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[Bioc-devel] NanoporeRNASeq not found in the devel Bioc3.12 package list

4 messages · CHEN Ying, Martin Morgan, Shepherd, Lori

Original
CHEN Ying
# 
Hello,

I received an email saying our package bambu built in Bioc3.12 produce errors, which I found was due to the dependent ExperimentData package NanoporeRNASeq was not built in the Bioc3.12 package list. However, when I check the Bioc3.13 package list, both bambu and NanoporeRNASeq were built successfully.

I was wondering will NanoporeRNASeq still be included in the Bioc3.12 version? If so, when will the status be reflected on Bioc3.12 package list?

Thank you
Regards
CHEN Ying
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Martin Morgan
# 
I believe that NanoporeNSeq was added to the experiment data build 'manifest' after the most recent build (on Mondays and Thursdays) started, so it will not be available until Monday experiment data package builds are complete, and bambu has been built with those packages available -- I think this will be on the build report available Tuesday afternoon, US Eastern time zone.

Martin

?On 10/23/20, 11:37 PM, "Bioc-devel on behalf of CHEN Ying" <bioc-devel-bounces at r-project.org on behalf of chen_ying at gis.a-star.edu.sg> wrote:

    Hello,

    I received an email saying our package bambu built in Bioc3.12 produce errors, which I found was due to the dependent ExperimentData package NanoporeRNASeq was not built in the Bioc3.12 package list. However, when I check the Bioc3.13 package list, both bambu and NanoporeRNASeq were built successfully.

    I was wondering will NanoporeRNASeq still be included in the Bioc3.12 version? If so, when will the status be reflected on Bioc3.12 package list?

    Thank you
    Regards
    CHEN Ying
    This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person.


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2 days later
CHEN Ying
# 
Hi Martin,

Thanks for answering my queries. Sorry about this, but there seems to have another issue related to NanoporeRNASeq package now, where on Windows, there is an error saying "database is locked" when trying to load data from ExperimentHub in building the vignette. I am not sure what I am supposed to do.

Please advise on the matter.

Thank you
Regards,
CHEN Ying
Shepherd, Lori
# 
We are looking into the issue.  This happens with a numer of packages and we think it has to do with multiple resources trying to access without an official locking mechanism in place.  I'm investigating the Hubs issue and hope to have it resolved soon.  There is nothing more you need to do on your end.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263