[Bioc-devel] spliceSites Vignette build error

Wolfgang Kaisers Wolfgang.Kaisers at uni-duesseldorf.de
Fri Mar 4 09:41:30 CET 2016

Dear All,

the package check  on bioc-LATEST return an error during the vignette 
A broken dependency to another package of mine in CRAN seems to be the 

The check using the last version available on CRAN is OK on my computer 
and I added a dependency "refGenome (>= 1.5.8)" into the DESCRIPTION 
But the error is not resolved.

How shall I handle this?

Wolfgang Kaisers

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The error in detail:
The build error message arises from the vignette 'spliceSites.Rnw':
Error: processing vignette 'spliceSites.Rnw' failed with diagnostics:
  chunk 34
Error in as.data.frame(y) :
   trying to get slot "ev" from an object (class "data.frame") that is 
not an S4 object

The error is thrown by the function 'uniqueJuncAnn' (in line 294 chunk 
34 spliceSites.Rnw).
Inside uniqueJuncAnn, there are two data.frames merged (in line 3386 of 
The right-hand object (uj at ev$gtf) refers to a 'refJunctions' object 
which is defined
in my CRAN package refGenome.

I recently changed the type of this object (which is present on CRAN 
since July 2015).

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