[BioC] Problems installing v 1.2

Jeff Gentry jgentry at jimmy.harvard.edu
Thu May 29 11:05:23 MEST 2003


> HDF5 did not install (see below)

You are referring to the actual HDF5 library and not the package (tho
obviously the package won't install w/o the library), right?

> Ruuid had an error in the complilation ( clear.c had a perse error
> before } type problem)

I can not replicate this at all, can anyone else?

> Graphviz I don't have installed ( it seems to want libpng.so.2, I have
> libpng.so.3 Hah!)

Again - you are talking about the actual AT&T Graphviz application,
correct?  If so, this might not be an insurmountable problem, but it is
best brought up to the AT&T folks:
http://www.research.att.com/sw/tools/graphviz/

> XML had an issue trying to find parser.h.

This should be taken up on the R-help list (r-help at stat.math.ethz.ch)

> Also, at the end of the install a message indicate repostools was not
> updated. Should it have been?

It was.  That bit is an (admittedly confusing, need to find a way around
that) artifact of how getBioC() works.  It first downloads reposTools
manually, then runs reposTools to update your BioC packages and their
dependencies.  Since reposTools is already up to date before it starts
using the reposTools functions, it appears to the system as if it was not
updated.  I will set up the getBioC() function to intercept that output
from reposTools and have it change this behavior so that it shows up as an
updated package.

-J



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