Comments on: Compiling EIGENSOFT on Ubuntu Januty

By: Mick

Mick — Wed, 21 Jul 2010 01:22:32 +0000

Hi Emily,

I think what happened it that the zip file comes with precompiled binaries for 64-bit Linux. U have to run “make clean” to remove, then recompile.

Cheers
Mick

By: Emily

Emily — Tue, 20 Jul 2010 19:03:03 +0000

Thank you so much! You have prevented my smashing an otherwise valuable computer.

By: Mick

Mick — Tue, 20 Jul 2010 01:59:39 +0000

Try running “make clean”.

By: Emily

Emily — Mon, 19 Jul 2010 16:53:42 +0000

Thank you Mick for your helpful tutorial.
I keep running into the same issue however, a segmentation fault when I try to “make eigenstrat” or “make pcatoy”

The error is:
collect2: ld terminated with signal 11 [Segmentation fault]
/usr/bin/ld: i386:x86-64 architecture of input file `eigenstrat.o’ is incompatible with i386 output

My naive understanding is that this is due to incompatibilities with a 64 bit OS.
Do you have any suggestions?

Thank you again.

By: Mick

Mick — Sun, 13 Jun 2010 21:33:33 +0000

Cool! Thanks Peter.

By: Peter

Peter — Sat, 12 Jun 2010 23:53:14 +0000

Awesome tutorial, Mick!

By: ross lazarus

ross lazarus — Thu, 04 Feb 2010 22:36:56 +0000

> anyone know if the Eigensoft author plans to move to gcc 4?

I doubt that there are any plans – it’s legacy code – once published, not much pressure to maintain it. One of the many joys of pressure to publish vs benefits to your academic career of the hard yards of maintenance (which is usually zero). I’m a Galaxy developer for the record

For doing ancestry PCA, there’s an interesting if quirky alternative called shellfish at http://www.stats.ox.ac.uk/~davison/software/shellfish/shellfish.php
The error message at the end of that page is an ominous sign…but that seems to be what they’re using at the Welcome trust?

At least it seems a little more up-to-date than eigensoft3 and the author does respond to email…

By: Mick

Mick — Wed, 23 Dec 2009 03:40:45 +0000

Peter, what version of Ubuntu (or other Linux disto) are you using?

Recently I upgraded to Ubuntu 9.10 (Karmic) and it doesn’t have the libg2c0 and related libraries. This appears to because it was part of gcc3.x and gcc4 (which Karmic uses) uses gfortran instead. It looks like to use Eigensoft one will have to stick with an older distro, or install the libg2c0 and gcc3 from Ubuntu Jaunty.

Anyone know if the Eigensoft author plans to move to gcc 4?

By: Tiger

Tiger — Wed, 16 Dec 2009 03:15:10 +0000

Very useful guide, Mick, it was such a relief to see your post and hence get the program running on my laptop. I agree with gioby that FF = “gfortran” works fine but not the other way around.

By: Peter

Peter — Thu, 10 Dec 2009 15:30:08 +0000

Well, i tried this as well, but i got no plot… Dont know why?
Are there special libraries necessary for the plot?
Thanks in advance
Peter