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List: bioc-devel
Subject: Re: [Bioc-devel] nebbiolo1 build error in Glimma
From: "Kern, Lori" <Lori.Shepherd () RoswellPark ! org>
Date: 2022-03-11 15:14:08
Message-ID: BL1PR12MB53017D1C0B9DD69301F928F2F90C9 () BL1PR12MB5301 ! namprd12 ! prod ! outlook ! com
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There was reported issues with the caching of the ZeiselBrainData. I have reset the \
cache and hopefully this should clear up over the weekend. If it does not we can \
further investigate on our end but I do not think there is anything you need to do at \
this time.
Cheers,
Lori Shepherd - Kern
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-bounces@r-project.org> on behalf of Shian Su \
<su.s@wehi.edu.au>
Sent: Thursday, March 10, 2022 6:59 PM
To: bioc-devel@r-project.org <bioc-devel@r-project.org>
Subject: [Bioc-devel] nebbiolo1 build error in Glimma
Hi all,
I’m trying to figure out why my package is failing to build on nebbiolo1 (Ubuntu \
20.04).
https://secure-web.cisco.com/19fh39OLbcA_qQ7Chvyt1bDyRmg1ntpwrey4SrccHwr-MDLK7rrYKrfH- \
g8L9Am3u-23Se7kNcbwnZBFkhqBy9FBI8pD4qBhVov0n_-JDbqkUhRRSg6FFO7iL9gCzlTjW1FYRBzNOOG3MuF \
pU_xfPqN2DogHJyrI7QSMQz06T85Lv27RFCprfTch3viKV1CaWhYUI2SlSFsEvUUdQTOx0ns22Klab6N4MAdg- \
wKP9nBWABomGKsNljueLVT07lor7Pa7MnUCbjV9vKt-aKZHUkbZP-laI9zrYS_8kETTjHGm9h0EwKs9nRSU3e2 \
1rAnui/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.15%2Fbioc-LATEST%2FGlimma%2Fnebbiolo1-buildsrc.html
I believe it spontaneously failed last November without any changes from me, so I had \
hoped it would go away on its own. The package has no problem building on the Mac and \
Windows servers, on my personal Mac, Windows and Ubuntu machines, and on the \
Bioconductor docker image. The offending lines appear to be
library(scRNAseq)
sce <- ZeiselBrainData(ensembl=TRUE)
Error: processing vignette 'single_cell_edger.Rmd' failed with diagnostics:
undefined columns selected
The only thing I can think of is that somehow ExperimentHub is behaving differently \
on that particular build server? Any help is appreciated.
Kind regards,
Shian Su
----
Shian Su
PhD Student, Ritchie Lab 6W, Epigenetics and Development
Walter & Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville VIC 3052, Australia
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Walter and Eliza Hall Institute of Medical Research
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