[BioC] Rgraphviz with rApache problems

[Robert M. Flight]

So that others might know, the problem was that regular users had a
different $LD_LIBRARY_PATH than the apache daemon, and therefore the
libraries could not be found when the application was being run as a
web user.

-Robert

On Tue, Oct 19, 2010 at 12:01, Robert M. Flight <rflight79 at gmail.com> wrote:
> Hello All,
> I'm hoping someone here can help me out.
> I am trying to run a web application using RApache, that I have
> running on a test machine, but am having difficulty with on the actual
> service machine. This application depends on Rgraphviz to generate
> figures as output. I have installed graphviz 2.2-6, as well as
> Rgraphviz 1.26.0, and can run "example(layoutGraph) with only X11 font
> problems (old system, not relevant to generated output) either as a
> regular user, the apache user, or as root.
> However, when I try and load the Rgraphviz library in my web
> application, I get the following error:
>
> RApache Warning/Error!!!
>
> Loading required package: Rgraphviz
> RApache Warning/Error!!!
>
> Loading required package: graph
> RApache Warning/Error!!!
>
> Loading required package: grid
> RApache Warning/Error!!!
>
> Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
> call: value[[3L]](cond) error: unable to load shared library
> '/usr/local/lib64/R/library/Rgraphviz/libs/Rgraphviz.so':
> libdotneato.so.0: cannot open shared object file: No such file or
> directory Check that (1) graphviz is installed on your system; (2) the
> installed version of graphviz matches '2.2'; this is the version used
> to build this Rgraphviz package; (3) graphviz is accessible to R,
> e.g., the path to the graphviz 'bin' directory is in the system 'PATH'
> variable. See additional instructions in the 'README' file of the
> Rgraphviz 'source' distribution, available at
> http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html Ask
> further questions on the Bioconductor mailing list
> http://bioconductor.org/docs/mailList.html
>
> I can't really figure out where this is looking for
> "libdotneato.so.0", because when I run R I have no problems. I did
> make a symbolic link to the actual file, could this be part of the
> problem? I could really use some direction on this.
>
> Thanks,
>
> -Robert
>
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> Rapache 1.1.9
> Rgraphviz 1.26.0
> graphviz 2.2-6
>
>
> Robert M. Flight, Ph.D.
> University of Louisville Bioinformatics Laboratory
> University of Louisville
> Louisville, KY
>
> PH 502-852-0467
> EM robert.flight at louisville.edu
> EM rflight79 at gmail.com
>
> Williams and Holland's Law:
>        If enough data is collected, anything may be proven by
> statistical methods.
>