[BioC] Cannot load bioconductor's packages installed
sfalcon at fhcrc.org
Tue Oct 25 15:44:47 CEST 2005
On 24 Oct 2005, zhengqi04 at mails.gucas.ac.cn wrote:
> I am a new user from China of Bioconductor and having some problems
> while using it at present.
Welcome. I hope we will be able to help get you going.
> The version of R installed is 2.1.1, and that of bioconductor
> is the also the latest (must be version 1.7 as I get it installed
> following the 'bioconductor installation' procedure. Wish these were
> helpful in solving my problems.
Actually, if you are using R 2.1.1, then biocLite will automatically
install Bioc 1.6 (previous release) because that is the Bioconductor
version compatible with R 2.1.1.
For the most up to date code, use R 2.2.0 which will allow you to
install Bioc 1.7 packages via the same biocLite method.
> The biggest problem I have met is that I can not load the package
> "graph" that has already been installed. I downloaded it using
> "biocLite("graph") and the installation progress was certainly
> finished without errors or warnings,
Hmm, it should have installed the Ruuid package as a dependency. Are
you sure it did not encounter an error installing Ruuid?
> "> library("graph")
> error: assign("nullgraphID", getuuid()) :
> cannot find the function"getuuid"
> error: package'graph' writing and loading R failed
> error: loading 'graph' package/namespace failed."
> And these were all the packages I had loaded then:
> "> search()
>  ".GlobalEnv" "package:ALL" "package:cMAP"
>  "package:Ruuid" "package:cluster" "package:hgu133a"
>  "package:KEGG" "package:annotate" "package:GO"
>  "package:Biobase" "package:tools" "package:methods"
>  "package:stats" "package:graphics" "package:grDevices"
>  "package:utils" "package:datasets" "Autoloads"
>  "package:base" "
The error message means that Ruuid was not found/functional. Here are
a few things to try:
1. library(Ruuid) to test whether or not Ruuid is installed.
3. If Ruuid _is_ having installation problems, you may need to install
some of the glib-devel rpm packages. The output from the
installation should help.
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