[BioC] help in downloading some packages.

Michael Dondrup Michael.Dondrup at uni.no
Thu Oct 7 15:37:44 CEST 2010

let's keep it on the list.
you can use apt-get install. Not sure about the package names there, try
apt-cache search libxml2 
to find out. Also these dependencies on XML affect other package installation, try to get XML 
installed first, then continue with biobase. Of course, *in principle* these dependencies to external libraries
should be listed in the package documentation/README file somewhere 
(and i guess for XML they are...)


Am Oct 7, 2010 um 2:44 PM schrieb Veerendra GP:

> I am using ubuntu 9.04-  Tha jaunty jackalop. so, can i use the same command to download it? 
> On Thu, Oct 7, 2010 at 6:00 PM, Michael Dondrup <Michael.Dondrup at uni.no> wrote:
> [snip]
> > * 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 ISO C89... none needed
> > checking how to run the C preprocessor... gcc -E
> > checking for sed... /bin/sed
> > checking for pkg-config... /usr/bin/pkg-config
> > checking for xml2-config... no
> > Cannot find xml2-config
> > ERROR: configuration failed for package 'XML'
> > ** Removing '/home/veerendra/R/i486-pc-linux-gnu-library/2.8/XML'
> > * Installing *source* package 'AnnotationDbi' ...
> ^this
> you cannot install package XML which is a dependency of other packages, because you need libxml2
> I guess you are using red-hat, centos or smth, you didn't give the sessionInfo().
> Install libxml2 and libxml2-devel using your package manager, aka.:
> # yum install libxml2 libxml2-devel
> or apt-get install ^^ on debian  
> -- 
> Veerendra.

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