[BioC] install biomaRt failed - configuration failed for XML and RCurl

[Steffen Durinck]

Hi,

Which source is your Yast using? I find libxml2 with my X86_64 SUSE 10.0
using Yast and the following source:

http://mirrors.kernel.org/opensuse/distribution/SL-10.0-OSS/inst-source

You can download Curl from:

http://curl.haxx.se/download.html

Cheers,
Steffen

zhihua li wrote:
> thanks netters.
>
> my system is x86_64-unknown-linux-gnu, SUSE LINUX 10.0.
>
> i tried yast2 but couldn't find corresponding library files for
> libxml2 and librcurl. does anyone know about some source containing
> these packages?
>
> thank you very much!
>
>> From: Diego Diez <diez at kuicr.kyoto-u.ac.jp>
>> To: zhihua li <lzhtom at hotmail.com>
>> Subject: Re: [BioC] install biomaRt failed - configuration failed for
>> XML 
> and RCurl
>> Date: Wed, 13 Sep 2006 11:56:22 +0900
>>
>> Hi Zhihua,
>>
>> On Sep 13, 2006, at 10:41 AM, zhihua li wrote:
>>
>>> Hi, netters,
>>>
>>> recently i've been trying to install biomaRt. I'm using Suse and
>>> have R 2.3.0 installed.
>>>
>>>> source("http://www.bioconductor.org/biocLite.R")
>>>> biocLite("biomaRt")
>>>
>>> Then I was told XML and RCurl are dependencies. And the program
>>> proceeded to download XML,RCurl and biomaRt, followed by installing
>>> them one by one. but when XML was being installed, an error message
>>> came up:
>>>
>>> checking for xml2-config... no
>>> Cannot find xml2-config
>>> ERROR: configuration failed for package 'XML'
>>>
>>> The same for RCurl. And then, not surprisingly, installation of
>>> biomaRt failed too.
>>>
>>> I don't know what happened. It seems that XML and RCurl has been
>>> downloaded, and all the other checkings were ok, except for the
>>> configuration files. Could anyone tell me how to solve the problem?
>>>
>>> Thank you very much!
>>
>>
>> You need to give some more information about your system, try the
>> output of sessionInfo(). Anyway, it seems that the building script
>> cannot find the development libraries for libxml2 which are needed
>> for building the XML package. You may need to install it if it is not.
>>
>> HTH,
>>
>> Diego.
>>
>>
>
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-- 
Steffen Durinck, Ph.D.

Oncogenomics Section
Pediatric Oncology Branch
National Cancer Institute, National Institutes of Health
URL: http://home.ccr.cancer.gov/oncology/oncogenomics/

Phone: 301-402-8103
Address:
Advanced Technology Center,
8717 Grovemont Circle
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