On Oct 1, 2014, at 4:20 PM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Wed, Oct 01, 2014, Ross Walker wrote:
>
>>
>> Again I reiterate my point. Why are we requiring lots of non-default
>> packages to be installed?
>
> I don't agree with Ross here. What do you think "default" is? A stock
> Ubuntu system won't even have a fortran compiler, much less a C-shell, or all
> kinds of other things that Amber requires. Are you sure the CC server
> is really just the "default" OS?
>
> On the web page, we list the "non-default" packages that are needed: for
> Ubuntu:
>
> sudo apt-get install csh flex patch gfortran g++ make xorg-dev libbz2-dev
>
> Add to this recommended packages for xparmed and mdoutanalyzer:
>
> sudo apt-get install python-tk python-dev python-matplotlib python-numpy
> python-scipy
>
> This is a big list, but it does include python-dev. The big change in the
> development version is that the absence of python-dev now (as I understand
> it) breaks the build (at the configure stage?), rather than just ending up
> with a non-functional xparmed.py program. Is there some (reasonably easy)
> way that lack of python-dev could be made to be less fatal, and to still
> build the stuff that doesn't depend on it?
Yes, that’s what we have now. The main reason it was made fatal was because unlike other Python requirements, it can’t be detected at runtime (and activated when it’s installed). It has to be available at compile-time.
> Note that for Fedora and openSuSE, the list of non-default packages is also
> quite large (see the web page). Is it really true that (a) RedHat version
> ??.? has everything one needs *execpt* python-dev and (b) there are a
> significant number of users that use that exact version and don't have root
> access?
There’s probably a lot of RHEL-based systems that are used by people that don’t have root access, but I agree with your points above. No programs are devoid of dependencies, and I think that, in general, python-dev is a more common dependency than gfortran… And even if users can’t install something as root, they would have to request that certain programs (like gfortran) be installed, anyway.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Oct 01 2014 - 14:30:02 PDT
