I always followed http://cran.r-project.org/bin/linux/ubuntu/ to install R
on Ubuntu 8.1. I had no errors before!

> install.packages("XML")
Warning in install.packages("XML") :
  argument 'lib' is missing: using '/usr/local/lib/R/site-library'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.fhcrc.org/src/contrib/XML_1.98-1.tar.gz'
Content type 'application/x-gzip' length 648274 bytes (633 Kb)
opened URL
==================================================
downloaded 633 Kb

* Installing *source* package 'XML' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package 'XML'
** Removing '/usr/local/lib/R/site-library/XML'

The downloaded packages are in
 /tmp/RtmpqCLrkQ/downloaded_packages
Warning message:
In install.packages("XML") :
  installation of package 'XML' had non-zero exit status
>



On Mon, Dec 1, 2008 at 1:42 PM, Hervé Pagès <hpages@fhcrc.org> wrote:

> Hi Tiandao,
>
> What OS do you have? How did you install R? It looks like you cannot
> install an R package with native code at all. Please try
>
>  > install.packages("XML")
>
> and show us the complete output.
> You could also try the R-help mailing list (r-help@r-project.org)
> since your problem doesn't seem to be Bioconductor-specific.
>
> Cheers,
> H.
>
>
> Tiandao Li wrote:
>
>> Hello,
>>
>> I tried to install BioC 2.3 on a new laptop (HP AMD Turion x2). However I
>> constantly had the following warnings, I tried several times for the last
>> few days. I never had this kind of errors before.
>>
>> sudo R
>>
>>  source("http://bioconductor.org/biocLite.R")
>>>
>>
>>  biocLite()
>>>
>>
>>  warnings()
>>>
>> Warning messages:
>> 1: In install.packages(pkgs = pkgs, repos = repos, dependencies =
>> dependencies, ... :
>>  installation of package 'Matrix' had non-zero exit status
>> 2: In install.packages(pkgs = pkgs, repos = repos, dependencies =
>> dependencies, ... :
>>  installation of package 'preprocessCore' had non-zero exit status
>> 3: In install.packages(pkgs = pkgs, repos = repos, dependencies =
>> dependencies, ... :
>>  installation of package 'IRanges' had non-zero exit status
>> 4: In install.packages(pkgs = pkgs, repos = repos, dependencies =
>> dependencies, ... :
>>  installation of package 'affy' had non-zero exit status
>> 5: In install.packages(pkgs = pkgs, repos = repos, dependencies =
>> dependencies, ... :
>>  installation of package 'affydata' had non-zero exit status
>> 6: In install.packages(pkgs = pkgs, repos = repos, dependencies =
>> dependencies, ... :
>>  installation of package 'Biostrings' had non-zero exit status
>> 7: In install.packages(pkgs = pkgs, repos = repos, dependencies =
>> dependencies, ... :
>>  installation of package 'matchprobes' had non-zero exit status
>> 8: In install.packages(pkgs = pkgs, repos = repos, dependencies =
>> dependencies, ... :
>>  installation of package 'vsn' had non-zero exit status
>> 9: In install.packages(pkgs = pkgs, repos = repos, dependencies =
>> dependencies, ... :
>>  installation of package 'gcrma' had non-zero exit status
>> 10: In install.packages(pkgs = pkgs, repos = repos, dependencies =
>> dependencies, ... :
>>  installation of package 'simpleaffy' had non-zero exit status
>> 11: In install.packages(pkgs = pkgs, repos = repos, dependencies =
>> dependencies, ... :
>>  installation of package 'affyPLM' had non-zero exit status
>> 12: In install.packages(pkgs = pkgs, repos = repos, dependencies =
>> dependencies, ... :
>>  installation of package 'affyQCReport' had non-zero exit status
>>
>>  sessionInfo()
>>>
>> R version 2.8.0 (2008-10-20)
>> i486-pc-linux-gnu
>>
>> locale:
>>
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> loaded via a namespace (and not attached):
>> [1] tcltk_2.8.0 tools_2.8.0
>>
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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