[Bioc-devel] Warning: 'rgl_init' failed

Dear Bioc-devel I have obtained the following warning by building binaries in celaya2 OS X 10.11.6 The Captain/x86_64, in windows works fine: ** byte-compile and prepare package for lazy loading Warning in rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server Warning:

Re: [Bioc-devel] Request R code this paper

Hi Joris, I think that it's a spam email. I've gotten a similar if not the same version directly already. Best, Leo On Tue, Jan 7, 2020 at 10:48 AM Joris Meys wrote: > Dear, > > you mailed the developers mailing list of Bioconductor, i.e. the list for > people who develop packages for the

Re: [Bioc-devel] Updating for 3.11

Hi, On 1/7/20 10:47, Karl Stamm wrote: > I was notified recently my package has build errors going in to bioc 3.11. > So begins the biannual saga of updating everything to see what's new. > My package has quite a few dependencies, so it's normal for someone to > change their API and break my

Re: [Bioc-devel] Updating for 3.11

I'm not an expert on macOS, but generally one wants to follow documented R procedures. Instructions for installing binary versions of R on macOS, including managing multiple versions, are provide at http://mac.r-project.org/man/R-admin.html#Installing-R-under-macOS. The section about

Re: [Bioc-devel] Updating for 3.11

Thanks for the note Karl, and sorry for the break. For others, the change in DESeq2::lfcShrink is that now type="apeglm" is the default instead of type="normal". For the past two releases, users have been getting a message when they run with the default argument that type="normal" performs worse

[Bioc-devel] Updating for 3.11

I was notified recently my package has build errors going in to bioc 3.11. So begins the biannual saga of updating everything to see what's new. My package has quite a few dependencies, so it's normal for someone to change their API and break my scripted usage. This time a default parameter

Re: [Bioc-devel] Request R code this paper

Dear, you mailed the developers mailing list of Bioconductor, i.e. the list for people who develop packages for the Bioconductor suite. Please mail the authors of the paper instead. If you know the package they used, the source code of each package can be found on the bioconductor website.

Re: [Bioc-devel] Change maintainer mail

Yes it should be. The automatic build failure messages and when we reach out to maintainers individually, we utilize the maintainer email provided in the package DESCRIPTION. Let me know when your package builds cleanly and I will remove it from the deprecation list. Cheers, Lori Shepherd

[Bioc-devel] Change maintainer mail

Hi, I am Juan Cruz Rodriguez, maintainer of the MIGSA package , I have noticed that it was giving error on the build, however, I was not being informed because of my other mail jcrodrig...@bdmg.com.ar is not working anymore. I have

Re: [Bioc-devel] Cannot reproduce build error

Hi Jose, evaluomeR 1.3.4 (master branch) is in BioC 3.11 (current BioC devel) so make sure that you use R 4.0 (current R devel) to develop/test the master branch of your package. This is what the build system uses to build/check all the packages in BioC 3.11. Also make sure that all your

[Bioc-devel] Cannot reproduce build error

Hello everyone, I am having some troubles to reproduce the building error of our package: http://bioconductor.org/checkResults/devel/bioc-LATEST/evaluomeR/ The error is related to the vignette generation, since inside of it