconv
- Change USE_GNOME=pkgconfig|gnomehack to USES=pathfix|pkgconfig while here

Reviewed by:	bapt, kwm

- adopt optionsNG
- trim historical header
- tighten COMMENT

Approved by:	portmgr (miwi)

- Take maintainership

- Reassign to the heap at maintainer's request

- update png to 1.5.10

- Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS)
- Fix all ports that add {CPP,LD}FLAGS to *_ENV to modify flags instead

PR:             157936
Submitted by:   myself
Exp-runs by:    pav
Approved by:    pav

Bump PORTREVISION after open-mofit update

- Get Rid MD5 support

- 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)

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

- Update to 6.0.0
- Unbreak

PR:             135376
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

- Mark BROKEN does not compile

Submitted by:   maintainer via private mail

- Update to 5.0.0

PR:             ports/122437
Submitted by:   Fernan Aguero <fernan at 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}.

- Fix after objformat removal

Reported by:    pointyhat

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.

Add missing USE_ICONV

SHA256ify

Approved by:    krion@

- Update to 2.10.0

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

- Fix OPTIONS handling

Pointy hat to:  sem

BROKEN: Broken distinfo file

[new port] biology/embassy

PR:             ports/74330
Submitted by:   Fernan Aguero <fernan(at)iib.unsam.edu.ar>