Thanks Martin,
I have dropped the @ call.
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
*From: *Martin Morgan
*Sent: *Wednesday, 10 March 2021 11:36 AM
*To: *stefano ;
I see, so it seems to be an issue of build failures of packages and not of
docker itself.
Thanks again for the help!
Best,
Reto
‐‐‐ Original Message ‐‐‐
On Tuesday, March 9, 2021 6:18 PM, Vincent Carey
wrote:
> note that diffcyt does not currently build at
>
It looks like you're assigning to assays, `assays(x) <- ...`, so you need to
import `assays<-`, and not just `assays`.
But this
assays(new_obj)@listData <-
looks VERY BAD. The internal structure of the assays slot (accessed with @)
should NEVER be accessed directly; use the public 'API'
Hello,
I have a trouble for tidySummarizedExperiment package BiocCheck()
This is BiocCheck version 1.26.0. BiocCheck is a work in progress.
Output and severity
of issues may change. Installing package...* Checking Package
Dependencies...* Checking if other packages can import this one...
*
Hi Robert, Kozo,
Thank you both for your responses!
I’ve now set up a testable tryCatch for my Cytoscape-using function that
returns NULL on connection fail error, rather than stopping the function
completely.
Catherine
> On Mar 6, 2021, at 1:12 PM, Kozo Nishida wrote:
>
> EXTERNAL EMAIL:
I am setting up a repo/docker for the coming Bioc2021 workshops, and apparently
packages ‘GenomeInfoDb’, ‘MultiAssayExperiment’ are not available for this
version of R [1] (they indeed fail on devel). Surprisingly, they seemed to be
available earlier in the day - my action failed for a
note that diffcyt does not currently build at
https://bioconductor.org/checkResults/3.13/bioc-LATEST/ -- its errors need
to be
repaired for your build to succeed
On Tue, Mar 9, 2021 at 11:07 AM Reto Gerber via Bioc-devel <
bioc-devel@r-project.org> wrote:
> Dear all,
>
> I would like to
This deadline is extended by one week, until March 16. Submit a talk,
digital poster, Birds-of-a-feather session, or a syllabus for a software
demo or long workshop at BioC2021 on Aug 4-6! We can confirm that the
conference will be virtual. https://bioc2021.bioconductor.org/submissions/.
On Thu,
Hi,
There are a few things here,
1. You don't have to install BiocManager again, it's pre-installed in the
docker image we provide 'bioconductor_docker'.
2. You also don't need to use install2.r script, just list all the packages you
need in the BiocManager::install command.
3. I don't
Dear all,
I would like to reproduce a build error (on Bioc devel) using docker. The issue
is that the docker image fails to build. I use the following Dockerfile:
> FROM bioconductor/bioconductor_docker:devel
> RUN install2.r --error broom.mixed\
> BiocManager \
> devtools \
> dirmult\
>
Thanks Mike, for getting to this.
Best,
Nitesh
On 3/9/21, 10:35 AM, "Bioc-devel on behalf of Murphy, Alan E"
wrote:
Hey Mike,
Thank you very much for the suggestion, this worked perfectly. I'll
definitely be stealing this code for future reference.
Kind regards,
Alan.
Hey Mike,
Thank you very much for the suggestion, this worked perfectly. I'll definitely
be stealing this code for future reference.
Kind regards,
Alan.
From: Mike Smith
Sent: 09 March 2021 11:14
To: Murphy, Alan E
Cc: bioc-devel@r-project.org
Subject: Re:
I've used something like this approach in the past. All the normal caveats
about making sure you've got a backup apply.
Find the names of largest objects in the pack file (not necessarily in size
order). In this case they're almost all .rda files.
git rev-list --objects --all | grep -f <(git
Hi both,
Thank you for your suggestions. Yes, I am still having problems with the size
of my git history in the EWCE package. To clarify, I have already tried the BFG
cleaner to no avail even when I set the max limit to 1 MB (see my first email
for details).
The issue is that a
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