[Bioc-devel] Change to Biobase release branch causing package failure?

[Martin Morgan]

Hi Richard --

First, let me apologize for not announcing the change I made to the
release branch of Biobase.

The change (on July 10) was in response to a user bug report.

  https://stat.ethz.ch/pipermail/bioconductor/2007-July/018189.html

I was faced with the dilemma of allowing Biobase to continue to
produce data objects that were not as intended, or correcting the
problem at the risk of breaking other packages.

We will work to keep changes to the release branch to a minimum, and
to diligently report these changes to bioc-devel in the future.

Please let me know (off-list) if you would like something more formal
to include with your challenge.

Best,

Martin

Richard Pearson <richard.pearson at postgrad.manchester.ac.uk> writes:

> Hi
>
> I think a recent change to Biobase has caused my package (puma) to fail 
> to build in the release branch when previously it was fine. Could 
> someone confirm that this could indeed be the case? I want to be sure of 
> this because I have recently had a paper rejected and the first reason 
> given was that the reviewers found that they could not get the package 
> to work. I think I have now fixed the problem but I would like to 
> challenge the rejection decision saying it was due to something which 
> was beyond my control.
>
> I believe the change that caused this was committed with the following 
> message on svn:
>
>       Harmonize dimnames of ExpressionSet assayData elements, if
>       possible
>    
>       * 'harmonize' means to ensure that all dimnames are
>       consistent with names from phenoData, featureData
>    
>       * Only possible if elements differ with NULL dimnames, not
>       if elements have different dimnames; in this case, signal an
>       error about conflicting dimnames
>
> I had an example which created an ExpressionSet which had different 
> column names for different assayData elements, which previously caused 
> no problems.
>
> This leads me to wonder whether the second "rule" for updating the 
> release branch (http://wiki.fhcrc.org/bioc/HowTo/Update_Release_Branch) 
> needs to be tightened to include something like:
>
> 2. It is very important not to change the signature of any functions, 
> not to add or remove functions, /and not to change functions such that 
> new errors might be given by the function/.
>
> Best regards
>
> Richard.
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org