[BioC] hexbin in R 2.2.0 - installation problem

[Nicholas Lewin-Koh]

Hi Naomi,
The colorspace dependency will be removed in the next version of hexbin. 
Most of the functionality I needed is now in grDevices. This
should be in the development version in the next couple days.

Also, I just committed some code last night to mix hexbin with lattice
so that now one can do hexploms and conditional plots. Thanks to
Deepayan for that.

Nicholas
>
> Message: 4
> Date: Wed, 19 Oct 2005 14:26:42 -0400
> From: Naomi Altman <naomi at stat.psu.edu>
> Subject: [BioC] ANCOVA in limma
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <6.2.5.6.2.20051019142403.033e61e8 at stat.psu.edu>
> Content-Type: text/plain; charset="us-ascii"; format=flowed
> 
> We would like to adjust our ANOVA-type analysis by using the 
> covariate "age".  Because limma is based on contrast, rather than 
> "type III SS", it seems to me that the only way to proceed with an 
> ANCOVA-type analysis is to orthogonalize the design matrix against 
> the covariate.  Is there a more straight-forward method?
> 
> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
> University Park, PA 16802-2111
> 
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Wed, 19 Oct 2005 14:58:43 -0400
> From: Naomi Altman <naomi at stat.psu.edu>
> Subject: [BioC] hexbin in R 2.2.0 - installation problem
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <6.2.5.6.2.20051019145353.03423508 at stat.psu.edu>
> Content-Type: text/plain; charset="us-ascii"; format=flowed
> 
> I just downloaded R 2.2.0 for Windows, after which I installed 
> several Bioconductor packages using the packages menu.
> 
> I downloaded hexbin and graph apparently without incident, except 
> that "colorspace" was not found.
> 
> However, I cannot run hexbin:
> 
>  >library(hexbin)
> 
> Loading required package: colorspace
> Error: package 'colorspace' could not be loaded
> In addition: Warning message:
> there is no package called 'colorspace' in: library(pkg, 
> character.only = TRUE, logical = TRUE, lib.loc = lib.loc)
> 
>  > hexbin
> Error: object "hexbin" not found
> 
> 
> "graph"  apparently installed "Ruuid".  I got the following message 
> when installing hexbin
> 
> dependency ''colorspace'' is not available
> 
> trying URL 
> 'http://www.bioconductor.org/bin/windows/contrib/2.2/hexbin_1.4.0.zip'
> Content type 'application/zip' length 1135841 bytes
> opened URL
> downloaded 1109Kb
> 
> package 'hexbin' successfully unpacked and MD5 sums checked
> 
> The downloaded packages are in
>          C:\temp\Rtmp18070\downloaded_packages
> updating HTML package descriptions
> 
> 
> 
> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
> University Park, PA 16802-2111
> 
> 
> 
> ------------------------------
> 
> Message: 8
> Date: Wed, 19 Oct 2005 13:53:04 -0700
> From: Seth Falcon <sfalcon at fhcrc.org>
> Subject: Re: [BioC] hexbin in R 2.2.0 - installation problem
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <m2ek6hns9b.fsf at macaroni.local>
> Content-Type: text/plain; charset=us-ascii
> 
> Hi Naomi,
> 
> On 19 Oct 2005, naomi at stat.psu.edu wrote:
> 
> > I just downloaded R 2.2.0 for Windows, after which I installed 
> > several Bioconductor packages using the packages menu.
> >
> > I downloaded hexbin and graph apparently without incident, except 
> > that "colorspace" was not found.
> 
> I'm guessing:
>  1. you did the installation using the menus
>  2. you had selected only the bioconductor repository to select
>     packages from.
> 
> Unfortunately, this doesn't allow the tools to install dependencies
> from other package repositories, namely CRAN, where colorspace is
> hosted.
> 
> This isn't your fault and it is something we will try to address for
> the future.
> 
> I think you can resolve your issue with hexbin by installing the
> colorspace package from CRAN.
> 
> You might also try select both bioconductor and CRAN repositories form
> the menu and then reinstalling hexbin (note: I haven't tried this, but
> I think it has a good chance of working).
> 
> Best,
> 
> + seth
> 
>