[BioC] "GOstat" package not installing

[Hervé Pagès]

Hi Ashwin,

Note that in order to compile the XML package on a Linux system, you
not only need to have the libxml2 package (I'm talking about Linux packages
here i.e. RPM or .deb packages) but also the include files and other stuff
needed for developing and compiling against libxml2. This is generally
found in a package called something like libxml2-devel (on RPM-based Linux
distros like Fedora, RedHat, openSUSE, etc...) or libxml2-dev (on
Debian-based Linux distros like Debian, Ubuntu, etc...).

Cheers,
H.


Steve Lianoglou wrote:
> 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
> 
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-- 
Hervé Pagès

Program in Computational Biology
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