Remove expired ports:
2015-01-01 biology/boinc-simap: Project shutting down, see
http://boincsimap.org/boincsimap/forum_thread.php?id=88
2015-01-01 security/openssh-portable-base: Overwrite-base option/port/pkg will
be removed. There is no real need for foot-shooting.
2015-01-01 devel/cedet: Fails to build, use Emacs' builtin cedet package instead
2015-01-01 devel/ecb: does not work with newer Emacs versions, use the elpa
package instead

Fix pkg-plist

Submitted by:	bapt

biology/boinc-simap: clean up pkg-plist

Requested by:	bapt

biology/boinc-simap: Deprecate, project shutting down on 2015-01-01

Obtained from:	http://boincsimap.org/boincsimap/forum_thread.php?id=88

Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)

Drop maintainership BOINC ports, old machine running them gave up.

The hmmer binary was renamed upstream to indicate that it is now an
archive file, adjust the port so that fetch and extract work again.

Several fixes:
- install files as the BOINC user/group, this ensures that work units can
  be downloaded and sent
- try to remove ~boinc/projects if empty
- do not specify -o and -g parameters to ${INSTALL}, this ensures the
  package can be built as user
- only extract the hmmer binary from the hmmer distribution file, this
  ensures correct permissions when modifying app_info.xml as user
- Bump PORTREVISION

Reviewed by:	bapt

Use value of BOINC_CLIENT_HOME in pkg-message

- Add stagedir support
- Rewrap lines

Respect 'make check-sanity' for this port too.

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

Use bsd.port.options.mk instead of bsd.port.{pre|post}.mk

Remove compatibility with FreeBSD 7.X

While here pet Makefile headers.

Take over maintainership.

Approved by:	pav (previous maintainer)

Use the new project URL to let the application attach coorectly to the
project, and some cleanups:
- use optionsNG
- update commands in pkg-install.in
- improve %%AMD64%% comment handling
- convert Makefile header
- remove unused variable SIMAP_URL

Bump PORTREVISION

PR:		ports/174748
Submitted by:	myself
Approved by:	maintainer (pav@)

- Adjust BOINC_* variables to be consistent with new system in boinc-client

- Fix fetch and update WWW

- Get Rid MD5 support

- Update the libmap instructions for amd64/8

Submitted by:   Rick van der Zwet <info@rickvanderzwet.nl>

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

- update to jpeg-8

- Annotate that 8.x no longer needs libmap hack

Reported by:    rene

- Remove conditional checks relevant only on FreeBSD 5.x and older

Bump portrevision due to upgrade of devel/gettext.

The affected ports are the ones with gettext as a run-dependency
according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT
in Makefile (29 of them).

PR:             ports/124340
Submitted by:   edwin@
Approved by:    portmgr (pav)

implement @dirrmtry macro for the pkg-plist

- Runs on 7.0-CURRENT with compat6x

Reported by:    Rene Ladan <r.c.ladan@gmail.com>

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

- Add hmmer 5.09 application

- Update to 5.10

- Provide SSE optimized application as an option

- Instruct amd64 users to libmap libpthread.so.2 to libc_r.so.6

SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculated
protein similarities that plays a key role in many bioinformatics methods. It
contains about all currently published protein sequences and is continuously
updated.

The computational effort for keeping SIMAP up-to-date is constantly increasing.
Please help to update SIMAP by calculating protein similarities on your
computer.

WWW: http://boinc.bio.wzw.tum.de/boincsimap/