Approved by: tobez (implicit)
0.08 20/Feb/2006 15:14
Improved referential integrity between nodes,
taxa, and data.
Implemented Fastnexus parser
Node object silently implements Bio::Tree::NodeI
interface if BioPerl is installed
Tree object silently implements Bio::Tree::TreeI
interface if BioPerl is installed
Added convertor methods for XML and CIPRES
Implemented more Matrix methods
Implemented symbol tables in Bio::Phylo::Util::CONSTANT
Implemented visit method for listable objects
Implemented caching infrastructure for calculations
Changed object-model to inside-out arrays
Added Biodiversity measures code by Aki Mimoto
Moved constants and exceptions to Bio::Phylo::Util::*
Fixed memory leak due to circular references
- refine BROKEN to make portlint happier
- patch to use on Scalar::Util instead of WeakRef
- mark IGNORE under old perl which don't support weak reference
PR: 96656
Submitted by: leeym
Approved by: maintainer
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.
WWW: http://bioperl.org/
PR: ports/93675
Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.
WWW: http://bioperl.org/
PR: ports/93674
Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
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)
- Add a MASTER_SITE backup since oficial one just have last version and make
it fetchable again
Submitted by: maintainer by email
Reported by: krismail
variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain
database) and is also available as a general purpose alignment editor.
WWW: http://www.jalview.org
PR: 93054
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
PR.
Thanks for contributing.
Since the acroread7 port is a somewhat important port for our users, I
will hand it over to emulation@ if no _active_ *committer* takes it
before the ports freeze.
While I'm here:
- fix a little nit in the csound port (I think the intention was to
create no backup file instead of creating one with a "-e" extension)
- set ARCH to i386 in the amd64 case for the acroread7 port. This
is a work-around to be able to install everything when a dependency
is not already installed (ARCH is read-only in sub-makes, so the
dependencies can't change it). This should be removed when the
dependencies are fixed or converted to use bsd.linux-rpm.mk. [1]
Not objected to by: portmgr (explicit: krion; silence: rest)
Maintainer timeout: ~4 months
Submitted by: Sangwoo Shim <sangwoos@gmail.com> [1]
PR: 87985 [1]
unnecessary PORTEPOCH bump)
- Update MASTER_SITES and WWW line, provide backup download site
- Come up with better port description
- Reset maintainer to ports@
- Uphold CXX and CXXFLAGS
- Clean up Makefile slightly
- Don't install yet another copy of GPL and texts in French
- Add SHA256 hash to distinfo
- Shared lib version and PORTREVISION bumb for all affected ports.
While I'm here:
- Remove USE_MESA knob where it was (35 ports).
It marked as depricated for 2 years.
PR: ports/90247
Submitted by: Ermal Lu?i <eri--@albabsd.org>
