[Bioc-devel] ALLMLL dataset

Herve Pages hpages at fhcrc.org
Mon Mar 19 23:44:39 CET 2007

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 Error: AffyBatch out-of-date; use 'updateObject(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

Daily build results are here

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:


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


> R version 2.5.0 Under development (unstable) (2007-03-18 r40854)
> i686-pc-linux-gnu
> locale:
> 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

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