[Bioc-devel] Bioconductor Git Credentials

2019-05-06 Thread Josef Spidlen
Hello, I am trying to merge changes from https://github.com/jspidlen/flowUtils to g...@git.bioconductor.org:packages/flowUtils.git but don't seem to have access. So I tried https://git.bioconductor.org/BiocCredentials/account_activation/ but it tells me jspid...@gmail.com is not associated with a m

Re: [Bioc-devel] showAsCell, character feature request [Re: Possible bug in showAsCell, character]

2019-05-06 Thread Boris Steipe
Ummm ... substr(x, 1, n) ? :-) > On 2019-05-06, at 18:03, Laurent Gatto wrote: > > paste0(paste(strsplit(x, "")[[1]][1:n], collapse = "") ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] showAsCell, character feature request [Re: Possible bug in showAsCell, character]

2019-05-06 Thread Laurent Gatto
Ok, so it appears I have posted a bug of my own and a fix in the same email. Trying to be positive and turning this into an opportunity, I will change it into a feature request. The current showAsCell,ANY implementation results in the following annoyance: > x <- DataFrame(x = c('A veee

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

2019-05-06 Thread Turaga, Nitesh
Hi Simina, This is an issue with Github. So just to walk through what might be happening, this is a case when users set up 2FA (two factor authentication). You might want to to set up SSH keys for GitHub as well, and use the SSH protocol (given below instead of HTTPS) as your remote origin.

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

2019-05-06 Thread Simina Boca
Thank you again Nitesh! I'm now having some issues with pushing the origin master: C:\Users\smb310\Documents\GitHub\MultiMed [master ↑]> git push upstream master Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to the list of known hosts. Counting objects: 16, done. Delta

Re: [Bioc-devel] FCBF git push to RELEASE_3_9 was denied

2019-05-06 Thread Turaga, Nitesh
Hi Tiago, Let's take a look at the commit history you have, /t/FCBF ❯❯❯ git log commit 5b6ba9580a6d4a0fb1b7e2

Re: [Bioc-devel] Single Package Builder for New Submissions

2019-05-06 Thread Shepherd, Lori
The single package builder should now be fixed and produce build reports on version bumps. Thank you for your patience. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 __

[Bioc-devel] FCBF git push to RELEASE_3_9 was denied

2019-05-06 Thread Tiago Lubiana Alves
Good afternoon, I am having a problem with a package I submitted ( https://bioconductor.org/packages/release/bioc/html/FCBF.html). I broke it and, by the time I managed to fix it, the RELEASE_3_9 was already going on. I managed to push it upstream to the "master" branch. but upon hitting $git pus

[Bioc-devel] warnings with BiocStyle pdf compilation

2019-05-06 Thread Vincent Carey
*I don't often compile vignettes to pdf ... but a recent attempt led to:* *Warning message:* *LaTeX Warning: You have requested package `/Library/Frameworks/R.framework/Vers* *ions/3.6/Resources/library/BiocStyle/resources/tex/Bioconductor',* * but the package provides `Bioconduc

[Bioc-devel] Single Package Builder for New Submissions

2019-05-06 Thread Shepherd, Lori
We are experiencing some issues with the Single Package Builder relating to the release. Currently builds may not be executing with versions bumps or you may get a report with a Fatal error: cannot create 'R_TempDir' We are working on a solution and hope to have it running as normal soon. Th

Re: [Bioc-devel] permission denied

2019-05-06 Thread Shepherd, Lori
I just made sure your account is activated. Could you please try again and let us know if you are still having trouble? Sometimes the password reset emails accidently get marked as spam - could you also please make sure they did not end up in a trash/spam folder. Please email back if you the