[Bioc-devel] widgettools download problem w/ getBioC

Cyrus Harmon ch-bioc at bobobeach.com
Thu May 19 01:39:17 CEST 2005

On May 18, 2005, at 4:23 PM, Seth Falcon wrote:

> Cyrus Harmon <ch-bioc at bobobeach.com> writes:
>> 1. The repository is in an unstable state as it gets prepped for the
>> 1.6 release
> That would be the issue: getBioC (the current version on the site)
> doesn't know about the updated repository layouts.

That's what I figured. The web pages that describe current releases  
and timelines could use an update. (I think there's one page that  
says that 1.5 is scheduled for release in Nov. 04 :-) ).

> Since you asked, please try:
> source("http://www.bioconductor.org/getBioC-1.6.R")
> And then
> getBioC(...)

Will do. Before I go off and do this, a couple quick questions:

1. What R versions are supported? I'm happy to do this on both  
R-2.1.0 and R-SVN-current-as-of-today, but if either is known to not  
be supported, it will save me time tracking this down. I'm not too  
interested in pre-2.1.0 releases, although I imagine others might be.

2. What to do about previous bioconductor installations? Do we  
support getBioC for 1.6 on top of existing packages? Is there an  
expectation that users blow away there old versions? Either approach  
seems like it might be reasonable, but I'll skip testing the install- 
over-previous-bioconductor thing if that's unsupported/known-not-to- 

> The script now accepts a pkgs argument that should allow you to
> specify a character vector of Bioconductor packages to install.

Sounds good!

> if you want the default package set, then getBioC() should do it.
> The develOK arg is no longer supported.  The Bioconductor package
> repository you will access depends on the version of R you use.  2.0
> => Bioc 1.5, 2.1 => Bioc 1.6, and 2.2 => Bioc 1.7 (not yet available).

Again, sounds like an improvement.

> Would love to hear how this works/doesn't work for you.  And if you
> have time to report back, please indicate sessionInfo() output as
> well.
> Thanks!

My pleasure! Congrats on the impending (or completed? I'm still not  
sure...) release!


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