[Bioc-devel] ALLMLL dataset

[Herve Pages]

Wolfgang Huber wrote:
> Hi Ben,
> 
> with
> 
> library("ALLMLL")
> data("MLL.A")
> show(MLL.A)
> sessionInfo()
> 
> I get:
> Error: AffyBatch out-of-date; use 'updateObject(<AffyBatch>)'
> 
> updateObject(MLL.A) works beautifully, but I wonder whether it'd be 
> worth centrally updating the package on
> http://www.bioconductor.org/packages/2.0/data/experiment/html/ALLMLL.html


Hi Ben, Wolfgang,

This can easily be done with the new "svn + build system" pipe:

svn repo
--------
  IMPORTANT: Our Subversion repo for data packages is organized in a different
  way than for software packages. When you check out, you need to retrieve the
  skeletons (no data) of _all_ data-experiement pkgs (should be fast though):

    svn co https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs
    cd pkgs

  Then, if you also want to retrieve the data for your package, you need to
  do (Python required):

    ./add_data.py ALLMLL

  ... this will add a (nested) working copy of the data directory.

  When you commit changes, you have to commit separately changes to the
  data (by being inside ALLMLL/data/) and changes to the skeleton
  (by being inside ALLMLL/). Please refer to pkgs/README.txt for more
  information.

Daily build results are here
----------------------------
  http://bioconductor.org/checkResults/2.0-data-experiment/

The "version bump" feature
--------------------------
  Like for software packages, if your package is already published and you make
  changes to it, the new version will not replace the old version unless you have
  bumped z in the version number x.y.z. DON'T FORGET TO BUMP Z! or the last
  version of your package will not be pushed to:

    http://bioconductor.org/packages/2.0/data/experiment

Let me know if you need help with this...

Best,
H.


> 
> R version 2.5.0 Under development (unstable) (2007-03-18 r40854)
> i686-pc-linux-gnu
> 
> locale:
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
> [7] "methods"   "base"
> 
> other attached packages:
>     ALLMLL      affy    affyio   Biobase  fortunes
>    "1.2.0" "1.13.14"   "1.3.3" "1.13.39"   "1.3-2"
> R version 2.5.0 Under development (unstable) (2007-03-18 r40854)
> i686-pc-linux-gnu
> 
>    Wolfgang
> 
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
> 
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel