[Bioc-devel] drosophila2GENENAME problem?

[Seth Falcon]

Hi Cyrus,

Cyrus Harmon <ch-bioc at bobobeach.com> writes:
> I'm trying to use drosophila2GENENAME with the BioC 1.6 release and  
> running into some trouble. It seems that all of the gene names are  
> NA. Did something happen to these or am I doing something wrong
> here?

We're looking into it.

> In an attempt to figure out what's going on, I've stumbled across a  
> couple other things:
>
> 1. When doing install.packages2("drosophila2"), everything seems to  
> install OK, but the message about Installation complete From URL: is  
> less than helpful as it doesn't return the full URL of the downloaded  
> package, but rather the URL http://www.bioconductor.org/packages/data/ 
> annotation/stable/src/contrib . While I'm sure folks who are more  
> informed than I can ape the proper URL for the drosophila2 package, I  
> can't.

I'm not sure how useful the URL is, complete or not, but I will add it
to a list of improvements.  I think that we will be moving towards
increased use of install.packages which does output the complete URL,
but not as a summary message at the end, so it can be hard to catch.


> 2. The "Return to index" link on the http://bioconductor.org/data/ 
> metaData/html/ page is busted.
>
> I imagine that the web pages are still in a state of flux; if you  
> want me to hold off on bug reports on the bioc web pages, I'm happy  
> to do so.

Please hold off on bug reports on the web pages.  As you imagined,
things are in a temporary state and we will be putting effort into
website improvements over the next couple of weeks.

> btw, I'm successfully (for the most part) using BioC 1.6 on OS X  
> 10.4.1 with R-2.1.0 built w/ gfortran. Lots of moving rapidly
>        targets...

Glad to hear it!

+ seth