[R] non-zero exit status error when install GenomeGraphs

[Martin Morgan]

 On 09/04/2010 01:38 PM, David Winsemius wrote:
> (Caveat: I am not a bioc user.) The error messages suggest that you
> are missing dependencies. I looked at the documentation for
> GenomeGraphs and it does not list any dependencies, but I have no way
> of knowing how careful
> packageDescription("GenomeGraphs")$Depends
[1] "methods, biomaRt, grid"

and likewise for biomaRt. Also at
http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html for
the current (release) version, or replacing 'release' with '2.5' (from
the original poster's biocLite invocation) for the version relevant to
R-2.10
<http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html>
> or knowledgeable the authors may or may not have bben when they
> composed that document. The fact that you are 
Not sure what 'that document' means, but if it's the package vignette or
reference manual then that's not the appropriate place for stating
package dependencies -- like all R packages, this information belongs in
the package DESCRIPTION file, with dependencies enforced at installation
time. Also the Bioconductor build system only makes available packages
that do not produce errors on R CMD build and R CMD check, i.e.,
packages that have fully specified their dependencies. And the build
system is versioned, so the original poster is getting (Bioconductor)
packages that are appropriate for their system (though CRAN packages
come from CRAN and so are not versioned in sync with R).
> posting to the wrong mailing list and are not including what version
> of linux (although there is a hint it may be RedHat5) you are running
> suggests you could be fairly new at this.
>
> Is biocLite the correct function for installing a bioc package? It
> appears it may be, but I'm wondering if there is an 
Yes it is. It does install dependencies, to the same extent that
install.packages() does; biocLite is a wrapper around install.packages
that inserts the appropriate (for the R version) Bioconductor
repositories in front of CRAN repositories.

Likely the original poster has an installed version of the XML package,
but it is not installed correctly or the installation has become
compromised in some way, e.g., by removing or updating libxml in the
operating system. Your advice -- install (or otherwise troubleshoot) XML
-- is likely part of the right solution, but since XML comes from the R
repository and is therefore only known to build with the current version
of R, it makes sense for the original poster to update their version of
R first.

Martin
> argument for dependencies as there is in install.packages() that you
> need to set to TRUE? If biocLite has a ,... in its argument list (and
> the error message suggests that it does) then you may get better
> results with the same call with an addition of dependencies=TRUE.
>
> Or you could first install the packages that are reported missing: XML
> and biomaRt, and then try again as you did before.
>
> Links to the bioc mailing lists can be found here:
>
> http://www.bioconductor.org/help/index.html
>