And of course: the whole trick I described below only makes sense
if MTseeker doesn't rely on gmapR for its core functionality, that
is, if not having gmapR installed still allows the user to accomplish
something meaningful with MTseeker.
Otherwise the trick below will make MTseeker available on
Hi Tim,
No platform-specific dontrun capabilities AFAIK but you can use
something like:
if (requireNamespace("gmapR", quietly=TRUE)) {
...
...
}
in your man pages.
You would also need to move gmapR from Imports to Suggests.
Then make sure that MTseeker passes 'R CMD check' **w
Hi Elizabeth,
I agree that the setClassUnion() warning is rather esoteric, especially
the "consider setClassUnion()" part.
library(DelayedArray)
setClassUnion("matrixOrHDF5", c("matrix", "DelayedArray"))
# Warning message:
# subclass "DelayedArray1" of class "DelayedArray" is not local a
This underscores how setClassUnion() can lead to unintended consequences.
Inheritance is an extreme form of coupling, and subclasses are expected to
obey the contract specified by the super class. By defining a class union,
the developer is essentially inventing a contract without any commitment of
Hi,
Thanks for the quick and helpful comments! As suggested, I used the the
following code
\code{\link[BiocParallel:BiocParallelParam-class]{BiocParallelParam}}
And it worked perfectly and all warnings are gone now! But im still puzzled why
it only gave a warning on windows and not on linux.
There is .BBSoptions, which can be placed in the root of your package,
but this is insidious, as evidenced by your own use case -- gmapR
doesn't support windows, so your package doesn't support windows, so any
package that Depends: or Imports: your package doesn't support windows,
so actually 1
Just to emphasize that the 'right' solution from the Bioc perspective is
to make sure that the vignette is evaluated
https://stackoverflow.com/a/44094582/547331
rather than to add a pdf to inst/doc -- no sense in providing the user
with a 'picture of code' when there are no guarantees that t
I think pull requests on
https://github.com/Bioconductor/bioconductor.org/blob/master/content/developers/package-submission.md
would be welcome.
Martin
On 10/10/18 11:51 AM, Ludwig Geistlinger wrote:
While this might be obvious to most of us, it seems to be less clear to others.
In particul
Hi --
I recently diagnosed a WARNING that kept popping up in my package's build
by following the advice of: https://stackoverflow.com/a/42673584/3878253
Since I wasn't the only one who benefited from this answer, I thought I'd
share with the broader Bioconductor community my experience with it (t
On Wed, Oct 10, 2018 at 3:25 PM Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:
> As far as Levi’s comment about PEP8. It’s possible to design something
> similar with Jim Hester’s “lintr” package, which purely defines a style
> guide for code.
>
> https://github.com/jimhester/lintr
As I
Hi,
It looks like vignette in TCGAWorkflow hasn't changed except for updating to
use BiocManager. This often points to a breaking change in an upstream
dependency (244 in your case) or it could be a problem on the builder.
The code chunk causing problems in devel is the call to ELMER::get.TFs()
As far as Levi’s comment about PEP8. It’s possible to design something similar
with Jim Hester’s “lintr” package, which purely defines a style guide for code.
https://github.com/jimhester/lintr
> On Oct 10, 2018, at 3:16 PM, Levi Waldron wrote:
>
> A related comment came up in a conversation
A related comment came up in a conversation I recently had with a potential
Bioconductor developer I met recently, who commented that even as an
experienced Python or CRAN developer, it is difficult to orient oneself to
the Bioconductor "style" and infrastructure for developers. He gave the
example
Hello,
I am using `setClassUnion` in my package `clusterExperiment` in the following
code to allow for either matrix or DelayedArray:
setClassUnion("matrixOrHDF5",members=c("matrix", "DelayedArray"))
This causes the following warning in checking my package:
Warning: subclass "DelayedArray1" of
While this might be obvious to most of us, it seems to be less clear to others.
In particular, those who worked out their first package and wonder what's the
difference between having a package available on Github, CRAN, or Bioconductor.
I wonder whether it would be helpful for the Bioc webpage
it looks like gmapR does not support Windows, and as a result, my MTseeker
package cannot build on tokay1, so the Data package which requires it also
cannot build on tokay1. Are there platform-specific dontrun capabilities?
http://bioconductor.org/spb_reports/MTseekerData_buildreport_201810101032
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