[BioC] cannot install rsbml

[Sean Davis]

On Fri, Oct 3, 2008 at 3:32 AM, Richard Birnie
<richard.birnie at pro-cure.uk.com> wrote:
> Dear list,
>
> I'm trying to install the package rsbml from bioconductor. I followed the
> instructions on http://bioconductor.org/packages/2.2/bioc/html/rsbml.html
> i.e. ran the commands
> source("http://bioconductor.org/biocLite.R")
> biocLite("rsbml").
>
> The installation consistently fails with this error:
> ####################
> make: *** [check.o] Error 1
> chmod: cannot access `/usr/local/lib/R/site-library/rsbml/libs/*': No such
> file or directory
> ERROR: compilation failed for package 'rsbml'
> ** Removing '/usr/local/lib/R/site-library/rsbml'
> ####################
>
> It is true that the directory does not exist but I have no idea why or what I
> need to do about it. My session info is

It might help to post the entire output of the installation attempt.
The error you show above is a symptom, not a cause.  The rest of the
output might show the error.  Also, you probably want to upgrade your
R, as R-2.6.2 is a year old.

Sean

> ###################
> sessionInfo()
> R version 2.6.2 (2008-02-08)
> i486-pc-linux-gnu
>
> locale:
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] rcompgen_0.1-17 tools_2.6.2
> ###################
>
> I have libsbml installed which was done by running the following commands:
> ./configure --with-python --with-bzip2=no
> make
> sudo make install
>
> Can anybody suggest what I need to do.
>
> thanks,
> Richard
> --
> Dr Richard Birnie
> Research Scientist
> Pro-Cure Therapeutics Limited
> Biocentre
> Innovation Way, Heslington, York, YO10 5NY, UK
> Registered in England : Reg No. 421 6368
> telephone +44 (0)1904 435125
> Email richard.birnie at pro-cure.uk.com
> www.pro-cure.uk.com
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