[BioC] R2.10 and BioC 2.5 where to report bugs?

Paul Leo p.leo at uq.edu.au
Fri May 29 03:59:14 CEST 2009

HI Herve,
Many thanks, I was missing the tek8.5-dev , as suggested, on recompile
it is all working fine.  Bioconductor was installed as you suggested,
all good. 

I see now from the BioMaRt emails that my first question is answered
too!... this is the problem I had encountered at the time.

Thanks again

Hi Paul,

Paul Leo wrote:
> 2 quick questions
> 1)
> So I recent decided to stick with the subversion R2.10 and to recompile
> weekly and use BioC2.5. (linux-ubuntu) Sometimes, as I guess maybe
> expected, I get errors in various libraries .... Not sure is that is a
> "Good idea" or what others do..
> Dumb question, is there a different mailing list where these errors
> should be reported or are those reported here ...  given they are on the
> development version....
> 2)
> PS I have an irritating problem with tcltk...
> does anyone with ubuntu know if the tcl8.5 and tcl8.5-dev libraries are
> all that should  are required to fix this?
> pleo at BIOINFORM01-ubuntu:/media/Bioinform-D/Research/R.packages
> $ /home/pleo/R_latest/bin/R CMD INSTALL --clean tcltk2_1.0-8.tar.gz 

Note that it's almost always a bad idea to install packages this way.
For Bioconductor packages, we highly recommend you use biocLite() as
explained here:


This method will handle the dependencies for you -- and BioC packages
tend to have a lot! (Note that biocLite() also works for installing CRAN

Otherwise I confirm what Laurent Gatto said before: you need tk-dev on
Ubuntu. After you've installed it, you need to reinstall R (configure + make).
Don't forget to include the recommended packages (I think tcltk is one
of them) before you do 'configure + make'. There is no need to install
tcltk2_1.0-8.tar.gz separately.
When you are done, start R and check capabilities(). Then library(tcltk)...


> * installing to library ‘/home/pleo/R_latest/library’
> * installing *source* package ‘tcltk2’ ...
> ** R
> ** 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 ‘tcltk2’
> * removing ‘/home/pleo/R_latest/library/tcltk2’
> pleo at BIOINFORM01-ubuntu:/media/Bioinform-D/Research/R.packages$ 
> R version 2.10.0 Under development (unstable) (2009-05-24 r48603) 
> x86_64-unknown-linux-gnu 
> locale:
>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
>  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
>  [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8   
>  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> base     
> other attached packages:
> [1] biomaRt_2.1.0   lattice_0.17-25 MASS_7.3-0     
> loaded via a namespace (and not attached):
> [1] grid_2.10.0  RCurl_0.95-1 tools_2.10.0 XML_2.3-0
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