I'm new to R and RStudio and am currently taking online classes to learn more about data science. In one of my lectures, I'm being asked to create a project in RStudio prior to creating a repository in github and linking the project with git. In order to make a pre-existing project interact with git, the instructions in my lecture are telling me to navigate to the directory containing my project file by using the "cd" command followed by the location of the file and file name. My project file is currently located on my desktop so I typed in "cd ~ /Desktop/temporary_no_version_control" however, the directory doesn't seem to change and remains set on the original location of the file which was in Users/savannahkeiffer. Just so I could complete the assignment, I re-located the file to my user file and tried to follow the rest of the instructions which told me to type "git init" followed by "git add ." which is where I run into the "warning: could not open directory" warning.
I have a macbook which runs on OS X Maverick. I went into my system preferences > security and privacy and selected Full Disk Access where I manually allowed terminal to have access to all the files on my laptop. However, after closing and re-opening RStudio and attempting the commands again, I got the same error.
This is what I entered when I tried to change the directory
Savannahs-MacBook-Air-2:~ savannahkeiffer$ cd ~
/Desktop/temporary_no_version_control
Savannahs-MacBook-Air-2:~ savannahkeiffer$ git init
Reinitialized existing Git repository in
/Users/savannahkeiffer/.git/
And what I got when I changed the location of the project on my laptop in order to complete the assignment (after already giving access to terminal)
Savannahs-MacBook-Air-2:~ savannahkeiffer$ cd ~
/Users/savannahkeiffer/first project/temporary_no_version_control
Savannahs-MacBook-Air-2:~ savannahkeiffer$ git init
Reinitialized existing Git repository in
/Users/savannahkeiffer/.git/
Savannahs-MacBook-Air-2:~ savannahkeiffer$ git add .
warning: could not open directory 'Pictures/Photos
Library.photoslibrary/': Operation not permitted
warning: could not open directory 'Library/Application
Support/MobileSync/': Operation not permitted
warning: could not open directory 'Library/Application
Support/CallHistoryTransactions/': Operation not permitted
warning: could not open directory 'Library/Application
Support/com.apple.TCC/': Operation not permitted
warning: could not open directory 'Library/Application
Support/AddressBook/': Operation not permitted
And so on.. Is this a directory problem or a "git add ." command problem?
It looks like what happened is that when you typed the cd command, you left a space in between the tilde and the rest of the path, so you changed back into your home directory (represented by the tilde). Then, when you tried to do a git init, you tried to initialize your home directory as a Git repository, and then ran into the fact that macOS restricts some programs (in your case, not Terminal, but maybe still Git) from accessing certain directories.
In the shell, the tilde is just a fancy way of spelling the environment variable $HOME, which points to your home directory (in this case, /Users/savannahkeiffer), so it should immediately precede the rest of the path without a space in between.
The best thing to do in this case is switch into your project directory and then initialize a repository there:
cd ~/Desktop/temporary_no_version_control # note the lack of space after the tilde
git init
If you didn't intend for your home directory to be a repository (i.e., you're not storing your dotfiles in a repository there), then you will probably also want to remove the .git directory from your home directory by running rm -fr ~/.git. Be careful when typing this, as rm removes data without prompting and an unfortunate space could result in all your data being deleted.
Hello this was an issue I had also but in Windows. It was a simple fix, user error. I hadn't used gitbash for awhile so I forgot the process with working in gitbash. First mistake I made was after opening gitbash I directly executed the git status command. That's when I got the "warning: could not open the directory" message. You need to using the cd (change directory) command and the dir (directory) command to navigate to the folder that has the files you want to "git add ." and "git commit -m". Once you get to that folder you will be able to use the "git status" command to see your changes then proceed as normal. I had to post this because it took me hours before I realized what I was doing wrong. No other stack post pointed this obvious user mistake. Hope it helps you.
Related
I am spinning up an instance of rstudio server and I need the working directory of R to be a specific directory. I would also like the file pane in the bottom right corner to be pointing to the same directory. Is there a way to do this? Currently it runs from the home directory of whichever user is running the program. I have tried the --server-working-dir flag, and it does not seem to work. Here is the command I am using:
/usr/lib/rstudio-server/bin/rserver \
--server-daemonize=0 \
--server-user=user \
--server-working-dir=/some/path \
--auth-none=1 \
--auth-minimum-user-id=0
Any help would be useful here.
[edit] Just wanted to clarify that I would like the server to start in this directory. I am building a container that will be deployed multiple times, and I don't want the users to have to set their directories every time it is deployed.
If you want to modify the file pane in the right, you should edit /etc/rstudio/rsession.conf.
