[Bioperl-l] OS X bioperl, staden/read, install problems

[Jim Nolan]

I tried installing bioperl-1.2.3 again on a relatively naive machine 
(has bioperl 1.1.1, but no -ext). Installation went off without a 
hitch. I think I must have gotten the idea of installing bioper-ext 
from the www.bioperl.org/Core/external.shtml, after having looked 
there for some other dependency like SOAP::Lite. Modules that are 
this tricky to install (I did try to do the manual installation of 
the missing io_lib files) should have a big skull and crossbones on 
them to keep guys like me out. Or better yet, instructions in the 
readme to tell us how to do it right.

At any rate, I ask that the evaluation for modules outside the core 
release be minimized and that they not cause failure of make test.

Whining aside, thanks to everyone for making such a great resource 
free to all of us, and Thanks for getting me going again after the 
little detour.

Jim

At 3:59 PM -0400 10/8/03, Aaron J Mackey wrote:
>On Mon, 6 Oct 2003, Jason Stajich wrote:
>
>>  When I get together with Aaron at the end of the month I will try and go
>>  through it with him so I understand what is supposed to happen and/or how
>>  we might reorg bioperl-ext to be less problematic.
>
>The problem (over-and-over-again) has been that while people think they
>have the staden io-lib successfully installed, they don't (because they
>have to manually do a few things that the io-lib install doesn't do for
>them).  It's a royal pain, of course.  And then they try to install
>bioperl-ext, which doesn't successfully complete (you can, btw, install
>only parts of bioperl-ext, so the whole staden read lib stuff shouldn't
>prevent someone from installing the other alignment code).
>
>Then, if they ignore that and try to run the normal bioperl test suite,
>they get various odd cryptic errors about read not being successfully
>installed.
>
>-Aaron


-- 
---------------------------------------------------------
Jim Nolan			email:JNolan at tulane.edu
Department of Biochemistry SL43
Tulane University Health Sciences Center
1430 Tulane Ave.		Phone: (504)-584-2453
New Orleans, LA 70112-2699	FAX:   (504)-584-2739
http://www.tulane.edu/~biochem/faculty/nolan.htm
http://phage.bioc.tulane.edu
The requirements said: Windows 2000 or better.
So I got a Macintosh.