[Bioc-devel] Last minute error in the build

Hervé Pagès hpages at fredhutch.org
Mon Apr 30 19:21:06 CEST 2018

Hi Divy,

I will take care of this. You don't need to do anything.


On 04/30/2018 07:16 AM, Kangeyan, Divy wrote:
> Hi,
>      I am the author of *scmeth* package that was submitted during this
> cycle. I know that there will be a new bioconductor release tomorrow. My
> package has been passing all the builds until April 27th which is past
> April 25th, the deadline to pass R CMD check and R CMD build. Now I see
> errors in the nightly builds which probably happened over the weekend.
> Following is the error:
> Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
> HDF5Matrix object uses internal representation from DelayedArray
>    >= 0.5.11 and < 0.5.24 and cannot be displayed or used. Please update it with:
>        object <- updateObject(object, verbose=TRUE)
>    and re-serialize it.
> Execution halted
> The error looks like it is related to a deprecated object in my vignette. I
> am not sure whether this is something that I have to update in the new
> development version or something that I can resolve now. Considering the
> new release is tomorrow and all the builds passed beyond the deadline I am
> wondering whether the package will have a release version?
> Thank you,
> Divy
> 	[[alternative HTML version deleted]]
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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