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
[Bioc-devel] OrgDB entry for Homo sapiens and Mus musculus missing in AnnotationHub
3 messages · Alex Wong, Shepherd, Lori
1 day later
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 at r-project.org> on behalf of Alex Wong <alexchwong.github at gmail.com>
Sent: Saturday, October 12, 2024 7:49 PM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] OrgDB entry for Homo sapiens and Mus musculus missing in AnnotationHub
Sent: Saturday, October 12, 2024 7:49 PM
To: bioc-devel at r-project.org <bioc-devel at 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]]
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We apologize for the disruption. They have been reinstated and should now be available. 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 at r-project.org> on behalf of Alex Wong <alexchwong.github at gmail.com>
Sent: Saturday, October 12, 2024 7:49 PM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] OrgDB entry for Homo sapiens and Mus musculus missing in AnnotationHub
Sent: Saturday, October 12, 2024 7:49 PM
To: bioc-devel at r-project.org <bioc-devel at 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 at 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.