A 404 ERROR generally has to do with accessing web resources. I looked at your
vignette and it appears that this link
http://baderlab.org/netDx/supporting_data/refGene.hg18.bed
Does not exist. Resources accessed by Bioconductor should be publically
available. If that location is not
Yes what you described is correct and why the ERROR is occurring. So at the
next Bioconductor release (3.12) you will have a RELEASE_3_12 branch that
Bioconductor will created for Bioc 3.12 commits and the master branch will
continue to link to our devel branch.
Cheers,
Lori Shepherd
Forgot to cc the group.
Also, this is the correct link:
http://download.baderlab.org/netDx/supporting_data/refGene.hg18.bed
Hosting it on our end isn't an issue.
S
-- Forwarded message -
From: Shraddha Pai
Date: Fri, Jun 12, 2020 at 10:24 AM
Subject: Re: [Bioc-devel] netDx:
If you git clone the git.bioconductor.org repository for your package in a
different folder location you would be able to see the copy and commits we have
on our server (I understand not very convenient)
There is a delay from commits to updates on the building reports and landing
page. It is
Hi Lori,
Thanks for confirming. Indeed, the new set of netDx build errors on all
operating systems seem to be caused by an inability to fetch the hg18 gene
definitions from biomaRt. I would rather keep the example running (and
package maintenance) simple by just hosting the gene definition file
Thankyou Lori,
Is there a way to get a visual overview of recent commits at
https://git.bioconductor.org/packages/multicrispr? (as in e.g. github)
Asking because I cannot see recent commits (pushed to upstream successfully
yesterday) reflected in build
Owkies, thx!
Aditya
From: Shepherd, Lori
Sent: Freitag, 12. Juni 2020 17:42
To: Bhagwat, Aditya ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a
branch 'RELEASE_3_11' cannot be created from it
If you git clone the git.bioconductor.org
Sorry my mistake.
Looking at the devel branch -- it looks like accessing the ensembl archives is
the issue in biomart. Ensembl/biomart connectivity is known to be spotty. I
believe caching is already implemented in the biomart backend and you could
verify with the maintainer but if not
