[BioC] "GOstat" package not installing

[Steve Lianoglou]

Hi Ashwin,

On May 21, 2009, at 3:04 AM, Ashwin Kumar wrote:

> Hello group ,
>
> I am still having problems with installing the GOstats package & its  
> not a
> typo error ... I am pasting my workspace image along with the error it
> shows:

So it looks like GOstats actually isn't your problem (yet, anyway) and  
the real problem is that installing the XML library is failing on your  
system. See:

> * 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 xml2-config... no
> Cannot find xml2-config
> ERROR: configuration failed for package ‘XML’
> * Removing ‘/home/mlscub1/R/i486-pc-linux-gnu-library/2.9/XML’

Once XML fails, the packages that depend on it fail to load, and you  
get the cascading errors you're experiencing now. So, let's try to  
sort that out first.

The System Requirements section on the CRAN page for XML[1] says it  
requires libxml2 (>= 2.6.3). By the looks of your errors, your  
system's inability to find "xml2-config" suggests libxml2 isn't  
installed.

Could you (or get your sysadmin to) try to use whatever package  
manager your linux distro uses to install libxml2 and then try your  
biocLite install again?

-steve

[1] XML Package: http://cran.r-project.org/web/packages/XML/index.html

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University

http://cbio.mskcc.org/~lianos