[Bioc-devel] OrgDB entry for Homo sapiens and Mus musculus missing in AnnotationHub

[Kern, Lori]

Thank you for letting us know.  We will investigate the issue.



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 Alex Wong <alexchwong.github using gmail.com>
Sent: Saturday, October 12, 2024 7:49 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] OrgDB entry for Homo sapiens and Mus musculus missing in AnnotationHub

Hi there,

It seems that OrgDB entries for human and mouse have recently been removed
from AnnotationHub for Bioc 3.19, then re-entered into Bioc devel. This
database change breaks (my package) SpliceWiz for Bioc 3.19 but continues
to work for Bioc devel.

Reprex: the following returns `TRUE` for Bioc devel but `FALSE` in Bioc
3.19:

'''

library(AnnotationHub)
ah <- AnnotationHub()
ah_orgList <- subset(ah, ah$rdataclass == "OrgDb")
supportedSpecies <- unique(ah_orgList$species)
any(supportedSpecies == "Homo sapiens")

'''

Kind Regards,
Alex Wong

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org mailing list
https://secure-web.cisco.com/1kazDKWent6xiUzkCsbo2cWivkmSkU0bfAdwbrdmS0x3yC7ZimF2wC6vQShICdYqTzXeM2NQLFRtBchIXhXv2aaHGmbYXtDppkiJ-wgqldQDhkkqRf0YHr_jcDJsUZd2loBJaSpkFe3wibjyFFJ-wssR_5440maV8GE32UwGvTwMKQX-ijkPx4pByAPNce_o377e4KdCwm8NMluezgTBTPovf6lcomK0hY3SBIdUPUbWdcdGEG5XOuvKsyrkv3m8qc66Jgor0pmRXpoin9Xpt2EEMSISQyOw2z1NMTUxeVrI8FnzZAJlgyGHnzQjMcq8l/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]]