[BioC] Bioconductor Install Problems

[Smith, Troy (NIH/NCI)]

Hello all,

 

We have installed R-2.0.0 on a Red Hat ES 3.0 server and have been trying to
install all of the Bioconductor pkgs for a few days using the following
methods:

 

            >getBioC

            >update.packages2()

            >install.packages2()

            #R CMD INSTALL package name

 

We continually encounter the same two issues.  An example of the first issue
when trying to install KEGGSOAP:

 

                        [1] "Attempting to download KEGGSOAP from
http://www.bioconductor.org/repository/release1.5/package/Source"

[1] "Download complete."

[1] "Installing KEGGSOAP"

* Installing *source* package 'KEGGSOAP' ...

** R

** save image

Loading required package: XML 

Loading required package: SSOAP 

Loading required package: RCurl 

Error in library.dynam(lib, package, package.lib) : 

                         shared library 'RCurl' not found

In addition: Warning messages: 

1: Package  'RCurl' contains no R code in: loadNamespace(package,
c(which.lib.loc, lib.loc)) 

2: S3 method(s) '[<-.CURLOptions', '[[<-.CURLOptions' were declared in
NAMESPACE but not found 

Error: package 'RCurl' could not be loaded

Execution halted

ERROR: execution of package source for 'KEGGSOAP' failed

>From URL:  http://www.bioconductor.org/repository/release1.5/package/Source

                         KEGGSOAP version 0.6.5

 

Warning message: 

Installation of package KEGGSOAP had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)

 

We have tried upgrading from R1.9.1 (using Bioconductor 1.4) to R2.0.0 to
R2.0.1.  We have tried fresh installs of R2.0.0 and R2.0.1 on this server,
as well as alternate Red Hat ES 3 boxes. 

 

The second issue involves RGraphviz when we use >getBioC("all").  The
following message pops up:

 

                        Package RGraphviz requires special libraries to be
installed.

 

We are pointed to the faq on www.bioconductor.org
<http://www.bioconductor.org/> , which states Graphviz 1.12 or above
required.  The system currently has the following Graphviz packages
installed:

 

                        graphviz-devel-1.16-1

graphviz-tcl-1.16-1

graphviz-1.16-1

 

We have also tried more recent versions, both RPM and from source.

 

Our current expertise of both R and Bioconductor is limited, and our
developers who actually use these applications are investigating on their
own, however we though we would ask the experts.   Any assistance you are
able to provide is greatly appreciated.

 

Thanks

Troy

 

Troy D Smith

Network Engineer

NCICB/LPG Systems Group

Contractor, Terrapin Systems

 

Terrapin Systems

6905 Rockledge Drive, Suite 200

Bethesda, MD 20817

 

301.530.9106 x323 Corporate Voice

301.530.9105 Corporate Fax

 

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