notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)

Two new features

Two new features were added on 2020-05-30:
  1. Repology links - each port now has a link to repology.org. See issue 148 for details.
  2. Ports I maintain report - port maintainers can now subscribe to a daily report of commits to the ports they maintain. See Watch ports I maintain at Report Subscriptions. Details at issue 138
non port: biology/phyml/Makefile
SVNWeb

Number of commits found XX: 26

Fri, 10 Jul 2020
[ 09:45 fernape ] Original commit   Revision:541852
541852 biology/phyml/Makefile
541852 biology/phyml/distinfo
biology/phyml: update to 3.3.20200621

From ChangeLog:
https://github.com/stephaneguindon/phyml/releases/tag/v3.3.20200621

This release fixes a few minor bugs (see recent commits). The manual also gives
extra XML configuration information in order to apply fancy substitution models
(e.g., CAT-like) on single- or multiple-gene data sets

Reported by:	portscout
Tue, 21 Apr 2020
[ 21:51 danilo ] Original commit   Revision:532429
532429 biology/phyml/Makefile
- Swap back from net/openmpi3 to net/openmpi
Sun, 12 Apr 2020
[ 09:06 danilo ] Original commit   Revision:531485
531485 biology/phyml/Makefile
- Move OpenMPI support to net/openmpi3. OpenMPI 1 is deprecated.
Fri, 6 Dec 2019
[ 13:04 pkubaj ] Original commit   Revision:519139
519139 biology/phyml/Makefile
biology/phyml: disable -march=native

Ports shouldn't build for the host CPU, it also breaks compilation on non-x86.

Approved by:    mentors (implicit approval)
Tue, 10 Sep 2019
[ 21:04 fernape ] Original commit   Revision:511777
511777 biology/phyml/Makefile
511777 biology/phyml/distinfo
biology/phyml: update to 3.3.20190909

While here, add license.

Reported by:	portscout
Mon, 20 May 2019
[ 09:17 wen ] Original commit   Revision:502098
502098 biology/phyml/Makefile
502098 biology/phyml/distinfo
- Update to 3.3.20190321
Sat, 22 Sep 2018
[ 18:00 yuri ] Original commit   Revision:480425
480425 benchmarks/imb/Makefile
480425 benchmarks/mdtest/Makefile
480425 biology/phyml/Makefile
480425 math/parmetis/Makefile
Change 4 ports from net/mpich2 to net/mpich

mpich2 is the obsolete version 2.x, mpich is at the current version 3.x

Ports:
biology/phyml benchmarks/mdtest benchmarks/imb math/parmetis
Sat, 23 Jun 2018
[ 15:53 fernape ] Original commit   Revision:473138
473138 biology/phyml/Makefile
473138 biology/phyml/distinfo
biology/phyml: update to v3.3.20180621

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D15967
Tue, 15 May 2018
[ 03:17 wen ] Original commit   Revision:469992
469992 biology/phyml/Makefile
469992 biology/phyml/distinfo
- Update to 3.3.20180214
Sat, 10 Mar 2018
[ 23:35 linimon ] Original commit   Revision:464132
464132 audio/zita-convolver/Makefile
464132 biology/phyml/Makefile
464132 games/trigger-rally/Makefile
Remove now-useless, commented-out lines.

Approved by:	portmgr (tier-2 blanket)
Thu, 1 Feb 2018
[ 07:26 wen ] Original commit   Revision:460569
460569 biology/phyml/Makefile
460569 biology/phyml/distinfo
- Update to 3.3.20180129
Wed, 27 Dec 2017
[ 07:36 linimon ] Original commit   Revision:457351
457351 audio/zita-convolver/Makefile
457351 audio/zita-convolver/files/patch-Makefile
457351 biology/phyml/Makefile
457351 games/trigger-rally/Makefile
457351 games/trigger-rally/files/patch-GNUmakefile
Disable the extra flag "-march=native" on arm to fix builds.

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com -exp run
Sat, 9 Dec 2017
[ 01:39 linimon ] Original commit   Revision:455815
455815 audio/zita-convolver/Makefile
455815 biology/phyml/Makefile
455815 databases/pg_citus/Makefile
455815 devel/critcl/Makefile
455815 games/crafty/Makefile
455815 sysutils/lscpu/Makefile
These are also broken on aarch64 in the same way as armv6/7.

