[BioC] Unable to use GEOquery (SOLVED)

[Sean Davis]

On Thu, Apr 17, 2008 at 9:39 AM, Juan C Oliveros Collazos
<oliveros at cnb.csic.es> wrote:
> Sean,
>
>  I did what you said and now GEOquery is running properly.
>
>  I think biocLite also installs a number of additional packages needed for
> GEOquery to work.
>
>  Thanks a lot!

That is great to hear, Juan.  Just to be clear, you should ALWAYS use
biocLite to install packages.  It will save you a great deal of
headache in the future.

Sean

>  Sean Davis wrote:
>
> > On Thu, Apr 17, 2008 at 6:21 AM, Juan C Oliveros Collazos
> > <oliveros at cnb.csic.es> wrote:
> >
> > > Hi all,
> > >
> > >  I just downloadad and installed the package "GEOquery" from
> bioconductor
> > >  web site. The installation carried-out with no errors.
> > >
> >
> > Hi, Juan.  You might want to try again.  First, remove the package
> > with remove.packages('GEOquery').  Then, type:
> >
> > source('http://bioconductor.org/biocLite.R')
> > biocLite('GEOquery')
> >
> > Does this fix the problem?
> >
> > Sean
> >
> >
> >
> > >  However, when I try to load the library: "library(GEOquery)", I get the
> > >  following error:
> > >
> > >
> -------------------------------------------------------------------------
> > >  > library(GEOquery);
> > >  Error in makeClassRepresentation(Class, properties, superClasses,
> > >  prototype,  :
> > >   element 2 is empty;
> > >    the part of the args list of 'list' being evaluated was:
> > >    (header = list(), )
> > >  Error : unable to load R code in package 'GEOquery'
> > >  Error: package/namespace load failed for 'GEOquery'
> > >
> ------------------------------------------------------------------------
> > >
> > >
> > >  This is the sessionInfo() output:
> > >
> ------------------------------------------------------------------------
> > >  > sessionInfo();
> > >  R version 2.6.0 (2007-10-03)
> > >  i686-pc-linux-gnu
> > >
> > >  locale:
> > >
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> > >
> > >  attached base packages:
> > >  [1] tools     stats     graphics  grDevices utils     datasets  methods
> > >  [8] base
> > >
> > >  other attached packages:
> > >  [1] Biobase_1.16.1 limma_2.12.0
> > >
> > >  loaded via a namespace (and not attached):
> > >  [1] rcompgen_0.1-15
> > >  ----------------------------------------------------------------------
> > >
> > >  Looking at this output, It seems that the package is not installed.
> > >  However, when i do "installed.packages()" GEOquery appears in the list!
> > >
> > >  I can not figure-out where the error is...
> > >
> > >  Any help?
> > >
> > >  Thanks in advance!
> > >
> > >  Best,
> > >
> > >  Juan Carlos
> > >
> > >  _______________________________________________
> > >  Bioconductor mailing list
> > >  Bioconductor at stat.math.ethz.ch
> > >  https://stat.ethz.ch/mailman/listinfo/bioconductor
> > >  Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> > >
> > >
> >
> >
>
>  --
>  Juan Carlos Oliveros
>  BioinfoGP, CNB-CSIC
>
>  ** NEW EMAIL ADDRESS: oliveros at cnb.csic.es **
>