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

[James W. MacDonald]

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.

It wouldn't be if it were true. However, this is an old annotation 
package that was part of the 1.7 release of Bioconductor that was 
designed to work with R-2.2.0. Direct downloading of BioC packages can 
easily result in unintended version mismatches like this.

The correct paradigm for installing BioC packages is to use biocLite(), 
which is a wrapper to install.packages() that will automatically point 
to the correct repository for a given version of R.

source("http://www.bioconductor.org/biocLite.R")
biocLite("hgu95av2")

Additionally, R-help is not the correct list for questions about 
Bioconductor packages. There is a separate list at 
bioconductor at stat.math.ethz.ch.

Best,

Jim


> 
> Duncan Murdoch
> 
> ______________________________________________
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> and provide commented, minimal, self-contained, reproducible code.


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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