Approved by:	portmgr (tier-2 blanket)
[ 00:42 linimon ] Original commit   Revision:455813
455813 audio/zita-convolver/Makefile
455813 biology/phyml/Makefile
455813 databases/percona56-server/Makefile
455813 databases/pg_citus/Makefile
455813 databases/soci/Makefile
455813 devel/arpc/Makefile
455813 devel/critcl/Makefile
455813 devel/cxxtools/Makefile
455813 devel/libffcall/Makefile
455813 devel/ppl/Makefile

(Only the first 10 of 21 ports in this commit are shown above. View all ports for this commit)
Mark more ports broken that fail on both armv6 and armv7.

Approved by:	portmgr (tier-2 blanket)
Mon, 4 Sep 2017
[ 00:01 sunpoet ] Original commit   Revision:449234
449234 biology/phyml/Makefile
449234 biology/phyml/distinfo
Update to 3.3.20170530

Changes:	https://github.com/stephaneguindon/phyml/releases
Fri, 1 Apr 2016
[ 13:29 mat ] Original commit   Revision:412344
412344 Mk/Uses/gecko.mk
412344 Mk/bsd.fpc.mk
412344 Mk/bsd.gecko.mk
412344 Mk/bsd.port.mk
412344 accessibility/accerciser/Makefile
412344 accessibility/at-spi/Makefile
412344 accessibility/at-spi2-atk/Makefile
412344 accessibility/at-spi2-core/Makefile
412344 accessibility/caribou/Makefile
412344 accessibility/dasher/Makefile

(Only the first 10 of 1009 ports in this commit are shown above. View all ports for this commit)
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
Fri, 26 Feb 2016
[ 13:03 wen ] Original commit   Revision:409605
409605 biology/phyml/Makefile
409605 biology/phyml/distinfo
409605 biology/phyml/pkg-descr
- Update to 3.2.0
- Update pkg-descr

PR:		205890
Submitted by:	tkato432@yahoo.com
Sun, 28 Dec 2014
[ 19:14 bapt ] Original commit   Revision:375747
375747 biology/phyml/Makefile
Convert to USES=autoreconf
Fri, 31 Jan 2014
[ 12:32 miwi ] Original commit   Revision:341987
341987 biology/phyml/Makefile
- Stage support
Fri, 20 Sep 2013
[ 15:55 bapt ] Original commit   Revision:327709
327709 biology/ariadne/Makefile
327709 biology/artemis/Makefile
327709 biology/avida/Makefile
327709 biology/babel/Makefile
327709 biology/biococoa/Makefile
327709 biology/biojava/Makefile
327709 biology/blast/Makefile
327709 biology/blat/Makefile
327709 biology/boinc-simap/Makefile
327709 biology/chemeq/Makefile

(Only the first 10 of 94 ports in this commit are shown above. View all ports for this commit)
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
Wed, 14 Aug 2013
[ 22:35 ak ] Original commit   Revision:324744
324744 accessibility/atkmm/Makefile
324744 accessibility/jovie/Makefile
324744 accessibility/kaccessible/Makefile
324744 accessibility/kmag/Makefile
324744 accessibility/kmousetool/Makefile
324744 accessibility/kmouth/Makefile
324744 accessibility/qt4-accessible/Makefile
324744 accessibility/speech-dispatcher/Makefile
324744 archivers/ark/Makefile
324744 archivers/bicom/Makefile

(Only the first 10 of 1725 ports in this commit are shown above. View all ports for this commit)
- Remove MAKE_JOBS_SAFE variable

Approved by:	portmgr (bdrewery)
Mon, 4 Feb 2013
[ 10:07 araujo ] Original commit   Revision:311601
311601 biology/phyml/Makefile
311601 biology/phyml/distinfo
311601 biology/phyml/files
- Update to 20121109.

