[Bioc-devel] nebbiolo1 build error in Glimma

[Kern, Lori]

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 using r-project.org> on behalf of Shian Su <su.s using wehi.edu.au>
Sent: Thursday, March 10, 2022 6:59 PM
To: bioc-devel using r-project.org <bioc-devel using 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_-JDbqkUhRRSg6FFO7iL9gCzlTjW1FYRBzNOOG3MuFpU_xfPqN2DogHJyrI7QSMQz06T85Lv27RFCprfTch3viKV1CaWhYUI2SlSFsEvUUdQTOx0ns22Klab6N4MAdg-wKP9nBWABomGKsNljueLVT07lor7Pa7MnUCbjV9vKt-aKZHUkbZP-laI9zrYS_8kETTjHGm9h0EwKs9nRSU3e21rAnui/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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