[BioC] AnnBuilder built package not supported in R 2.2.0

[Ting-Yuan Liu]

Hi Brian,

Could you try again?  I believe there are some problems in the KEGG site 
last week, and I also believe these problems have been solved.  You should 
not get the error in the parseKEGGGenome() function again.

HTH,
Ting-Yuan
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________

On Fri, 24 Feb 2006, Brian Parker wrote:

> Hi,
> 
> Actually, I just wasn't installing the generated package properly using 
> R CMD INSTALL (see my response to James MacDonald above) (...actually, 
> that might be a useful newbie FAQ to add to the AnnBuilder vignette...).
> 
> The one remaining problem I have now is that I am finding that the KEGG 
> site is unresponsive, and on most runs I get the following error message-
> "
> Warning message:
> Built for UCSC is not valid! in: getUCSCBuilt(organism)
> Error in parseKEGGGenome() : Faild to obtain KEGG organism code
> "
> Is there any simple workaround to skip the KEGG data?
> 
> BTW, thanks for the AnnBuilder function!
> Brian Parker
> 
> John Zhang wrote:
> 
> >You will have to tell us a little bit more about what you have done. Did you 
> >built the package and then had the package installed using R 2.2.0 or 2.2.1 or 
> >built the package using R < 2.0.0 and tried to install the package using R > 
> >2.0.0? 
> >
> >
> >  
> >
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> >
> >>Date: Thu, 23 Feb 2006 11:42:30 +1100
> >>From: Brian Parker <brian.parker at rsise.anu.edu.au>
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> >
> >>Hi,
> >>
> >>I have tried generating an example annotation file using AnnBuilder 
> >>following the example in the AnnBuilder vignette.
> >>The example package "myPkg" appears to build OK, but when I try to use 
> >>it I get the following error-
> >>    
> >>
> >>>library(myPkg)
> >>>      
> >>>
> >>Error in library(myPkg) : 'myPkg' is not a valid package -- installed < 
> >>2.0.0?
> >>
> >>I have tried R 2.2.0 and 2.2.1 under Windows.
> >>Any suggestions?
> >>
> >>Thanks,
> >>Brian Parker
> >>
> >>_______________________________________________
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> >>    
> >>
> >
> >Jianhua Zhang
> >Department of Medical Oncology
> >Dana-Farber Cancer Institute
> >44 Binney Street
> >Boston, MA 02115-6084
> >
> >  
> >
> 
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