[BioC] basicplot functionality (flowCore/rflowcyt)

[M. Jankowski]

> 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.

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)
>