R help - Feb 2007 - Problems with 'delay'/'delayedAssign' when installing data package

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?

Thanks - Wolfram

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

Hi Wolfram,

Wolfram Fischer <wolfram at fischer-zim.ch> writes:
> 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
That is not the recommended way to install Bioconductor packages (and
of course, this is not the recommended place to ask questions about
them: there is a dedicated bioconductor list).

Based on this:
> 	** Removing '/usr/local/lib64/R-2.4.1/library/hgu95av2'
I take it you are using R-2.4.1 on a 64-bit Linux platform.  It is
good that you are using an up-to-date version of R.  To install
Bioconductor packages, please try:

  R> source("http://bioconductor.org/biocLite.R")
  R> biocLite("hgu95av2")
  ## or to get everything geneplotter depends and suggests
  R> biocLite("geneplotter", dependencies=TRUE)

The error you are seeing is due to the fact that you have downloaded a
very old version of the data annotation package.  These packages are
maintained and updated version appropriate for current R are
available.  The easiest way is to install using biocLite, but you can
also get to the current stuff from the website.

+ seth