[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 at 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.

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 at 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.

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.Shepherd at RoswellPark.org>
Envoy? : lundi 5 ao?t 2024 14:02
? : Julien Wollbrett <julien.wollbrett at unil.ch>; bioc-devel at r-project.org <bioc-devel at 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-bounces at r-project.org> on behalf of Julien Wollbrett <julien.wollbrett at unil.ch>
Sent: Monday, August 5, 2024 7:45 AM
To: bioc-devel at r-project.org <bioc-devel at 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 at 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.


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.

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.Shepherd at RoswellPark.org>
Envoy? : lundi 5 ao?t 2024 14:02
? : Julien Wollbrett <julien.wollbrett at unil.ch>; bioc-devel at r-project.org <bioc-devel at 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-bounces at r-project.org> on behalf of Julien Wollbrett <julien.wollbrett at unil.ch>
Sent: Monday, August 5, 2024 7:45 AM
To: bioc-devel at r-project.org <bioc-devel at 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 at 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.

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.