Re: [R-pkg-devel] suggestion: conda for third-party software

2020-01-07 Thread Ivan Krylov
On Tue, 7 Jan 2020 15:49:45 +0100 Serguei Sokol wrote: > Currently, many R packages include TPS as part of them thus bloating > their sizes and often duplicating files on a given system.  And even > when TPS is not included in an R package but is just installed on a > system, it is not so

Re: [R-pkg-devel] suggestion: conda for third-party software

2020-01-07 Thread Sokol Serguei
Thanks for this hint. Le 07/01/2020 à 20:47, Kevin Ushey a écrit : The newest version of reticulate does something very similar: R packages can declare their Python package dependencies in the Config/reticulate field of a DESCRIPTION file, and reticulate can read and use those dependencies to

Re: [R-pkg-devel] rhub, docker and Bioconductor

2020-01-07 Thread Ivan Krylov
On Tue, 7 Jan 2020 13:54:38 + Christian Martin Hennig wrote: > Are there any other options apart from rhub/docker to get wiser about > my errors and issues (error on debian-clang in a routine that shows > nothing suspicious on my machine I cannot answer your original questions, but I can

Re: [R-pkg-devel] suggestion: conda for third-party software

2020-01-07 Thread Kevin Ushey
The newest version of reticulate does something very similar: R packages can declare their Python package dependencies in the Config/reticulate field of a DESCRIPTION file, and reticulate can read and use those dependencies to provision a Python environment for the user when requested (currently

Re: [R-pkg-devel] rhub, docker and Bioconductor

2020-01-07 Thread brian knaus
I was tracking down problems with my package yesterday that were specific to r-devel and I had trouble reproducing the errors. I believe the issue is that the rhub and the docker/rocker r-devel were not using the most recent version of r-devel. My solution was to add r-devel to my travis ci.

[R-pkg-devel] suggestion: conda for third-party software

2020-01-07 Thread Serguei Sokol
Best wishes for 2020! I would like to suggest a new feature for R package management. Its aim is to enable package developers and end-users to rely on conda ( https://docs.conda.io/en/latest/ ) for managing third-party software (TPS) on major platforms: linux64, win64 and osx64. Currently,

Re: [R-pkg-devel] rhub, docker and Bioconductor

2020-01-07 Thread Christian Martin Hennig
That's good to know. I'm still at a loss what to do though. How are you checking your packages on systems that are not available to you, other than using rhub? Chances are if something from Bioconductor is required by one of the packages that I require, I can't get rid of it, right? Thanks,

Re: [R-pkg-devel] rhub, docker and Bioconductor

2020-01-07 Thread Gábor Csárdi
It is an R-hub bug: https://github.com/r-hub/rhub/issues/318 Gabor On Tue, Jan 7, 2020 at 2:05 PM Christian Martin Hennig wrote: > > I should maybe add that I'm not even sure why I need Bioconductor, the > package has: > > Imports: MASS, cluster, mclust, flexmix, prabclus, class, diptest, >

Re: [R-pkg-devel] rhub, docker and Bioconductor

2020-01-07 Thread Christian Martin Hennig
I should maybe add that I'm not even sure why I need Bioconductor, the package has: Imports: MASS, cluster, mclust, flexmix, prabclus, class, diptest, robustbase, kernlab, grDevices, graphics, methods, stats, utils, parallel Suggests: tclust, pdfCluster, EMMIXskew, mvtnorm Christian On 1/7/20

[R-pkg-devel] rhub, docker and Bioconductor

2020-01-07 Thread Christian Martin Hennig
Hi there, I'm trying to track down some errors and issues of my fpc package. As I can't reproduce any of these on my machine, I'm using rhub and docker. I'm getting Bioconductor related issues with both local_check_linux("fpc_2.2-3.tar.gz", image = "rhub/debian-clang-devel") and