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

Patrick Aboyoun paboyoun at fhcrc.org
Tue May 26 00:14:35 CEST 2009

To address your first issue, the choice of (stable) release quality  
vs. (unstable) development quality software depends on circumstance.  
The former tends to be recommended for end users who would like to use  
established portions of the software or need to be able to audit their  
analyses. The latter tends to be recommended for end users who would  
like to use parts of the software that is undergoing active  
development or developers who are working on software components of  
their own for the next release.

In general, you should contact the package maintainer if you find any  
issues with their packages in BioC 2.5 (devel). Just make sure you  
follow the standard reporting procedure: 1) ensure you are using the  
latest version of their package and its dependencies, 2) provide a  
reproducible example, and 3) supply a printout of the sessionInfo().

If you are using the relatively new sequence analysis infrastructure  
(IRanges/Biostrings/BSgenome/ShortRead/etc.) and believe there is an  
issue of debate over what has been implemented and what you consider  
to be best practices, you can post your issue to the Bioc-sig-seq  
mailing list. A number of BioC developers are striving to make  
Bioconductor as prominent in the sequence analyses space as it is in  
the microarray analyses space and the more user feedback we get, the  
stronger our offering can be.


Quoting Paul Leo <p.leo at uq.edu.au>:

> 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
> * 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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