[BioC] basicplot functionality (flowCore/rflowcyt)

[Deepayan Sarkar]

On 8/12/07, M. Jankowski <mjankowski at gmail.com> wrote:
> > The support for filters in flowViz was added after the current bioc
> > release. If you go to the page for the devel version, you'll find a
> > link to a (somewhat terse) vignette with examples:
> >
> > http://bioconductor.org/packages/2.1/bioc/html/flowViz.html
> >
> > To use this (the filter stuff), you either need to run R-devel, or
> > manually install flowViz for R 2.5.x (I don't think there will be any
> > problems if you do that, but I can't guarantee it).
> >
> > -Deepayan
>
> Deepayan,
>
> Thank you for your answer to my question. I feel like I am getting on
> the right track to visualize flow data. When I attempted to install
> flowViz 1.1.4:
>
> > install.packages("flowViz_1.1.4.tar.gz", repos=NULL)
>
> I receive this error (the whole sequence is below):
>
> > Error in importIntoEnv(impenv, impnames, ns, impvars) :
>         object 'ecdfplot' is not exported by 'namespace:latticeExtra'
>
> Do I need to install the dev version of lattice or just go ahead and
> install R-dev? I'm guessing that ecdfplot is not in the current widely
> available version of lattice. I appreciate any advice you might have
> for me.

The dependency is actually a different package called 'latticeExtra'.
Just get the latest version from CRAN.

-Deepayan


> Thanks!
> Matt
>
> > install.packages("flowViz_1.1.4.tar.gz", repos=NULL)
> Warning in install.packages("flowViz_1.1.4.tar.gz", repos = NULL) :
>          argument 'lib' is missing: using '/home/mdj/R/i486-pc-linux-gnu-library
> /2.5'
> * Installing *source* package 'flowViz' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Loading required package: flowCore
> Loading required package: Biobase
> Loading required package: tools
>
> Welcome to Bioconductor
>
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: rrcov
> Scalable Robust Estimators with High Breakdown Point (version 0.3-06)
> KernSmooth 2.22 installed
> Copyright M. P. Wand 1997
> Loading required package: rgl
> Loading required package: geneplotter
> Loading required package: annotate
> Loading required package: lattice
> Loading required package: MASS
> Error in importIntoEnv(impenv, impnames, ns, impvars) :
>         object 'ecdfplot' is not exported by 'namespace:latticeExtra'
> Execution halted
> ERROR: lazy loading failed for package 'flowViz'
> ** Removing '/home/mdj/R/i486-pc-linux-gnu-library/2.5/flowViz'
> ** Restoring previous '/home/mdj/R/i486-pc-linux-gnu-library/2.5/flowViz'
> Warning message:
> installation of package 'flowViz_1.1.4.tar.gz' had non-zero exit status in: inst
> all.packages("flowViz_1.1.4.tar.gz", repos = NULL)
> >
>