hexbin in R 2.2.0 - installation problem
0
0
Entering edit mode
@nicholas-lewin-koh-63
Last seen 10.2 years ago
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 > >
graph hexbin limma graph hexbin limma • 1.0k views
ADD COMMENT

Login before adding your answer.

Traffic: 624 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6