[Bioc-devel] Updated biocLite -- please try!

Robert Castelo robert.castelo at upf.edu
Thu Jun 16 08:15:12 CEST 2011

hi Martin, and the rest of the list,

one issue that i believe could be improved at this point, and as far as
i know is not addressed in any automatic way, is the way in which
packages that rely on external libraries like, for instance Rgraphviz,
react to errors when they are installed.

i believe these packages should have a non-empty 'SystemRequirements'
field in their DESCRIPTION file and if this was detected by biocLite(),
then, if an error occurs, i think it would be nice if biocLite() would
offer the user the possibility of showing a README file from the package
(like the Rgraphviz/README file, for instance), that contains in fact
the crucial information about what to do to install the package in
relationship with the external library (what configure.args argument has
to be specified, etc.). if this is complicated, then at least showing
the 'SystemRequirements' line would be a minimal amount of information
that could help. configure already tells things but it is not
straightforward to interpret the output of configure for the

i know most of us reading this mailing list have no problem to download
the source tarball and find out what to do, but i'm sure many
non-developer users get stuck with this issue of the external libraries


On Tue, 2011-06-14 at 15:21 -0700, Martin Morgan wrote:
> Hi BiocDevelopers --
> As mentioned previously, we have revised how biocLite works. Please try
>     source("http://bioconductor.org/scratch-repos/biocLite.R")
> and then installing your favorite package
>    biocLite("MyFavoritePackage")
> The 'source()' command will download, install (first time only!) and 
> load the 'BiocInstaller' package.
> biocLite does behave differently. It'll check for out-of-date packages 
> and ask, after installing MyFavoritePackage, whether you'd like to 
> update them. With no arguments, biocLite() installs just Biobase, 
> IRanges, and AnnotationDbi. biocLite(character()) will look for 
> out-of-date packages to update. And ?biocLite will provide a help page(!).
> The revised behavior should only occur in the 'devel' version of R, 
> R-2.13 should behave as before.
> Any feedback most welcome.
> Martin

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