Re: [Bioc-devel] how can I declare that a package doesn't/can't fully support Windows

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

Re: [Bioc-devel] how can I declare that a package doesn't/can't fully support Windows

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'

Re: [Bioc-devel] Problem with setClassUnion and DelayedArray

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

Re: [Bioc-devel] Problem with setClassUnion and DelayedArray

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

Re: [Bioc-devel] Roxygen documentation under windows

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.

Re: [Bioc-devel] how can I declare that a package doesn't/can't fully support Windows

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

Re: [Bioc-devel] Files in the 'vignettes' directory but no files in 'inst/doc'

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

Re: [Bioc-devel] Why bioconductor?

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

[Bioc-devel] Files in the 'vignettes' directory but no files in 'inst/doc'

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

Re: [Bioc-devel] Why bioconductor?

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

Re: [Bioc-devel] Invalid Parameter - /figure-html

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

Re: [Bioc-devel] Why bioconductor?

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

Re: [Bioc-devel] Why bioconductor?

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

[Bioc-devel] Problem with setClassUnion and DelayedArray

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"

Re: [Rd] unlockEnvironment()?

On Wed, 10 Oct 2018, William Dunlap via R-devel wrote: > R lets one lock an environment with both an R function, > base::lockEnvironment, and a C function, R_LockEnvironment, but, as far as > I can tell, no corresponding function to unlock an environment. Is this > omission on principle or just

[Rd] unlockEnvironment()?

R lets one lock an environment with both an R function, base::lockEnvironment, and a C function, R_LockEnvironment, but, as far as I can tell, no corresponding function to unlock an environment. Is this omission on principle or just something that has not been done yet? I ask because several

[Bioc-devel] Why bioconductor?

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

[Bioc-devel] how can I declare that a package doesn't/can't fully support Windows

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?

Re: [Rd] R_ext/Altrep.h should be more C++-friendly

Thank you, I updated my example package so that it works with both. https://github.com/romainfrancois/altrepisode/blob/96af0548a9ecc08701d119ea427e16940a82882b/src/altrepisode.h We

Re: [Rd] R_ext/Altrep.h should be more C++-friendly

Thanks for the suggestion. Committed in R_devel. Best, luke On Mon, 8 Oct 2018, Michael Sannella wrote: > I am not able to #include "R_ext/Altrep.h" from a C++ file.  I think > it needs two changes: > > 1. add the same __cplusplus check as most of the other header files: >     #ifdef