IMO for very dependency you require, you need to detect what it is and
provide an intelligible quick cure in explanatory text so when failures
occur they won't spam the AMBER list (as much)...
On Wed, Oct 1, 2014 at 2:26 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> 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 - 15:00:02 PDT
