Hello,
Gviz hasn't been updated for the past two months but has a CHECK warning and
there are almost no answered questions on the support website in the past three
months. Is it worthwhile developing plotting functions based on Gviz if it is
likely to become defunct next year?
And why exactly is it becoming defunct? That is the first time I hear that it
will be. The warning message is:
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'GenomeAxisTrack,ANY,ANY,ANY'
All user-level objects in a package (including S
On 10/20/2017 03:00 AM, Dario Strbenac wrote:
Hello,
Gviz hasn't been updated for the past two months but has a CHECK warning and
there are almost no answered questions on the support website in the past three
months. Is it worthwhile developing plotting functions based on Gviz if it is
likel
Dear all,
I am the clipper package maintainer.
According to the "Build/check report" for BioC 3.6,
the clipper package has an error while compiling the vignette.
I try to reproduce the error in my computer using the devel version but the
R CMD check and installation goes smoothly.
Anyone has sug
On 10/20/2017 03:43 AM, Paolo Martini wrote:
Dear all,
I am the clipper package maintainer.
According to the "Build/check report" for BioC 3.6,
the clipper package has an error while compiling the vignette.
I try to reproduce the error in my computer using the devel version but the
R CMD check
Thanks a lot.
Yesterday I was unable to get the error because the graphite I downloaded
was not the latest version (it had a build failure).
I'll fix clipper asap.
Thanks again.
Paolo
2017-10-20 10:12 GMT+02:00 Martin Morgan :
> On 10/20/2017 03:43 AM, Paolo Martini wrote:
>
>> Dear all,
>>
>>
Dear developers,
We have requested a maintainer change for the MAIT package.
This has been approved by the Bioconductor team and the new maintainer
has completed the git form using his public ssh key.
However, he does not possess the permissions to clone or push the
repository, probably bec
The key and the permissions have changed and the userid Sola-Santos should have
access with the key that was submitted with that user name.
If there are still permission issues please send the command being used with
output.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Hello,
may I ask a question about the R version dependence?
Currently I am trying to submit a package to Bioconductor repository. When
my package was built at bioconductor.org, I got a warning message
"* WARNING: Update R version dependency from 2.3.0 to 3.4."
So I changed the R dependency to 3
We strongly recommend the version of R that is used on our builders when
building and checking your package. This is also to ensure that the package
dependencies are also in a version that is compatible with a new package. We
can't guarantee that a package will work with a previous version of
I've submitted a package for the next release and just pushed an update
with a version bump, but a rebuild doesn't seem to be triggered. I set up a
webhook as explained in
https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md,
but I see from my repo's Settings tab that there was
What is the name of your package?
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Bioc-devel on behalf of Leslie Myint
Sent: Friday, Octobe
Hi Paolo,
FYI 3 days ago I contacted Gabriele Sale (maintainer of graphite
and co-author of clipper) about this. See below.
Cheers,
H.
---
Hi Gabriele,
A recent update to the graphite package introduced the following
change:
l
Hi,
On 10/19/2017 05:50 PM, Ryan Thompson wrote:
Hi Chunlei,
One thing you could do to make the interface more traditional is to have a
global "query" function that takes a client object as an additional
argument.
Usage would be something like:
gene_client <- BioThingsClient("gene")
query("CD
We restarted our server. Could You please try one more time to push a version
bump for package?
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
Fro
I want to raise a question about this from the perspective of intersystems
interfacing. You can use reticulate to import your python into R, once you
have installed the python library for biothings_client
library(reticulate)
bt = import("biothings_client")
mv = bt$get_client("variant")
myv = m
On Thu, Oct 19, 2017 at 9:23 PM, Chunlei Wu wrote:
> Thank you all for the feedback. Just to give some extra context, here we
> have the Python and Javascript versions of the biothings_client:
>
>
> https://github.com/biothings/biothings_client.py
>
> https://github.com/biothings/biothings_client
As long as the logic has been pushed down into the server, the R interface
should be lightweight, and there's no need to introduce a dependency on
python.
On Fri, Oct 20, 2017 at 9:27 AM, Vincent Carey
wrote:
> I want to raise a question about this from the perspective of intersystems
> interfac
As the developer of all these three biothings_clients, we, of course, like to
keep the same pattern for R, and R6 looks the closest to me. But it looks like,
from R users' perspective, this is not a popular pattern to use
Yes, there will probably be way more users of R wanting to use BioThings
It was the mpra package. I just bumped and pushed, and I did get a rebuild
triggered.
Thanks so much!
On Fri, Oct 20, 2017 at 12:17 PM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:
> We restarted our server. Could You please try one more time to push a
> version bump for package?
>
>
>
Hello,
I noticed that October 24 is "Deadline for packages passing ‘‘R CMD build’’ and
‘‘R CMD check’’ without errors or warnings." and "Identify packages to be
‘deprecated’ in the new devel, Bioconductor 3.7." and "... or those with errors
and unresponsive maintainers." If the Release Schedule
On 10/20/2017 07:00 PM, Dario Strbenac wrote:
Hello,
I noticed that October 24 is "Deadline for packages passing ‘‘R CMD build’’ and ‘‘R CMD check’’ without
errors or warnings." and "Identify packages to be ‘deprecated’ in the new devel, Bioconductor
3.7." and "... or those with errors and unr
Good day,
Thanks for the clarification. I appreciate your regular insights on the support
forum over the years. It seems that Gviz will be stable enough to use, although
the same maintainer's domainsignatures package has strikethrough across its
name in the 3.6 build report, indicating its depr
On 10/20/2017 09:00 PM, Dario Strbenac wrote:
Good day,
Thanks for the clarification. I appreciate your regular insights on the support
forum over the years. It seems that Gviz will be stable enough to use, although
the same maintainer's domainsignatures package has strikethrough across its
n
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