[BioC] flow Installation Problems

[Florian Hahne]

Hi John,
it seems that you are having a general problem with your TclTk 
installation on your system. The issue is really the installation of 
rpanel, which relies on TclTk to be present. rpanel is a dependencies of 
the feature package, which again is a dependency of flowCore. So in a 
way the problem is passed down all the way from there. You should 
install both tcl and tk (on a Debian system try sudo apt-get install tcl 
tk), recompile R and run biocLite again.
Hope that fixes the issue. TclTk is used by many R packages and you 
might run in a lot of problems without it.
Florian



John Campbell wrote:
> I am having trouble installing the flowCore package, because of  issues with
> the "rpanel" and "feature" packages, maybe related to TclTk support. Below
> is my sessionInfo information and more details from the flowCore
> installation log. I just downloaded R 2.9.0 on April 22, 2009 and installed
> BioConductor using:
>
>
> source("http://bioconductor.org/biocLite.R")
> biocLite()
> biocLite("flowCore")
>
>   
>> sessionInfo()
>>     
> R version 2.9.0 (2009-04-17)
> i686-pc-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.9.0
>
>
> Errors with flowCore installation
> ===============================
> source("http://bioconductor.org/biocLite.R")
> biocLite("flowCore")
>
>
> 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: robustbase
> Loading required package: pcaPP
> Loading required package: mvtnorm
> pcaPP 0.1-1 loaded
> Scalable Robust Estimators with High Breakdown Point (version 0.5-01)
> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
>   there is no package called 'feature'
> ERROR: lazy loading failed for package ‘flowCore’
> * Removing ‘/home/jcampbell/programs/R/lib/R/library/flowCore’
>
> The downloaded packages are in
>         ‘/tmp/RtmpWDdduP/downloaded_packages’
> Updating HTML index of packages in '.Library'
> Warning messages:
> 1: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   installation of package 'rpanel' had non-zero exit status
> 2: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   installation of package 'feature' had non-zero exit status
> 3: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   installation of package 'flowCore' had non-zero exit status
>
> * Installing *source* package ‘rpanel’ ...
> ** R
> ** data
> ** demo
> ** inst
> ** preparing package for lazy loading
> Error in firstlib(which.lib.loc, package) :
>   Tcl/Tk support is not available on this system
> Error : package 'tcltk' could not be loaded
> ERROR: lazy loading failed for package ‘rpanel’
> * Removing ‘/home/jcampbell/programs/R/lib/R/library/rpanel’
> * Installing *source* package ‘feature’ ...
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> KernSmooth 2.22 installed
> Copyright M. P. Wand 1997
> Warning in library(pkg, character.only = TRUE, logical.return = TRUE,
> lib.loc = lib.loc) :
>   there is no package called 'rpanel'
> Error : package 'rpanel' could not be loaded
> ERROR: lazy loading failed for package ‘feature’
> * Removing ‘/home/jcampbell/programs/R/lib/R/library/feature’
>
> Thank you,
> John Campbell
>
> 	[[alternative HTML version deleted]]
>
>   
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-- 
Florian Hahne, PhD
Computational Biology Program
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
PO Box 19024
Seattle, Washington 98109-1024
206-667-3148
fhahne at fhcrc.org