I am new to using Rproject and Github. I have created some .R files .stan and .Rdata files in Rstudio.
I would like know a way how I can connect these files to a Github repository (which I have not created yet) so that I can collaborate them with others.
Reading through https://happygitwithr.com/rstudio-git-github.html , it appears that an Rproject is required to do this.
how do I add the existing .R, .stan and .RData files to a new Rproject?
Thanks
Since you are new. I recommend you install GitHub Desktop and read this if you are unfamiliar with it. log in using your GitHub credentials. Then go to File>New Repository and add your folder as a repository (you don't really need to have it as an Rproject although it is a good idea). You can simply commit everything with a message and then use "Push origin" to push it to GitHub.
Hope it helps.
Related
I’ve made a package on RStudio and I successfully put it on Github. I just have to add a README file. I acknowledge that this should be the easiest possible thing to do, but I’m pretty new at git and still learning.
I’m wondering if adding a README on the Github repository would be reflected in the local branch in Rstudio? If possible, I don’t want to have some files added on the Github repo and not have them locally on RStudio. Or if I’d be better off creating a README locally in RStudio and then pushing it to Github?
If the latter, would anyone have any suggestions on how to do that?
I've been building an R package via an R project file (.Rproj) in R studio with the project file linked to my github. When I was working on it this morning, all was as it should be, but when I returned to it this afternoon, the .Rproj file had mysteriously vanished. All other files and folders associated with the package are where they should be (e.g., the "R" folder with the scripts for the package's functions, the DESCRIPTION file, the man folder, etc.) but the .Rproj file is gone. I have not deleted it and it is not in my trash can, nor does git have any record of it for some reason.
If I do a search for the file name in the windows search bar (I'm suing windows 7, btw) the file shows up and says that it is in the correct location, but if I click on it, I get an error message saying that the file has been moved or deleted. Similarly, if I try to navigate to where the file should be via "open project" in R, there is a greyed out ".Rproj.user" folder that I don't recall having seen before, but no project file.
I'm at my wits end for what is going on. The package on github appears to all still be correct (as do the files on my computer), but without being able to find or access the .Rproj file I can't easily edit the package and push the changes to github.
Does anyone have any idea what is going on or how to retrieve my package file? Since I have all the source files for it, I could always build a new project using the source files, but then I need that to link up to my github which is linked to a now non-existent project file, and everything becomes really messy and tedious quickly.
PS I have restarted both my computer and R. It didn't help.
You can probably just create a "new" project in the existing folder to generate a new .Rproj file.
The .Rproj file doesn't actually do that much. It mostly lets RStudio know that "this folder is the root directory of a project named X". Git keeps its own hidden files in the directory to track things (that RStudio will look for if it's a project).
If you haven't done this, I'd also recommend adding your .Rproj files to your .gitignore file - Rproj files are user-specific so shouldn't be tracked in version control. (If you used RStudio to create the git repo, this will be done automatically.)
Packrat is often recommended as the virtual environment for R, but it doesn't fully meet my need of contributing to R open source. Packrat's "virtual environment" is stored directly in the project directory, requiring me to modify the .gitignore to ignore them when I make a pull request to the open source upstream.
In contrast, something like conda stores the virtual environment somewhere else, leaving no trace in the project codebase itself.
So how do R open source contributors deal manage dependencies during package development? Ideally the solution would work well with devtools and Rstudio.
There is nothing wrong in having Packrat in .gitignore.
You can use .git/info/exclude file thus avoiding touching the .gitignore.
Is there any way to save your workspace code to a file? I would like to save each version of my program in R using RStudio, simply by running the code itself.
Mick,
I suggested you use git which is available from Rstudio. Basically speaking, you firstly need to install git for your platform.
Then you need to create a directory which is already under version control. After this you simply need to create a project from Rstudio and enable version control feature. Then the remote repository will be cloned into the specified directory and Rstudio's version control features will then be available for that directory.
Details regarding how to set up version control in Rstudio can be found here:
https://support.rstudio.com/hc/en-us/articles/200532077-Version-Control-with-Git-and-SVN
I want to create a master repository on our server, from which I can clone a local version onto my computer.
I am using R Studio v0.98.994.
So far, this is what I have tried doing:
Create a folder for the master repository to live in. I do this using 'new project' in R studio, and tell it to make a git repository.
I can then open up another new project, located on my C drive, and use R studio to clone, by telling it to open an existing project and setting the URL as the location of the master project.
However, then when I make changes and commit to my local repository (which works fine) I cannot push to the master repository, I get an error exactly as described in this question: git push fails: `refusing to update checked out branch: refs/heads/master`
So it appears that R Studio creates non-bare repositories?
Now I thought, well okay, I will use git bash to initialise the repository and then connect to that within R studio.
I do so, but cannot then find a way to use that repository in R Studio.
I am very new to Git, so it is entirely probable that this is one of those 'read the instructions' questions, in which case I am very sorry - and could someone possibly point me towards some guidance for this situation? I have spent the better half of a day googling around this error and haven't yet managed to pull together the pieces :( I also apologise; this doesn't feel like a very reproducible question.
It sounds like you are using Windows Git, with a setup on a local Windows machine (C: drive) and a server of some kind, mounted as the S: drive. There's a few things you should be aware of when doing this.
Shared Repositories
If you are intending for multiple people to share the same repository, you want to initiate a shared repository. See the --shared option in git-init for more details. Note that I'm not sure how having your repository on a Windows machine affects the sharing options. If you are just trying to keep your repository in two places, that makes things a lot easier.
Bare Repositories
Separate from the discussion of sharing is the discussion of bare repositories. If you don't intend to ever work with files in the server (i.e. it's just going to be a place to push changes so they are safely stored), you could initialize a bare repository. A bare repository contains the database structure of Git, but does not have the actual files in the directory.
A standard Git repository is a directory with a hidden folder in it named .git. This .git folder contains all the various data structures that Git uses to track changes. A bare repository is essentially a folder containing only the contents of .git.
The good thing about a bare repository is that no one can work in the repository itself (since there is no working directory, just the database). This means that no one could log into S: and edit the repository themselves. Instead, they would have to clone the repository, then push their changes back to the origin. The GitGuys have a good article about why this is ideal.
Note that shared repos and bare repos are not dependent or mutually exclusive. As a general practice, if you are having a "server repo" from which you pull and to which you push, you should have it be bare, regardless of whether the project is shared.
A Non-Shared Workflow
Since it's not clear if you are sharing or not sharing and you're on a Windows environment, which I don't know about from a sharing standpoint, I'm going to give you a simple example. Using git-bash, you should be able to change directories to wherever on S: you have your repositories. Then, use git init with the bare options as described by the link above to initialize a bare repository. Navigate to where you want your repository to live on C:, and then do git clone to get a working copy.
Add a README file or something else so you can do your initial commit, and then commit and do git push origin master to push your changes to the S: repository. Once all that is done, THEN initialize the RStudio Git project. RStudio should defer to your existing configuration, and things should hopefully work.