We agreed a deprecation cycle should be implemented.
We are pushing up changes to BiocFileCache, AnnotationHub, and ExperimentHub so
instead of an ERROR and failing out, it will give a warning with deprecation
notice and use the old default cache.
After the next release however, we will
Log into the support site,
Click on your profile,
Click edit your profile,
Add package name to the Watched Tags field
Click submit.
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New
>From a Bioconductor R perspective, we can't tell if the package would work
>with a lesser version of R or lower versions of any package dependencies. We
>accept packages and have requirements to ensure packages can run.
You can always have another github branch
I believe in the past we
R CMD check sometimes wants dependency on specific R versions, for example
when the file format changed (forgot which version .. was it 3.6). But that
warning is emitted when it tests the package utilizes version-specific
stuff.
I get that Bioc doesn't check under older versions. That is
Dear All,
I just committed some changes to my package, but I get this error about
adding package name to watched tags on the support site. How do I fix this?
Regards,
Daniel
* Checking for support site registration...
Maintainer is registered at support site.
* ERROR: Maintainer must
But why is it even a warning? The submission policy is that warnings are
discouraged. This means that developers will adapt to this warning.
The check is also against the policies on the website which state you don't
need a formal dependency.
Best,
Kasper
On Thu, Apr 8, 2021 at 3:53 PM Kern,
> I believe in the past we tried suggesting removing a R dependency altogether
> but that R CMD check complained not having an R dependency? Maybe someone
> remembers more about this.
There are no such requirements in 'R CMD check'. The only requirement
around 'Depends: R (>= x.y.z)', if
On Thu, Apr 8, 2021 at 11:22 AM Kasper Daniel Hansen
wrote:
>
> R CMD check sometimes wants dependency on specific R versions, for example
> when the file format changed (forgot which version .. was it 3.6). But that
> warning is emitted when it tests the package utilizes version-specific
Dear All,
I got this error in the latest build of my package. I think this has to do
with Rgraphviz during the test on MacOS. Do I need to do anything
about this?
Regards,
Daniel
Quitting from lines 36-43 (cyanoFilter.Rmd)
Error: processing vignette 'cyanoFilter.Rmd' failed with diagnostics:
Hi,
Might just be bad luck. The Single Package Builder (SPB) and daily
builds (BBS) run on the same machines and share the same R installation
and libraries. BBS was probably in the process of reinstalling Rgraphviz
at the time the SPB was running 'R CMD build' on your package.
Bump the
Thanks Nitesh! It looks like this worked, now we just need to squash the R CMD
Check issues that arose in the meantime :-)
Much obliged,
Timothy J. Triche, Jr., PhD
Assistant Professor of Bioinformatics, Van Andel Institute
330 Bostwick Avenue NE, Grand Rapids, MI, 49503
(616) 234-5316
The latest BiocCheck (well, it may have been around for a bit) _requires_
the package to have a R >= 4.1 dependency.
That seems new to me. Right now it's a bit irritating, because if you're
submitting a package that works with latest stable release, you are now
prohibited from installing it from
You could also preprend your cat so it outputs something like
INCLUDE_DIR=..
and then use grep and sed to trim it. Of course that can also end up being
brittle.
On Wed, Apr 7, 2021 at 10:48 PM Henrik Bengtsson
wrote:
> Correcting: the env var is R_LIBS_USER and nothing else.
>
> /Henrik
>
>
This requirement has been around for awhile. New package submissions are
checked against the devel version of Bioconductor. At the moment this is R
devel (R 4.1) and Bioconductor packages in devel for 3.13. Given that
Bioconductor releases are closely tied to a R release, and changes in R
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