[R-pkg-devel] Checkpoint package failing CRAN checks

Hi all, I'm the new (as of 6 months ago) maintainer of checkpoint. If you're not familiar with it, checkpoint is a package to help with reproducible analysis: you give it a particular snapshot date from the MRAN site, and it installs the packages that your project depends on from that

Re: [Bioc-devel] Problem in activating the Account for Bioconductor Git Credentials

Hi Nitesh, thank you very much! the email pa...@idsia.ch was the one with which I created the package 10 years ago, but lot of years ago I changed it in all documents of the package with the current one since I changed Institution. I was able to add my SSH key and to

Re: [Bioc-devel] TIMEOUT error in building vignette in package scruff

I can confirm that downgrading Rsubread to an older version eliminates the slowdown. Here are the timings I get on my laptop (Ubuntu 16.04.6 LTS) for 'R CMD build scruff' with different versions of Rsubread (all these timings use the same R-devel version and the latest master branch of

Re: [Rd] re-submission of package after CRAN-pretest notes

Hi Michael, At the risk of sounding like I'm just name-dropping, R. Gentleman once told me something along the lines of "version numbers are cheap, don't be afrai to use a lot of them". I get that its a bit annoying but its for good reason, imho. Any change, no matter how trivial will change the

Re: [Rd] add jsslogo.jpg to R sources?

On Wed, 8 Jan 2020, Iñaki Ucar wrote: On Wed, 8 Jan 2020 at 19:21, Toby Hocking wrote: Hi R-core, I was wondering if somebody could please add jsslogo.jpg to the R sources? (as I reported yesterday in this bug) https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17687 R already includes

Re: [Rd] add jsslogo.jpg to R sources?

On Wed, 8 Jan 2020 at 19:21, Toby Hocking wrote: > > Hi R-core, I was wondering if somebody could please add jsslogo.jpg to the > R sources? (as I reported yesterday in this bug) > > https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17687 > > R already includes jss.cls which is the document

Re: [Bioc-devel] TIMEOUT error in building vignette in package scruff

Hi Zhe, The code in the vignette seems to rely a lot on the Rsubread package to perform some very computationally intensive operations. Could it be that some recent changes to the Rsubread package are somehow related to the sudden slowdown of these operations? That's something I suggest you

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

It would also be worth looking at the basilisk package: https://github.com/LTLA/basilisk where the approach used there is to instead embed a Conda installation as part of the R package itself. This comes with the benefit that it's now the package author's responsibility to maintain the Conda

Re: [R-pkg-devel] debian-clang error with class

Great, thanks! On 1/8/20 7:18 PM, Fernando Roa wrote: Take a look at https://stat.ethz.ch/pipermail/r-package-devel/2019q4/004675.html Best, On Wed, Jan 8, 2020 at 3:09 PM Christian Martin Hennig mailto:christian.hen...@unibo.it>> wrote: Hi there, I have an ERROR in my fpc package on

[Rd] add jsslogo.jpg to R sources?

Hi R-core, I was wondering if somebody could please add jsslogo.jpg to the R sources? (as I reported yesterday in this bug) https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17687 R already includes jss.cls which is the document class file for Journal of Statistical Software. Actually, for the

Re: [R-pkg-devel] debian-clang error with class

Take a look at https://stat.ethz.ch/pipermail/r-package-devel/2019q4/004675.html Best, On Wed, Jan 8, 2020 at 3:09 PM Christian Martin Hennig < christian.hen...@unibo.it> wrote: > Hi there, > > I have an ERROR in my fpc package on debian-clang that I currently > cannot reproduce due to the fact

[R-pkg-devel] debian-clang error with class

Hi there, I have an ERROR in my fpc package on debian-clang that I currently cannot reproduce due to the fact that rhub is apparently affected by a bug on that platform that doesn't allow me to install Bioconductor packages. The description is "--- failure: the condition has length > 1 ---".

Re: [R-pkg-devel] pandoc lua filter error with win devel check

Hi, I added SystemRequirements: pandoc (>= 2.0) to DESCRIPTION as you suggested; submission failed, the automatic check of package submission to CRAN had the error I got before with check_win_devel: "pandoc.exe: unrecognized option `--lua-filter=refs/multiple-bibliographies.lua' Error:

Re: [Bioc-devel] Warning: 'rgl_init' failed

Hi Fernando, This is a warning only and is on our side (i.e. it's an issue with how our Mac builders are set up). It can safely be ignored. Cheers, H. On 1/7/20 23:58, Fernando Pérez Sanz wrote: > Dear Bioc-devel > > I have obtained the following warning by building binaries in celaya2 OS >

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

On Tue, Jan 7, 2020 at 10:42 PM Sokol Serguei wrote: > > 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

[Bioc-devel] TIMEOUT error in building vignette in package scruff

Hi all, I am the maintainer of package scruff. Recently I encountered a timeout error in creating vignette in the development branch of the package. I tried increasing the number of cores for parallelization from 2 to 3 but it still timed out. I did not make any changes to the R codes in the

Re: [Rd] re-submission of package after CRAN-pretest notes

On 8 January 2020 at 10:06, Michael Friendly wrote: | It used to be the case that when I submitted a package and it gave notes | or warnings in the CRAN checks, I was required to bump the package | version before re-submission. | | I hope this is no longer the case.  I recently submitted a

[Rd] re-submission of package after CRAN-pretest notes

It used to be the case that when I submitted a package and it gave notes or warnings in the CRAN checks, I was required to bump the package version before re-submission. I hope this is no longer the case.  I recently submitted a package that gave one fairly trivial NOTE, fixed that, and would

Re: [Bioc-devel] Updating for 3.11

I agree with Martin that the R administration guide should be frequently consulted on Mac OS and other systems (and would have save me a couple hours of trouble shooting the other week). However it's not always updated for the most recent Mac OS perversions, as I found:

Re: [Bioc-devel] Problem in activating the Account for Bioconductor Git Credentials

Hi Paola, It seems your email is registered to pa...@idsia.ch on the Bioconductor Git repository. I've changed it on my end. You should be able to activate your account https://git.bioconductor.org/BiocCredentials/account_activation/ with the new email address. Once

Re: [R-pkg-devel] Significant warnings during package checks

On 08/01/2020 7:48 a.m., MONSUUR OLAWALE via R-package-devel wrote: Hi R-package-devel team, I submitted my package on CRAN and below errors and warnings seemed to have appeared in the during the automatic check but that did not actually appear when I compile. Any suggestions on how this

[R-pkg-devel] Significant warnings during package checks

Hi R-package-devel team, I submitted my package on CRAN and below errors and warnings seemed to have appeared in the during the automatic check but that did not actually appear when I compile. Any suggestions on how this problem could be resolved? * checking whether package BASiNET can be

[Bioc-devel] Problem in activating the Account for Bioconductor Git Credentials

Dear All, I am the author and Maintainer of the package mBPCR. I was adviced to fix some issues in the package. Thus, I am trying to create a new GitHub repository for my package and I need to activate my account for Bioconductor Git Credentials. But, the website told me that:

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

Le 08/01/2020 à 08:50, Ivan Krylov a écrit : 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

Re: [Rd] Another wish (?) for R 4.0.0: print(*, width = )

> Henrik Bengtsson > on Tue, 7 Jan 2020 13:31:18 -0800 writes: > On Tue, Jan 7, 2020 at 6:14 AM brodie gaslam via R-devel > wrote: >> >> For whatever my 2c are worth I think this would be nice. I'm still uncomfortable at having to call `options` in my package