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
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
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
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:
Is there a way to mark a ticket as a potential regression in the bug
tracker? I think the following issue is a regression:
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17684
I've just tested (2020-06-12 r78687) and what I believe to be a
regression is still there. I don't think the bug
Thanks everyone for getting a solution.
Brian's solution works for me too.
Thanks again!!
Wayne
-Original Message-
From: Prof Brian Ripley
Date: Friday, June 12, 2020 at 3:00 AM
To: "Fox, John" , Simon Urbanek
Cc: Wayne Oldford , "r-devel@r-project.org"
Subject: Re: [Rd] tcltk
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
Ah, thanks, Brian, so the issue is that Catalina is now embedding Exif tags
while previous versions didn’t. Tcltk never supported them, but it only came up
now as Catalina is generating them. I’ll check if tcltk has ever fixed it.
Sent from my iPhone
> On 12 Jun 2020, at 19:00, Prof Brian
On 12/06/2020 03:49, Fox, John wrote:
Dear Simon,
On Jun 11, 2020, at 9:00 PM, Simon Urbanek wrote:
Wayne,
that one is unrelated, but interesting - you can fix it with
sudo install_name_tool -change \
/usr/local/lib:/opt/X11/lib/libtk8.6.dylib \
/usr/local/lib/libtk8.6.dylib \
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