[BioC] Cannot load bioconductor's packages installed

Seth Falcon sfalcon at fhcrc.org
Tue Oct 25 15:44:47 CEST 2005

Hi there,

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()
> [1] ".GlobalEnv"        "package:ALL"       "package:cMAP"
> [4] "package:Ruuid"     "package:cluster"   "package:hgu133a"
> [7] "package:KEGG"      "package:annotate"  "package:GO"
> [10] "package:Biobase"   "package:tools"     "package:methods"
> [13] "package:stats"     "package:graphics"  "package:grDevices"
> [16] "package:utils"     "package:datasets"  "Autoloads"
> [19] "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.
2. biocLite("Ruuid")
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.

Best Wishes,

+ seth

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