Re: [R-pkg-devel] NOTE: Examples with CPU time > 2.5 times elapsed time

2023-12-04 Thread Ben Bolker
Wow. On Mon, Dec 4, 2023, 5:43 PM Ivan Krylov wrote: > Dear Artur, > > You've got a well-written package. There are some parts I wasn't able > to understand (e.g. changing the class of a variable by reference using > SET_CLASS and later changing it back), but there are no obvious places > where

Re: [R-pkg-devel] NOTE: Examples with CPU time > 2.5 times elapsed time

2023-12-04 Thread Ivan Krylov
Dear Artur, You've got a well-written package. There are some parts I wasn't able to understand (e.g. changing the class of a variable by reference using SET_CLASS and later changing it back), but there are no obvious places where a mistake could be hiding. On Fri, 1 Dec 2023 23:43:32 + Artur

Re: [R-pkg-devel] Update timing of machines on CRAN?

2023-12-04 Thread Uwe Ligges
Thanks for your offer to providing us with capable multicore servers and support staff for continuing support of recent Fedora systems. Best, Uwe Ligges On 04.12.2023 18:09, andrew--- via R-package-devel wrote: I do think that its a reasonable ask that the test machines be running operating

Re: [R-pkg-devel] Update timing of machines on CRAN?

2023-12-04 Thread andrew--- via R-package-devel
I do think that its a reasonable ask that the test machines be running operating systems within their vendor support periods. -Andrew Robbins From: R-package-devel on behalf of Josiah Parry Sent: Monday, December 4, 2023 11:34 AM To: Tomas Kalibera Cc: R Packa

Re: [R-pkg-devel] Update timing of machines on CRAN?

2023-12-04 Thread Josiah Parry
Unfortunately, it is often important for us to pay attention to what machines our code is being tested on. I think the point is more or less that we often find ourselves trying to make super small adjustments for machines and builds that are used by a number of users in the single digits. The vast

Re: [R-pkg-devel] Update timing of machines on CRAN?

2023-12-04 Thread Tomas Kalibera
On 12/4/23 15:44, SHIMA Tatsuya wrote: Thanks for your answer. Unlike Windows Server, which has a long support period, Fedora's support period is usually about one year, so it is surprising that the old Fedora continues to be used. And, unlike Windows, Linux uses the distribution standard pa

Re: [R-pkg-devel] Update timing of machines on CRAN?

2023-12-04 Thread SHIMA Tatsuya
Thanks for your answer. Unlike Windows Server, which has a long support period, Fedora's support period is usually about one year, so it is surprising that the old Fedora continues to be used. And, unlike Windows, Linux uses the distribution standard packages for builds, which causes problems

Re: [R-pkg-devel] I'm trying to include phyloseq as a CRAN package dependency and for the life of me I can't figure it out

2023-12-04 Thread Uwe Ligges
On 03.12.2023 21:19, Sharon Bewick wrote: I had this package included in a previous upload and it didn’t cause errors. However, now it is getting flagged as an error. I’ve included biocViews: phyloseq in the DESCRIPTION file, but that did not help. Unfortunately, I cannot make phyloseq a we

Re: [R-pkg-devel] I'm trying to include phyloseq as a CRAN package dependency and for the life of me I can't figure it out

2023-12-04 Thread Martin Morgan
CRAN knows about Bioconductor packages, so add phyloseq to Depends: , Imports:, or Suggests: as appropriate. These CRAN packages seem to Import phyloseq, for instance > db = available.packages(repos = "https://cloud.R-project.org";) > rownames(db)[grepl("phyloseq", db[,"Imports"])] [1] "adaptive

[R-pkg-devel] I'm trying to include phyloseq as a CRAN package dependency and for the life of me I can't figure it out

2023-12-04 Thread Sharon Bewick
I had this package included in a previous upload and it didn’t cause errors. However, now it is getting flagged as an error. I’ve included biocViews: phyloseq in the DESCRIPTION file, but that did not help. Unfortunately, I cannot make phyloseq a weak dependency. It can be installed through Bio

Re: [R-pkg-devel] Example files for functions reading binary files

2023-12-04 Thread Uwe Ligges
On 03.12.2023 16:12, Josiah Parry wrote: Rafael, I believe the issue is that packages cannot include binary *executables.* If you have a binary file (such as a parquet file) in inst/extdata, I do not think that would be a problem. It would be a good idea to ensure that that file is small, tho