Re: [Bioc-devel] Error: invalid graphics state in creating vignettes

Hi JIanhong, that did work. Thank you very much! Best, Sunyoung On Apr 29, 2019, at 10:47 AM, Jianhong Ou, Ph.D. mailto:jianhong...@duke.edu>> wrote: Hi Sunyoung, Sorry for the change of motifStack which makes you struggling. Please have a try following codes for plotting:

Re: [Bioc-devel] pushing changes to an existing package

Thank you, it seems to work now! Do you have any idea of why the ".git" had been moved to ".g?" Just curious if it was something on my end. Cheers, Simina On Thu, May 2, 2019 at 2:15 PM Turaga, Nitesh wrote: > Once your access works you should see yourself as maintainer with Read and > Write

Re: [Bioc-devel] pushing changes to an existing package

No idea Simina. Maybe a typo? Best, Nitesh This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby

Re: [Bioc-devel] pushing changes to an existing package

Once your access works you should see yourself as maintainer with Read and Write access on MultiMed and CancerMutationAnalysis. Best Nitesh This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent

Re: [Bioc-devel] pushing changes to an existing package

Hi Simina, Now that the RELEASE_3_9 branch and pushes are available to everyone, I can help you with this. It seems like your upstream branch is a little funny looking, is this how it got pasted in or maybe it's a mistake. What you gave: (I understand that the mailto: stuff may have been

[Bioc-devel] Access to Bioc git server resumed

Dear Maintainers, Access to Bioc git server is now active again. Maintainers will now have access to RELEASE_3_9 and master branch. Make sure you sync your packages with the latest release changes before making any updates.

Re: [Bioc-devel] pushing changes to an existing package

No worries, thanks for letting me know! Cheers, Simina On Thu, May 2, 2019, 1:02 PM Turaga, Nitesh wrote: > Hi Simina, > > We are going through the release process for Bioc 3.9 now, so all commits > are blocked until further notice. > > I can get back to helping you debug this issue once we

Re: [Bioc-devel] pushing changes to an existing package

Hi Simina, We are going through the release process for Bioc 3.9 now, so all commits are blocked until further notice. I can get back to helping you debug this issue once we are done with the release. https://stat.ethz.ch/pipermail/bioc-devel/2019-May/015050.html Best, Nitesh On May 2,

Re: [Bioc-devel] When to use generics?

Thank you all for the discussion and input. I have decided to use generics for the time being since I am working with 3 classes and might add a fourth one later on. Also, worst case scenario, reverting from generics to "if statements wrapper" functions should not be too terrible. Many thanks,

Re: [Bioc-devel] permission denied

Thanks for help! Unfortunately, I can't even login to activate my account with the email used to maintain the package (ruizh...@gmail.com) To double check whether there is an account existing with my email address, I try to use the password reset and never received the email to reset the password.

Re: [Bioc-devel] readVcf problems in package check

Hi Herve, Thanks so much for your response! I realize that you all aren't obligated to support CRAN packages. When I was developing polyRAD I considered submitting Bioconductor, but I didn't want to have to convert my 'RADdata' class from S3 to S4. The polyRAD package also isn't very deeply

Re: [Bioc-devel] Bioconductor version 3.9 branching today

Minor typo, we'll be creating the Bioconductor 3.9 branch (RELEASE_3_9) starting at 11AM. > On May 2, 2019, at 9:28 AM, Turaga, Nitesh > wrote: > > Dear Bioc developers, > > Today we'll be creating the Bioconductor 3.8 branch (RELEASE_3_9) starting at > 11am EST. All commits to

[Bioc-devel] Bioconductor version 3.9 branching today

Dear Bioc developers, Today we'll be creating the Bioconductor 3.8 branch (RELEASE_3_9) starting at 11am EST. All commits to git.bioconductor.org will be blocked for a few hours starting at 11AM. We'll post back when push access is restored and you can resume

Re: [Bioc-devel] Deleting a branch on Bioconductor git

Hi Kevin, I'm actually surprised you were able to push a branch at all. I'll delete this branch. Best, Nitesh > On May 2, 2019, at 7:52 AM, Kevin Wang wrote: > > Hi all, > I accidentally pushed a branch called “RELEASE_3_9” to the “scMerge" package > that I am maintaining on

Re: [Bioc-devel] 'MoonlightR' Bioconductor package ERROR

Yes that should be a good tutorial to follow to sync to Bioconductor. As of right now there is no RELEASE branch to sync too because the RELEASE_3_8 branch was frozen on April 15. but as of tomorrow the release branch will be RELEASE_3_9 and the devel branch is the master branch. Cheers,

[Bioc-devel] Deleting a branch on Bioconductor git

Hi all, I accidentally pushed a branch called “RELEASE_3_9” to the “scMerge" package that I am maintaining on Bioconductor. I now understand that this is not the correct way to manage this Bioconductor package and may interfere with the upcoming release. However, when I tried to delete this

Re: [Bioc-devel] 'MoonlightR' Bioconductor package ERROR

Please fix the ERROR as soon as possible to avoid potential deprecation. We will temporarily be freezing the master (devel) branch later today (for an hour or two) to create the new release 3.9 branch in preparation for tomorrows Bioc3.9 release. Once this branching happens, the ERROR will

Re: [Bioc-devel] permission denied

Have you checked your ssh keys on the credentials app? You can add additional keys associated with your username there. https://git.bioconductor.org/BiocCredentials Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm &

[Bioc-devel] permission denied

Hi all, My package TreeSummarizedExperiment has recently been accepted. I got the error about permission denied when following the guidelines in the page ( https://bioconductor.org/developers/how-to/git/new-package-workflow/) to run the following commands $git remote add upstream