[BioC] R2.10 and BioC 2.5 where to report bugs?
hpages at fhcrc.org
Fri May 29 02:44:28 CEST 2009
Paul Leo wrote:
> 2 quick questions
> 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....
> 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
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
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)
>  LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
>  LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
>  LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8
>  LC_PAPER=en_AU.UTF-8 LC_NAME=C
>  LC_ADDRESS=C LC_TELEPHONE=C
>  LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
>  stats graphics grDevices utils datasets methods
> other attached packages:
>  biomaRt_2.1.0 lattice_0.17-25 MASS_7.3-0
> loaded via a namespace (and not attached):
>  grid_2.10.0 RCurl_0.95-1 tools_2.10.0 XML_2.3-0
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