Package Details: phyml 1:3.2.20160530-1

Git Clone URL: https://aur.archlinux.org/phyml.git (read-only)
Package Base: phyml
Description: Builds phylogenies from DNA or protein sequences using a maximum likelihood approach
Upstream URL: http://www.atgc-montpellier.fr/phyml/
Licenses: GPL2
Submitter: None
Maintainer: mschu
Last Packager: mschu
Votes: 6
Popularity: 0.012849
First Submitted: 2009-04-02 01:54
Last Updated: 2016-05-31 16:23

Dependencies (0)

Required by (0)

Sources (1)

Latest Comments

Rhinoceros commented on 2015-02-08 01:28

Okay, I've done a bit more homework, and I realised that split packages normally have one build() section, and hence it's probably not a good idea to use a split package in this case.

I've created a new package phyml-mpi, just because it's a bit easier as per reasons in my previous post. Let me know if you want to adopt it, anyway. Cheers.

Rhinoceros commented on 2015-02-02 21:39

Thanks for the fix.

With MPI, configuring upstream phyml with --enable-mpi creates a separate binary phyml-mpi. This does not conflict with phyml. Hence, I attempted to change the package name to phyml-mpi, so I could install both. However, pacaur (for example) won't let me change the package name, although packer does, although this means that packer/pacaur -Syu won't pick up the package in future.

I wonder if there is any disadvantage to compiling with --enable-mpi by default? If so, then perhaps this package could enable this by default, with optdepends openmpi. If it *is* better to install both, another option might be to make phyml a split package, so that users can install/upgrade both without having to download the source twice.

mschu commented on 2015-02-02 13:42

Concerning MPI, just change the option in the PKGBUILD. A separate package is only needed when it's used by more people in my opinion.

mschu commented on 2015-02-02 13:41

You are right, I made a mistake reading the URL and still had the old version cached instead of deleting it.

Should be fixed now (for real).

Rhinoceros commented on 2015-02-02 11:11

It's still 404-ing for me. Isn't it 20141029 that you want? Also, would you consider maintaining phyml-mpi (i.e. multi-threaded)? i.e. just configure it with --enable-mpi? I'm happy to do it otherwise, but might make more sense for you to if you are willing.

mschu commented on 2015-02-02 10:05

It seems the git download URL changed slightly.

Fixed that, and some autoconf issue. Not bumping $pkgrel because it is built from the same source (same md5sum).

Rhinoceros commented on 2015-02-02 03:43

Ugh, apologies. The stable version was released 26 Feb 2014, but is actually from April 2012. However, the current PKGBUILD still 404s.

Rhinoceros commented on 2015-02-02 03:22

When trying to build, phyml-20140926.tar.gz now 404s. Upstream is being strange. The stable release from 23 Feb was deleted, but now there is a stable release from 26 Feb 2014.

https://github.com/stephaneguindon/phyml-downloads/releases

wookietreiber commented on 2014-10-16 12:26

This appears to be the latest version:

https://github.com/stephaneguindon/phyml-downloads/releases/download/development/phyml-20140926.tar.gz

talavis commented on 2014-09-12 11:37

Seems like the current devel version is 20140911 now.

pkgver=20140911
sha1sums=('c554287908951bf3a0cf932a5d65fe3cdcf4453a')

mschu commented on 2014-06-17 08:48

Yes it does, and that makes sense given that the stable version is almost 2 years old now.

Rhinoceros commented on 2014-06-17 04:05

This now pulls the unstable developmental version, not the stable?

Rhinoceros commented on 2014-06-06 04:12

Thanks for that. This is strange; it seems like they've reverted the latest stable version back to 20120412. The current PKGBUILD 404s. I modified the PKGBUILD with the new source [1] and it builds and installs fine. However, `phyml -h` suggests that I've installed "PhyML 20140606" (although perhaps that's just the build date?).

[1] http://pastebin.com/GMT8VxAY

mschu commented on 2014-06-05 08:48

Updated to 20140604, but I can not reproduce your error. Please make sure you have an up-to-date system and tell me the version of autoconf/automake.

Rhinoceros commented on 2014-06-05 06:18

makepkg -s fails for me.
http://pastebin.com/FwPei51c

Also, the newest version is 20140223.
https://github.com/stephaneguindon/phyml-downloads/releases

tegenf commented on 2013-07-12 10:24

Hello, had problems with building the pkg. It failed claiming that the dir ./compile is missing. It suggested to add the option '--add-missing' to automake.
I did just that in the PKGBUILD file. That fixed my problem!

iosonofabio commented on 2013-04-09 07:54

That's ok, you did better. The binary works, btw.

mschu commented on 2013-04-08 09:26

Updated to the latest Google Code version (20130219). If you like to have a 3.1 binary version, feel free to maintain it :-)

iosonofabio commented on 2013-04-08 09:03

I made one PKGBUILD, which uses binaries though:

http://pastebin.com/RzitS997

iosonofabio commented on 2013-04-08 08:46

PhyML 3.1 is available:

http://www.atgc-montpellier.fr/phyml/versions.php

In addition, depends and makedeps should be added.

mschu commented on 2011-02-09 17:43

Adopted and updated :)

Anonymous comment on 2010-11-04 16:08

is it possible to make an update to v3.0 ?