[Bioc-devel] Extensive updates to DiffBind: help reviewing docs and/or beta testing?

I've checked in extensive updates to the DiffBind ChIP/ATAC analysis package to reflect current best practices. I'm looking for help/advice in the following areas: 1. Reviewing the documentation (particularly the updated vignette), and/or beta-testing the code by running analyses on real dat

Re: [Bioc-devel] BiocCheckGitClone error

I pushed famat.Rproj after .gitignore was created and pushed with "famat.Rproj" in it. That's why i don't understand why famat.Rproj is still in the clone folder. Garanti sans virus. www.a

Re: [Bioc-devel] BiocCheckGitClone error

So I think the file probably got pushed up before you added it to .gitignore. So you would probably want to git rm the files, commit, and push. Then you could add them back in after and if they were still listed in the .gitignore then they would be ignored. Lori Shepherd Bioconductor Core

Re: [Bioc-devel] BiocCheckGitClone error

This time I used Git clone folder. Though, when I push famat package in github, .gitignore file isn't uploaded, so I created a .gitignore file in the github repository with "famat.Rproj" in it before pushing the whole package. Unfortunately, the "famat.Rproj" file is still in the git clone folder..

Re: [Bioc-devel] Bioconductor package DegNorm

We do not see any changes in the version on Bioconductor git.bioconductor.org. You need to push the changes to that location not your github location and there needs to be a valid version bump for the changes to propagate. Firstly, please check your remotes git remote -v upstream should poin

Re: [Bioc-devel] Bioconductor package DegNorm

Hi Lori, I have made changes to some of the R functions a few months ago, also I have changed version etc (recently fixed a few bugs). But I noticed in the current Bioconductor version, such changed have never been included. Could you advise what happened? Or anything additional should I do

Re: [Bioc-devel] BiocCheckGitClone error

We run BiocCheckGitClone on a raw clone of the github directory. If you are running it locally and had .gitignored those files before pushing to github then you should be okay. A way to test this would be to do a git clone​ of your github repository, in a different, temporary location to se

[Bioc-devel] BiocCheckGitClone error

Hello, When i run R CMD and BiocCheck, i get no error or warnings. But, when running BiocCheckGitClone, i'm getting this error : System files found that should not be tracked : famat.Rproj, .Rhistory The issue is that both files are in .gitignore, but this error isn't removed... I'm using BiocChec