Hello Lori,
Thanks for the quick reply.
The last build worked for the development version on nebbiolo2. It still failed
on nebbiolo1.
Should I bump the version to force the build or is there still an issue with
the resource causing the error?
Julien Wollbrett
________________________________
De : Kern, Lori <lori.sheph...@roswellpark.org>
Envoy� : lundi 5 ao�t 2024 14:02
� : Julien Wollbrett <julien.wollbr...@unil.ch>; bioc-devel@r-project.org
<bioc-devel@r-project.org>
Objet : Re: Build error in nebbiolo1 for package BgeeCall
I redownloaded the resource that was causing the error
ah_resources[["AH50453"]]
It should resolve on the next build.
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-boun...@r-project.org> on behalf of Julien
Wollbrett <julien.wollbr...@unil.ch>
Sent: Monday, August 5, 2024 7:45 AM
To: bioc-devel@r-project.org <bioc-devel@r-project.org>
Subject: [Bioc-devel] Build error in nebbiolo1 for package BgeeCall
Hello,
I am the maintainer of the BgeeCall package. There is an issue in the build of
the package on nebbiolo1 since at least the last Bioconductor release.
The error comes from the vignette when I try to load data from the
AnnotationHub package. I am not able to reproduce the error locally. Do you
have any idea what the problem could be?
block of code that produce the error:
library(AnnotationHub)
library(rtracklayer)
ah <- AnnotationHub()
ah_resources <- query(ah, c("Ensembl", "Caenorhabditis elegans", "84"))
annotation_object <- ah_resources[["AH50789"]]
# remove MtDNA not tag as C. elegans genome
annotation_object <- dropSeqlevels(annotation_object, "MtDNA", "coarse")
transcriptome_object <- import.2bit(ah_resources[["AH50453"]])
The error message is :
Quitting from lines 94-102 [unnamed-chunk-4] (bgeecall-manual.Rmd)
Error: processing vignette 'bgeecall-manual.Rmd' failed with diagnostics:
UCSC library operation failed
Best Regards,
Julien Wollbrett
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://secure-web.cisco.com/1gpDzGj1QyNtCP15WFNBS3geGyv5HTrFBSrrc9amDbtkPW7P8e6fFrK-cLxtbU1JNmrlJ0maGYuO3DVBeshxscACZqjU85GSfNMGvojl5qRtCMqg2ks6Q08TQHl6YpSYI3ltg8srvY2o2d4BdbOxKXh8woQMHRKeQ9WXoLQxkC-MymwIqRk6-4HAr4vtgx1Rs5XrjP1qTgi7uYj1hCG4mHUi5VDohqDpDR0wX_Koo2smHWg-Gk7FTylL8ySTqqir7HTtCZzVB6auSUACYIC_CM_UiRyeP7pehCevgNjwLCS1ZMgSEGVa5qh8DCRSMo5Bt/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
This email message may contain legally privileged and/or confidential
information. If you are not the intended recipient(s), or the employee or agent
responsible for the delivery of this message to the intended recipient(s), you
are hereby notified that any disclosure, copying, distribution, or use of this
email message is prohibited. If you have received this message in error, please
notify the sender immediately by e-mail and delete this email message from your
computer. Thank you.
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
