Hi Anjia and Hi Ting-Yuan,

It's nice to see this topic has been discussed here. I have the similar (or
the same) problem as Anjia's even after installing R 2.2.0 on my ubuntu
linux. Here are the details.

The error under R 2.2.0 is:

> source("http://www.bioconductor.org/biocLite.R")
> biocLite("Biobase")

Running bioCLite version 0.1  with R version  2.2.0

Running biocinstall version 1.1  with R version  2.2.0
trying URL
'
http://www.bioconductor.org/packages/bioc/1.7/src/contrib/Biobase_1.8.0.tar.gz
'
Content type 'application/x-gzip' length 1285566 bytes
opened URL
==================================================
downloaded 1255Kb

* Installing *source* package 'Biobase' ...
** libs
/usr/lib/R/bin/SHLIB: line 102: make: command not found
ERROR: compilation failed for package 'Biobase'
** Removing '/usr/local/lib/R/site-library/Biobase'

The downloaded packages are in
        /tmp/RtmpuiBzwp/downloaded_packages
Warning message:
installation of package 'Biobase' had non-zero exit status in:
install.packages(pkgs = "Biobase", repos =
c("http://www.bioconductor.org/packages/bioc/1.7",

(Then I opened "/usr/lib/R/bin/SHLIB" and found the line 102)

eval ${MAKE} ${makefiles} ${makeargs} ${makeobjs}


I am a green hand to both Linux and C and can't fix the problem. My guess is
this is a problem specific to Linux Ubuntu Breezy Badger.

Can anyone help me with it? Thanks ahead.

Frank


On 11/28/05, Ting-Yuan Liu <tliu@fhcrc.org> wrote:
>
>
> Hi Anja,
>
> If you are using R 2.1.1, could you upgrade to R 2.2.0, which is the
> latest versionof R, please?
>
> After you upgrade to R 2.2.0, you can use the biocLite script to install
> BioConductor for you.  In an R command window, type the following:
>
> source("http://www.bioconductor.org/biocLite.R")
> biocLite()
>
> Please refer to the "Install - How To" page on the BioConductor official
> website.
>
> If you still have trouble in installing BioConductor, please report the
> error/warning messages and the result of sessionInfo() to the list again.
>
> HTH,
> Ting-Yuan
>
> ______________________________________
> Ting-Yuan Liu
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> Seattle, WA, USA
> ______________________________________
>
> On Sat, 26 Nov 2005, Anja Schiel wrote:
>
> > I have downloaded R version 2.1.1 via apt-get and have now a running R
> under Ubuntu Breezy Badger. But now I would like to use the Bioconductor
> packages and tried to install with BioC().
> No matter if I use the root account or my personal login, I always end
> up with at least 11 to 14 warnings and always the problem that all
> packages dependent on the Biobase package can not be installed.
>
> I should mention that I gave myself permission to all libraries and
> anyhow, other libraries such as limma are not affected.
>
> Warning messages:
> 1: installation of package 'Biobase' had non-zero exit status in:
> install.packages(pkgs = c("affy", "affydata", "affyPLM",
> "annaffy",   ...
> 2: installation of package 'Biostrings' had non-zero exit status in:
> install.packages(pkgs = c("affy", "affydata", "affyPLM",
> "annaffy",   ...
> 3: installation of package 'pamr' had non-zero exit status in:
> install.packages(pkgs = c("affy", "affydata", "affyPLM",
> "annaffy",   ...
> 4: installation of package 'affy' had non-zero exit status in:
> install.packages(pkgs = c("affy", "affydata", "affyPLM",
> "annaffy",   ...
> 5: installation of package 'annaffy' had non-zero exit status in:
> install.packages(pkgs = c("affy", "affydata", "affyPLM",
> "annaffy",   ...
> 6: installation of package 'edd' had non-zero exit status in:
> install.packages(pkgs = c("affy", "affydata", "affyPLM",
> "annaffy",   ...
> 7: installation of package 'genefilter' had non-zero exit status in:
> install.packages(pkgs = c("affy", "affydata", "affyPLM",
> "annaffy",   ...
> 8: installation of package 'multtest' had non-zero exit status in:
> install.packages(pkgs = c("affy", "affydata", "affyPLM",
> "annaffy",   ...
> 9: installation of package 'vsn' had non-zero exit status in:
> install.packages(pkgs = c("affy", "affydata", "affyPLM",
> "annaffy",   ...
> 10: installation of package 'geneplotter' had non-zero exit status in:
> install.packages(pkgs = c("affy", "affydata", "affyPLM",
> "annaffy",   ...
> 11: installation of package 'makecdfenv' had non-zero exit status in:
> install.packages(pkgs = c("affy", "affydata", "affyPLM",
> "annaffy",   ...
> 12: installation of package 'matchprobes' had non-zero exit status in:
> install.packages(pkgs = c("affy", "affydata", "affyPLM",
> "annaffy",   ...
> 13: installation of package 'gcrma' had non-zero exit status in:
> install.packages(pkgs = c("affy", "affydata", "affyPLM",
> "annaffy",   ...
> 14: installation of package 'affyPLM' had non-zero exit status in:
> install.packages(pkgs = c("affy", "affydata", "affyPLM",
> "annaffy",   ...
>
> So when I try to open affy the following error message appears.
>
> > library(affy)
> Loading required package: Biobase
> Error in library.dynam(lib, package, package.lib) :
>        shared library 'Biobase' not found
> In addition: Warning messages:
> 1: package 'Biobase' contains no R code in: loadNamespace(package,
> c(which.lib.loc, lib.loc))
> 2: S3 method 'as.data.frame.exprSet' was declared in NAMESPACE but not
> found
> Error: package 'Biobase' could not be loaded
>
> I used the woody URL to apt-get install, but I guess that should not
> make a difference.
>
> I checked the mail archive, but somehow this particular problem was not
> discussed. It seems that something goes wrong during compiling the
> Biobase package.
> Any suggestions would be very welcome, I am not necessarily an expert on
> Linux.
>
> Greetings and thanks in advance,
> Anja Schiel
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
>

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