Hi All, Getting through the new CPAS upgrade and working through setup of R scripts. A couple of questions:

Are GDD and Cairo packages necessary for the following scripts:

SASPECT

Normalization_function.R

and others found in:

http://peiwang.fhcrc.org/research-project.html

From Martin McIntosh's informatics group

In the new upgrade I thought SASPECT was loaded as a default somewhere but I couldn't find it

I am running tomcat on a RHEL4 with 5 updates and R wont allow me to install the GDD or cairo packages
Before I load and compile these packages from source I thought I would ask if I was missing something. I tried

install.packages('Cairo', 'http://www.rforge.net/')

install.packages(c("GDD", "Cairo"), repos="http://cran.r-project.org" )

install.packages(c("Cairo"), repos="http://www.cairographics.org" )

install.packages(c("GDD"), repos="http://www.rosuda.org/R/GDD/" )

install.packages('Cairo',,'http://www.cairographics.org')

None of these seem work, output is below. Any advice folks have is muchly appreciated. Thanks -Rich

###################################################################
checking for an ANSI C-conforming const... yes
checking for pkg-config... /usr/bin/pkg-config
checking whether pkg-config knows about cairo... no
configure: CAIRO_LIBS is unset, attempting to guess it.
configure: CAIRO_CFLAGS=
checking if R was compiled with the RConn patch... no
checking cairo.h usability... no
checking cairo.h presence... no
checking for cairo.h... no
configure: error: Cannot find cairo.h! Please install cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.
ERROR: configuration failed for package 'Cairo'
** Removing '/usr/local/lib/R/library/Cairo'

The downloaded packages are in
        /tmp/RtmptxmhYL/downloaded_packages
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages(c("GDD", "Cairo"), repos = "http://cran.r-project.org") :
  installation of package 'GDD' had non-zero exit status
2: In install.packages(c("GDD", "Cairo"), repos = "http://cran.r-project.org") :
  installation of package 'Cairo' had non-zero exit status