[Bioc-devel] Last minute error in the build

[Hervé Pagès]

Done:

 
https://github.com/Bioconductor/HDF5Array/commit/c525570bc927274c37d9f267a2cf194d8e545d91

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.

H.

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]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=RBt9k3A-vxuVohDsl55aCS2e531MTyn_iu2qGRh2-qI&s=OO19dRaLUk9SvbPL7BTpB_uWkqIJk-_78VSX_p_SznQ&e= 
>>
>>
> 

-- 
Hervé Pagès

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