[R] Problems with 'delay'/'delayedAssign' when installing data package

[Robert Gentleman]

Or you could check and see that this is several versions of Bioconductor 
in the past and rather than using the well documented and advertised 
method for obtaining data that are consistent with your version of R you 
have chosen to completely circumvent that procedure and loaded a package
for some obsolete version of R.

So, if you have newer R there are newer versions of this data from 
Bioconductor,
   http://bioconductor.org/packages/1.9/data/annotation/html/hgu95av2.html

shows that for a current R, we are at version 1.14.0 for this package.



Duncan Murdoch wrote:
> On 2/15/2007 3:57 AM, Wolfram Fischer wrote:
>> I downloaded:
>>     http://www.bioconductor.org/data/metaData/hgu95av2_1.7.0.tar.gz
>> described as:
>>     Package: hgu95av2 
>>     Title: A data package containing annotation data for hgu95av2 
>>     Version: 1.7.0 
>>     Created: Wed Jan 12 16:57:23 2005 
>>     Author: Lin,Chenwei 
>>     Description: Annotation data file for hgu95av2 assembled using data
>>        from public data repositories 
>>        Maintainer: Lin,Chenwei < clin at fhcrc.org > 
>>        LazyLoad: yes 
>>        Depends: R(>= 2.0.0) 
>>        License: LGPL 
>>        Packaged: Thu Mar  3 15:43:00 2005; biocbuild
>>
>> It is an example database of the geneplotter library.
>>
>> Trying to install, I got:
>> 	$ R CMD INSTALL hgu95av2_1.7.0.tar.gz 
>>
>> 	* Installing *source* package 'hgu95av2' ...
>> 	** R
>> 	** data
>> 	** preparing package for lazy loading
>> 	Error: 'delay' is defunct.
>> 	Use 'delayedAssign' instead.
>> 	See help("Defunct")
>> 	Execution halted
>> 	ERROR: lazy loading failed for package 'hgu95av2'
>> 	** Removing '/usr/local/lib64/R-2.4.1/library/hgu95av2'
>>
>> How to by-pass this problem?
> 
> There are two possibilities:  update the package to follow current R 
> usage (which is something the maintainer should do, but if the 
> maintainer is not active you may have to do it yourself), or run in an 
> old version of R (pre-2.2.0) from before delay() was made defunct.
> 
> You may also use this as a sign that the package is not being actively 
> maintained, since this change happened in R 2.2.0 in 2005.  I don't know 
> if that's reasonable for a collection of annotation data or not.
> 
> Duncan Murdoch
> 
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> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org