[Bioc-devel] Can't push to RadioGx upstream

Hello BioC core team, I am unable to push to the RadioGx upstream master, despite being able to push to CoreGx, PharmacoGx and ToxicoGx. The error is: ceeles@EELESPC-Desk:~/Development/RadioGx$ git push upstream master FATAL: W any packages/RadioGx b.haibe-kains DENIED by fallthru (or you

[Bioc-devel] No write permissions on PDATK

Hello Core Team, I am trying to push a fix for our package, PDATK, to Bioconductor but it seems I have lost write permissions on the repo, as indicated by `ssh -T g...@git.bioconductor.org | grep PDATK`. I also tried to login to the BiocCredentials app, but it

Re: [Bioc-devel] Best Practices for Renaming S4 Slots

and reimplement them in a new package. Doesn't that go against the spirit of reuse that is supposed to be encouraged by adoption of S4 classes? TL;DR - IMO API = interface; implementation is developer business Best, Chris From: Vincent Carey Sent: October 15, 2021 1:31 PM To: Chris Eeles Cc: Herv� Pag�s

Re: [Bioc-devel] Best Practices for Renaming S4 Slots

Message received. I will leave that branch for later. Is this information available on the Bioconductor website at all? It would have been useful to find out sooner. Best, Chris -Original Message- From: Bioc-devel On Behalf Of Chris Eeles Sent: October 15, 2021 1:10 PM To: Hervé Pagès

Re: [Bioc-devel] Best Practices for Renaming S4 Slots

the slots to be renamed so it would significantly delay required features if I were to wait. I plan to put in the work so that those using accessors shouldn't notice a difference. Best, Chris -Original Message- From: Hervé Pagès Sent: October 15, 2021 12:39 PM To: Chris Eeles ; bioc-devel

[Bioc-devel] Best Practices for Renaming S4 Slots

Hello BioC community, I am the lead developer for the CoreGx, PharmacoGx, RadioGx and ToxicoGx packages. We have recently been working on major updates to the structure of a CoreSet, which is inherited by the main class in all three of the other packages listed. While making these changes, we

[Bioc-devel] Can't push to upstream for ToxicoGx

Hello BioC core team, I am having a weird issue with pushing a fix to the ToxicoGx repo. I tried removing and re-adding the upstream branch, but the problem still persists. I can fetch and pull from the remote using my SSH key, I can also access our CoreGx repo (push and pull) using the same

[Bioc-devel] Bioconductor 3.14 R Version

Hello Bioc Core Team, I noticed that currently Bioconductor 3.14 is building using R 4.1.0 beta. Will this be changed to R 4.2 in the future? Best, --- Christopher Eeles Software Developer BHK

Re: [Bioc-devel] 3.12 builds

Hi Herve, Can you clarify what you mean by after tomorrow? The deadline is Friday, October 23rd correct? Is there a time of day submissions need to be made by? Best, --- Christopher Eeles Software Developer BHK Laboratory Princess Margaret Cancer Centre University Health Network -Original

Re: [Bioc-devel] Changing Package Maintainer

Hi Nitesh, Thanks for getting back to me. So in the future to change maintainers I can simply update the DESCRIPTION? I wasn’t sure based on the issues we had with the credentials account and didn’t want to assume. Best, Chris From: Nitesh Turaga Sent: July 8, 2020 8:13 AM To: Chris Eeles

[Bioc-devel] Changing Package Maintainer

Hello Bioconductor developers, Michael and I would like to change the package maintainer for the MetaGxPancreas and MetaGxBreast data packages from Michael to: Benjamin Haibe-Kains If someone could assist me with this it would be greatly appreciated. Best, --- Christopher Eeles Software

Re: [Bioc-devel] Bioconductor credentials issue

Hi Nitesh, I had to reset the password but yes I can. Best, Chris From: Nitesh Turaga Sent: Friday, June 19, 2020 10:40:41 AM To: Chris Eeles Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Bioconductor credentials issue Hi Chris, Let�s try

[Bioc-devel] Bioconductor credentials issue

Hello Bioconductor team, I am having issues accessing our labs Bioconductor repositories and also cannot login to the Bioconductor credentials website. I had a similar issue less than a month ago, which Nitesh from the core team helped me resolve. At that time I was able to login to

Re: [Bioc-devel] SSH Issues

* consensusOV * CoreGx Benjamin’s GitHub username is bhaibeka, if I just change the username back will that work? Sorry for an inconvenience. Best, Chris From: Nitesh Turaga Sent: June 3, 2020 1:15 PM To: Chris Eeles Cc: bioc-devel@r-project.org; Haibe-Kains, Benjamin Subject: Re: [Bioc

[Bioc-devel] SSH Issues

Hello Bioconductor team, I am having issues pushing updates to the development branch of the CoreGx package. When I try to push to upstream I get: "FATAL: W any packages/CoreGx gangeshberiuhn DENIED by fallthru (or you mis-spelled the reponame) Fatal: Could not read from remote repository.

[Bioc-devel] Package Submission Limbo

Hello Bioconductor team and community, My name is Christopher Eeles and I am a software developer in the Benjamin Haibe-Kains laboratory at Princess Margaret Cancer Research Centre in Toronto, Ontario, Canada. I am concerned due to inaction on the part of my reviewer for two of my package

Re: [Bioc-devel] To Push or Not To Push?

:25 PM To: Chris Eeles ; Bioc-devel@r-project.org Cc: Smirnov, Petr Subject: Re: [Bioc-devel] To Push or Not To Push? Hi Chris, That is the question :-) The last run of the builds got delayed (that's because we updated R to final 4.0.0 on all build machines on Friday) so we weren't able to update the

[Bioc-devel] To Push or Not To Push?

Hello Bioc-Devel community, We recently submitted CoreGx to Bioconductor and am happy to announce it was accepted. However, the package has not yet made it into the 3.11 build and we are concerned it may not make the release. Our existing Bioconductor package, PharmacoGx, has significant

[Bioc-devel] Resubmitting additional packages as separate issues

Hello Bioc-devel, I recently submitted three packages to Bioconductor Contributions (CoreGx, RadioGx and ToxicoGx). After consulting my reviewer I now wish to resubmit the two dependent packages (RadioGx and ToxicoGx) on separate issues. I deleted the comments from #1445 where I submitted the