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
[Bioc-devel] Last minute error in the build
4 messages · Kangeyan, Divy, Shepherd, Lori, Hervé Pagès
The package will have a release version. The branches are frozen now to proceed with the release branching. If the ERROR persists this just means you will have to update your fix on the RELEASE_3_7 branch and the devel (master) branch. There will be an email notification when pushes can resume to the git server. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Kangeyan, Divy <divyswar01 at g.harvard.edu>
Sent: Monday, April 30, 2018 10:16:59 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Last minute error in the build
Sent: Monday, April 30, 2018 10:16:59 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Last minute error in the build
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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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=
Herv? Pag?s 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 Phone: (206) 667-5791 Fax: (206) 667-1319
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, Herv? Pag?s 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=
Herv? Pag?s 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 Phone: (206) 667-5791 Fax: (206) 667-1319