[Bioc-devel] spliceSites Vignette build error

[Dan Tenenbaum]

Are you using R-devel on your computer?

----- Original Message -----
> From: "Wolfgang Kaisers" <Wolfgang.Kaisers at uni-duesseldorf.de>
> To: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Friday, March 4, 2016 12:41:30 AM
> Subject: [Bioc-devel] spliceSites Vignette build error

> Dear All,
> 
> the package check  on bioc-LATEST return an error during the vignette
> build.
> A broken dependency to another package of mine in CRAN seems to be the
> reason.
> 
> 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
> file.
> But the error is not resolved.
> 
> How shall I handle this?
> 
> Thanks
> Wolfgang Kaisers
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - -#
> 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
> spliceSites.r).
> 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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