Hello everyone

 

I have been trying to install bioconductor on ubuntu 7.10 gutsy using R
version 2.5.1, and getting a lot of error messages:

 

 Here are a few:

1: package âxtableâ is not available in: install.packages(pkgs = pkgs, repos
= repos, dependencies = dependencies,   ...

2: dependency âsurvivalâ is not available in: install.packages(pkgs = pkgs,
repos = repos, dependencies = dependencies,   ...

3: installation of package 'affyio' had non-zero exit status in:
install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
...

4: installation of package 'lattice' had non-zero exit status in:
install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
...

5: installation of package 'KernSmooth' had non-zero exit status in:
install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
...

 

I have installed r-base-core, build-essential, g77, reflas3, reflas3-dev,
r-base-dev, and r-recommended.

 

When I tried to install affyio by itself, I got the following error message:

> biocLite(c("affyio"))

Running biocinstall version 2.0.8 with R version 2.5.1

Your version of R requires version 2.0 of Bioconductor.

Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :

         argument 'lib' is missing: using '/usr/local/lib/R/site-library'

trying URL
'http://bioconductor.org/packages/2.0/bioc/src/contrib/affyio_1.4.1.tar.gz'

Content type 'application/x-gzip' length 59104 bytes

opened URL

==================================================

downloaded 57Kb

 

* Installing *source* package 'affyio' ...

creating cache ./config.cache

checking how to run the C preprocessor... cc -E

checking for main in -lz... no

updating cache ./config.cache

creating ./config.status

creating src/Makevars

** libs

gcc-4.2 -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic
-g -O2 -c read_abatch.c -o read_abatch.o

/bin/bash: gcc-4.2: command not found

make: *** [read_abatch.o] Error 127

chmod: cannot access `/usr/local/lib/R/site-library/affyio/libs/*': No such
file or directory

ERROR: compilation failed for package 'affyio'

** Removing '/usr/local/lib/R/site-library/affyio'

 

The downloaded packages are in

        /tmp/RtmpowXclV/downloaded_packages

Warning message:

installation of package 'affyio' had non-zero exit status in:
install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,

 

 

If anyone can offer suggestions or help, it would be appreciated.

 

Thanks,

R


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