PR:		ports/175014
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
Tue, 4 Dec 2012
[ 20:28 zi ] Original commit   Revision:308268
308268 biology/phyml/Makefile
- Reset MAINTAINER due to unrecoverable email bounce

Reported by:	portscout
Feature safe:	yes
Sat, 4 Dec 2010
[ 07:34 ade ] Original commit 
1.164 Mk/bsd.gnome.mk
1.63 Mk/bsd.php.mk
1.660 Mk/bsd.port.mk
1.1001 UPDATING
1.63 accessibility/atk/Makefile
1.58 accessibility/gnome-mag/Makefile
1.33 accessibility/kdeaccessibility/Makefile
1.34 archivers/arj/Makefile
1.17 archivers/kbackup/Makefile
1.10 archivers/kio_p7zip/Makefile

(Only the first 10 of 1730 ports in this commit are shown above. View all ports for this commit)
Sync to new bsd.autotools.mk
Tue, 5 Oct 2010
[ 19:57 ade ] Original commit 
1.12 archivers/par2cmdline-tbb/Makefile
1.36 archivers/rpm5/Makefile
1.10 archivers/torrentzip/Makefile
1.17 archivers/zipios++/Makefile
1.32 astro/boinc-setiathome-enhanced/Makefile
1.37 astro/orsa/Makefile
1.49 audio/audacity-devel/Makefile
1.40 audio/faac/Makefile
1.60 audio/faad/Makefile
1.23 audio/gspeakers/Makefile

(Only the first 10 of 235 ports in this commit are shown above. View all ports for this commit)
Round one migration of ports from automake{19,110} to automake111
Tue, 21 Jul 2009
[ 01:10 amdmi3 ] Original commit 
1.111 biology/Makefile
1.1 biology/phyml/Makefile
1.1 biology/phyml/distinfo
1.1 biology/phyml/files/patch-src-configure
1.1 biology/phyml/files/patch-src-configure.ac
1.1 biology/phyml/pkg-descr
PhyML is a software that estimates maximum likelihood phylogenies from
alignments of nucleotide or amino acid sequences. It provides a wide range of
options that were designed to facilitate standard phylogenetic analyses. The
main strengths of PhyML lies in the large number of substitution models coupled
to various options to search the space of phylogenetic tree topologies, going
from very fast and efficient methods to slower but generally more accurate
approaches. It also implements two methods to evaluate branch supports in a
sound statistical framework (the non-parametric bootstrap and the approximate
likelihood ratio test). PhyML was designed to process moderate to large data
sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long
can analyzed. In practice however, the amount of memory required to process a
data set is proportional of the product of the number of sequences by their
length. Hence, a large number of sequences can only be processed provided that
they are short. Also, PhyML can handle long sequences provided that they are
not numerous. With most standard personal computers, the "comfort zone" for
PhyML generally lies around 3 to 500 sequences less than 2,000 character long.

WWW: http://code.google.com/p/phyml/

PR:             136877
Submitted by:   Ben Allen <ben@sysadminschronicles.com>

Number of commits found XX: 26

Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD

This site
What is FreshPorts?
About the authors
Issues
FAQ
How big is it?
The latest upgrade!
Privacy
Blog
Contact

Search
Enter Keywords:
 
more...

Latest Vulnerabilities
apache24Aug 08
gitlab-ceAug 06
goAug 06
sqlite3*Aug 06
typo3-10Aug 04
typo3-9Aug 04
libX11Aug 01
xephyrAug 01
xorg-dmxAug 01
xorg-nestserverAug 01
xorg-serverAug 01
xorg-vfbserverAug 01
xwaylandAug 01
python38Jul 31
arkJul 30

14 vulnerabilities affecting 93 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities

Last updated:
2020-08-08 17:33:12


Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds

Statistics
Graphs
NEW Graphs (Javascript)
Traffic

Calculated hourly:
Port count 40273
Broken 90
Deprecated 600
Ignore 326
Forbidden 5
Restricted 147
No CDROM 76
Vulnerable 21
Expired 3
Set to expire 570
Interactive 0
new 24 hours 4
new 48 hours6
new 7 days21
new fortnight60
new month143

Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD
Valid HTML, CSS, and RSS.
Copyright © 2000-2020 Dan Langille. All rights reserved.