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

[Richard Pearson]

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.