[BioC] hexbin needs colorspace - but where is colorspace?

Naomi Altman naomi at stat.psu.edu
Tue Jul 19 16:38:31 CEST 2005

OK, true confession time.  I tend to leave my software well enough alone 
until I come up with a problem (as I just did).  So, I was running R. 2.0.1 
with what I thought was the most recent release of Bioconductor.   I do 
regularly hit the "update packages" button.

I have been installing Bioconductor by

installing R (on Windows)
using the pulldown menu to "install packages"

Hexbin was  in the "Install packages from Bioconductor" menu.  But that was 
the wrong version, so I went to the Bioconductor website, and tracked down 
the developer version of hexbin, which requires R 2.1.0.

I just upgraded to R 2.1.1.  Without starting over, it is hard to see what 
comes automatically with hexbin, as I have already downloaded all the 
relevant bits and pieces.

All I can say in my defense is that I do try to respond to more 
bioconductor questions than I pose, to even the score a bit.

Thanks everyone for your assistance.  I guess I had better reinstall all 
the Bioconductor software that I use to ensure I have the latest release.


At 09:55 AM 7/19/2005, Martin Maechler wrote:
> >>>>> "JimMcD" == James MacDonald <jmacdon at med.umich.edu>
> >>>>>     on Mon, 18 Jul 2005 15:23:19 -0400 writes:
>     JimMcD> library(reposTools)
>     JimMcD> install.packages2("colorspace")
>     JimMcD> HTH,
>     JimMcD> Jim
>     JimMcD> Also, if you are using the devel version you will probably 
> need to be
>     JimMcD> running R-2.2.0
>but really the grid-based  hexbin is in the current Bioconductor
>(1.6), at least for me,
>so I am a little perplexed why Naomi first needs to download it.
>I guess, Naomi, you somehow managed to keep an old version of
>hexbin around?  It may be because  getBioC() has changed and
>doesn't install "hexbin" anymore AFAIK, unless you explicitly
>ask for
>    getBioC("hexbin", lib = ...., destdir = ....)
>the need of which I had been wondering about as well..
>Also --- probably more a question to the bioconductor-release-managers :
>if you had used the above  getBioC(..) shouldn't you have gotten
>"hexbin"  *plus* all the packages it depends on, i.e., in your
>case "colorspace" as well?
>Naomi, can you tell us *how* you've installed hexbin?
>Martin Maechler, ETH Zurich
>     >>>> Naomi Altman <naomi at stat.psu.edu> 7/18/2005 3:15:30 PM >>>
>     Naomi> I downloaded hexbin from the developer site, since the release 
> version
>     Naomi> says
>     Naomi> to do so.
>     Naomi> But I then get the following message:
>     >> library(hexbin)
>     Naomi> Loading required package: grid
>     Naomi> Loading required package: colorspace
>     Naomi> Error: package 'colorspace' could not be loaded
>     Naomi> In addition: Warning message:
>     Naomi> there is no package called 'colorspace' in: library(pkg, 
> character.only
>     Naomi> = TRUE, logical = TRUE, lib.loc = lib.loc)
>     Naomi> I thought this might be a version problem, so I also
>     Naomi> reinstalled the most recent version of R - but to no
>     Naomi> avail.  I have not been able to locate colorspace.
>     Naomi> As always, any assistance would be most appreciated.

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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