[BioC] problem of package yg98 and XML

[Robert Gentleman]

Yes, others have had that problem and searching the mailing list  
archive would have pointed you to the correct solution. You do not have  
libxml installed on your computer and you will need to have it  
installed, the XML package uses software available through libxml.

  Robert

ps did you look at what you did get in the yg98 package and make sure  
that the information you want is not there (perhaps stored in a  
different place than you looked?) Reading the manual pages and  
searching the available mailing list archives is sometimes not an  
entirely irrelevant exercise.


On Jan 27, 2005, at 12:16 PM, Lin Tang wrote:

> Hi,
> I've tried to install the
> 1.6.8.tar.gz in my linux, but I found the
> package is missing symbol, refseq and unigene information. When I try  
> to
> load the symbol for probe ID with annoation package, it reports:
>
>  Object "yg98SYMBOL" not found.
>
> Is this the package problem?
>
> So I tried to use the annobuilder. But when I tried to install XML
> (XML_0.97-0.tar.gz), I have the following errors:
>
>> install.packages("XML","~/R")
> trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
> Content type `text/plain; charset=iso-8859-1' length 46868 bytes
> opened URL
> ==================================================
> downloaded 45Kb
>
> trying URL `http://cran.r-project.org/src/contrib/XML_0.97-0.tar.gz'
> Content type `application/x-tar' length 556400 bytes
> opened URL
> ==================================================
> downloaded 543Kb
>
> * Installing *source* package 'XML' ...
> checking for gcc... gcc
> checking for C compiler default output... 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 xml2-config... no
> Cannot find xml2-config
> ERROR: configuration failed for package 'XML'
>
>
> Has any one have the same problems?
>
> Thanks you.
>
> Lin
>
> _______________________________________________
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> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
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| Robert Gentleman              phone: (206) 667-7700                    
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| Head, Program in Computational Biology   fax:  (206) 667-1319   |
| Division of Public Health Sciences       office: M2-B865               
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| Fred Hutchinson Cancer Research Center                                 
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| email: rgentlem at fhcrc.org                                              
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