Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0

Yes, all builds of R 4.0 and above are now using Rtools40 on Windows. See: https://cran.r-project.org/bin/windows/Rtools/ AFAIK there has been no official announcement about this on the various R-* mailing lists but this is suggested by the output of 'R CMD config CC' which has changed from

[R-pkg-devel] More GitHub problems

Hello:   Is there a way to restore the functionality of a local clone of a GitHub repository after the SSH key it used was replaced?   I have a local clone that previously worked fine but now asks for a password that I don't think I have when I try "git push".   Thanks,  

Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0

Hi Herve, Ah, I see now. I was getting confused by the CRAN page that points to R-4.1.0 for Windows and says it "will eventually become the next major release of R". I see now that we should be using R-4.0.0 RC instead, which is the patched link. Can I confirm whether we should be using

Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0

Hi Gordon, The Bioconductor version to be released (BioC 3.11) uses R 4.0, not R 4.1. The latest Windows built of R 4.0 is available on CRAN here: https://cran.r-project.org/bin/windows/base/rpatched.html Note that the upcoming devel version of Bioconductor (BioC 3.12) will still be based

Re: [Bioc-devel] version inconsistence in the development version page and the build page of a bioconductor package, cogena

We don't update the pages with broken versions of packages. 3.21.1 as you showed has an ERROR so it will not propagate and the landing page will keep the last working version in this case 3.21.0. Please see the follow page that not only explains this but also has advice on the length 1 vector

Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0

Hi Martin, I may have jumped to the wrong conclusion as to the cause of the problem. The problem we are observing is that BiocManager::install does not currently work with R Devel for Windows 2020-04-18 (which the installer is calling R 4.1.0) while it still works fine with R Devel for Windows

[Bioc-devel] version inconsistence in the development version page and the build page of a bioconductor package, cogena

Hi, Bioconductor community, I found it is inconsistent in the versions of the development package, cogena. I am maintaining this package. For example, the build page of my package cogena is 3.21.1 ( https://master.bioconductor.org/checkResults/3.11/bioc-LATEST/cogena/malbec2-buildsrc.html),

Re: [R-pkg-devel] check_for_cran not responsive

On 20/04/2020 5:34 p.m., Eric Leifer wrote: Hello, I apologize if I'm asking this question in the wrong place, but I'm trying to check my R package for upload to CRAN using the check_for_cran command, and it's stuck after the following messages: - Building package - Uploading package -

[R-pkg-devel] check_for_cran not responsive

Hello, I apologize if I'm asking this question in the wrong place, but I'm trying to check my R package for upload to CRAN using the check_for_cran command, and it's stuck after the following messages: - Building package - Uploading package - Preparing build, see status at

Re: [Rd] stringsAsFactors and type.convert()

> Arni Magnusson > on Mon, 20 Apr 2020 16:50:16 + writes: > Dear Martin, > Thank you for the well-reasoned response. I realized I was rather late to make this suggestion for 4.0.0, changing a somewhat low-level function that can indeed affect packages. > I was just

Re: [Rd] stringsAsFactors and type.convert()

Dear Martin, Thank you for the well-reasoned response. I realized I was rather late to make this suggestion for 4.0.0, changing a somewhat low-level function that can indeed affect packages. I was just reviewing some R user scripts that were using type.convert(), mainly on data frames. In all

Re: [Bioc-devel] Problem with pushing package to Bioconductor

Try adding a new SSH key and retrying again. Best, Nitesh > On Apr 20, 2020, at 12:29 PM, Cao, Quy wrote: > > Dear all, > > I made some updates for my package PERFect on GitHub but I have some trouble > pushing it to Bioconductor. Here is what I have done: > > > 1. I have activated my

[R-pkg-devel] debugging memory sanitation errors

Hello so I keep getting my package turned back because of errors detected by UBSAN. I am trying to catch it using r-hub's platform with UBSAN but there are no errors thrown there. What would be a good way for me to debug this. Obviously I did R CMD check --as-cran on my own machine, and on Travis

[Bioc-devel] Problem with pushing package to Bioconductor

Dear all, I made some updates for my package PERFect on GitHub but I have some trouble pushing it to Bioconductor. Here is what I have done: 1. I have activated my GitCredentials account and it said that I have access to my package. 2. When I checked whether I have access to my package

Re: [Rd] stringsAsFactors and type.convert()

> Arni Magnusson > on Mon, 13 Apr 2020 22:20:19 + writes: > If read.table() is defaulting to "character" instead of "factor" data type, shouldn't type.convert() also default to "character" in R 4.0.0? > This would seem like a good time to change the default to

Re: [Rd] suggestion: "." in [lsv]apply()

I wouldn't drive my choices using unlikely edge cases but rather focus on the vast majority of practical cases. The popularity of tidyverse shows that this philosophy works well from a user's perspective. For the vast majority of practical cases it works well, and for the others you can either

Re: [Bioc-devel] Unable to access Bioconductor git repo

Hi Peter, The account was using peter.humb...@csiro.org. I've changed it to the gmail address. Please activate your account again, and try to add SSH keys. You'll gain access. https://git.bioconductor.org/BiocCredentials/account_activation/ Best, Nitesh > On Apr 18, 2020, at 7:26 PM, Peter

Re: [Rd] suggestion: "." in [lsv]apply()

Le 19/04/2020 à 20:46, Gabor Grothendieck a écrit : You can get pretty close to that already using fn$ in the gsubfn package: library(gsubfn) fn$sapply(split(mtcars, mtcars$cyl), x ~ summary(lm(mpg ~ wt, x))$r.squared) 4 6 8 0.5086326 0.4645102 0.4229655 Right, I thought about similar syntax

Re: [Bioc-devel] Unable to reproduce vignette build error

I am able to reproduce this locally. Make sure you are using R 4.0.0 and have updated versions of all Bioconductor packages BiocManager::valid() BiocManager::install() I did an "R CMD Stangle Installing_and_Using_BrainSABER.Rmd" to produce an R file of code for the vignette and also tried to

[Bioc-devel] Important Upcoming Release 3.11 Deadlines This Week!!

Some Important Release Deadlines are fast approaching. See also the release schedule online The last day for any NEW package to be accepted and released under Bioc 3.11 is this Wed. April 22th. Packages accepted after this day will remain in Bioconductor devel and included in the Bioc 3.12

Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0

The Bioconductor 3.11 builds transitioned in the last week to using the new tool chain, following CRAN's lead. As a sanity check (ours!) what makes you say > It appears that the Bioconductor developmental repository is using > rtools35 ? Martin Morgan On 4/19/20, 10:41 PM, "Bioc-devel

[Bioc-devel] EBImage/cytomapper check error on tokay2 i386

Hi all, the checks for my newly submitted package seem to be failing on tokay2 i386 for a couple of days now: https://bioconductor.org/checkResults/devel/bioc-LATEST/cytomapper/tokay2-checksrc.html And

[Bioc-devel] Unable to reproduce vignette build error

Dear Bioconductor Team, In the past week the vignette for our package BrainSABER has been failing to build on the automated builder with a 'subscript out of bounds' error. I am unable to reproduce this error on my local system (Windows x86_64 running devel versions of R and Bioconductor 3.11),