[Bioc-devel] Last minute error in the build

Hervé Pagès hpages at fredhutch.org
Mon Apr 30 19:32:53 CEST 2018



I also applied the fix to the new RELEASE_3_7 branch
of HDF5Array.

If you install the latest version of HDF5Array (1.8.0
in the RELEASE_3_7 branch and 1.9.0 in master), that should
clear the error you get when running the code in scmeth
vignette. The build system will pick-up the latest version
of HDF5Array so scmeth should go green again on the build
report tomorrow.


On 04/30/2018 10:21 AM, Hervé Pagès wrote:
> Hi Divy,
> I will take care of this. You don't need to do anything.
> Cheers,
> H.
> 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
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
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