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
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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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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