Re: [Bioc-devel] Issues with push on release branch

2021-02-03 Thread Giulia Pais
Didn't see them sorry, they are apparently in auto-generated files from vignette building, thanks for the help! Il 03/02/2021 18:05, Nitesh Turaga ha scritto: Hi, Martin, thanks for catching these lines. It's likely these lines are causing the merge conflict git hook to prevent your push. Gi

Re: [Bioc-devel] Updating a package due to reviewer comments and other questions

2021-02-03 Thread Kern, Lori
Additionally on the fread not being found: if you are using roxygen and devtools to develop you may need to run document() again for the changes to be made to the NAMESPACE. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinform

Re: [Bioc-devel] Updating a package due to reviewer comments and other questions

2021-02-03 Thread Martin Morgan
1. New features -- even those that improve the package ;) -- should be added to devel; your users will have access to them soon enough, and it provides a chance for the bugs and errors that new code inevitably introduces to be worked out. 2. If the data is used in the package per se, e.g., in a

Re: [Bioc-devel] Issues with push on release branch

2021-02-03 Thread Nitesh Turaga
Hi, Martin, thanks for catching these lines. It's likely these lines are causing the merge conflict git hook to prevent your push. Giulia, as long as you remove them and amend your commit you should be alright to push. Steps: 1. Remove merge markers 2. Amend your commit (git commit --amend)

Re: [Bioc-devel] Issues with push on release branch

2021-02-03 Thread Martin Morgan
Is it from lines like this https://github.com/calabrialab/ISAnalytics/blob/69341f6591c6765a4a70253f7ab85e64cca9845d/vignettes/collision_removal.bib#L18 in your github repository? Martin On 2/3/21, 11:32 AM, "Bioc-devel on behalf of Giulia Pais" wrote: Hello, I'm trying to push upda

[Bioc-devel] Issues with push on release branch

2021-02-03 Thread Giulia Pais
Hello, I'm trying to push updates to the release 3.12 branch of the bioconductor repo but I got an odd error from git: remote: Error: You cannot push without resolving merge conflicts. remote: remote: Please check the files in the commit pushed to the git-server remote: for merge conflict mark

[Bioc-devel] Updating a package due to reviewer comments and other questions

2021-02-03 Thread Tim Nieuwenhuis
Hello, I am the creator of the HPAStainR package and have received reviewer comments from a journal I sent an accompanying paper to, which leads me to these 3 questions about responding to paper reviewer comments. 1. Am I able to update my Release 3.12 version of the package based on the