And add two lines in below:
session-default-working-dir=/some/path
session-default-new-project-dir=/some/path
You can do this by edditing the (global) R profile startup script. Here's a step by step guide:
1) Run Rscript -e "R.home()" -- this will tell you the location of your R directory home. In my case (Mac) it is /Library/Frameworks/R.framework/Resources
2) Go to /Library/Frameworks/R.framework/Resources/etc -- e.g., $R_HOME/etc
3) sudo touch Rprofile.site if it doesn't exist, then sudo nano Rprofile.site
4) Add the following lines and save:
cat("hi\n")
setwd("/some/path/")
You should avoid overwriting the users home directory.
Amongs the [.Rprofile] files you should only edit the Rprofile.site as a last resort since it acts globally.
Suggested solution:
R read the "initialization file" at start, in the following order:
.Rprofile.site
.Rprofile (located in the current directory).
.Rprofile (in the users home directory).
In your case if you are planning to login to R-Studio server you will end up in the users home directory, so I would suggest you to just edit the [.Rprofile] in the home directory. In case the [.Rprofile] is missing you need to create it.
Add this line in your .Rprofile [in your home directory]:
setwd ('/your/path/')
Logout/login to your R-studio server session and you will notice that the "file pane to the right location" has changed accordingly to what you specified in your .Rprofile.
I'm trying to install Grav on Heroku following the learn.getgrav.org docs.
I've got the web app deployed successfully, however it tells me to bin/grav install.
I do that and it gives me the following output:
ERROR Missing .dependencies file in user/ folder
I do not know what to do at this point as it's happened everytime I've installed Grav.
Hope this will be solved.
Sadly this problem is all too common when copying files :(
hidden (dotted) files are not always copied.
.dependencies
.htaccss
using ls -l -a in the folder where you extracted the files originally Dowloads/grav I could see the files that were not copied to fix it
cp .dependencies .htaccss /var/www/grav/
When I install GRAV on my server each time, I always copy the Zip file to the server, unzip it in place, then remove the zip file - using this method I have never had a problem with the installing of GRAV
HTH Rich
I'm using Sourcetree on OS X. I'm working on a WordPress project. For some reason, changes I make in the 'themes' directory are not being shown as Unstaged files. If I add a test file to /wp-admin/ or /wp-content/ it shows the test file as unstaged. I can't figure out why themes files are not being tracked.
I checked .gitignore and it's empty.
Any help is appreciated. Thanks!
To clarify the question. If SourceTree fails to recognize un-tracked files here are some steps you should take.
Double check that you are not listing the file/directory in .gitignore
Open up a GIT console for that repository and run git status This should show whether any changes are detectable by GIT.
Go to the directory in which you are having problems and look to see if you have any .gitignore files or .git folders. If they exist then deleting them should allow you to add these files to your repository
Caution:
Sometimes having a Repo inside a repo is by design (often referred to as a sub-repository) and could cause issues if removed.
Edit:
I just replicated this scenario with two repos and source tree appeared to see the untracked files once the .git was removed.
Could you open up a terminal window to that themes directory and do an ls -a?
If you use SourceTree, open the terminal and use git add <fileName> -f to force shown any changes in this folder then you can push to Bitbucket
Is it possible to copy Atom from one Mac to another, including all installed packages, settings etc?
There are several ways to synchronize your settings and packages between Atom installations:
Git: Create a public or private Git repo and store the contents of your local ~/.atom folder in there. Ignore the following files/directories in a .gitignore file:
storage
compile-cache
dev
.npm
.node-gyp
Use a package like sync-settings. This will store your configuration in a GitHub Gist.
Dropbox (or similar): Move your ~/.atom folder to your Dropbox folder and then symlink it from there to its original location. This has the downside of syncing everything in ~/.atom, even the things you could ignore.
Use stars to select your favorite packages. On the Atom web site, create an account and mark your favorite packages with stars. Then use apm stars --install to install all starred packages on any machine. Downside: This only works for packages, not for settings.
More details:
https://discuss.atom.io/t/syncing-settings-packages-between-machines/1385
As a user who uses a dotfile management system such as RCM, I prefer independent config files.
For now, Atom doesn't officially provide a packages.cson file to manage plugins, but as the post Syncing settings & packages between machines mentioned, there is a plugin called package-sync that will generate a packages.cson file for us.
So with the help of package-sync, now I can just sync those mininal config files to have my Atom settings and packages consistent across multiple machines.
This is how to do it (Use ubuntu as an example):
Install Atom, and install package-sync through Edit-->Preferences-->Install as the screen shot shows:
Open your command pallete and type: Create Package List and there will be a packages.cson file under your ~/.atom folder.
Edit the gitignore file:
$ gedit ~/.atom/.gitignore
Make sure the content is:
blob-store
compile-cache
dev
storage
.node-gyp
.npm
.apm
packages/
atom-shell/
This is a screenshot of the .gitignore file:
This makes sure the content downloaded by Atom from the Internet will not get synced to your dotfiles repo.
Move the .atom folder to the dotfile repo:
$ mv ~/.atom ~/dotfiles/tag-atom/atom
Relink the folder:
$ ln -s ~/dotfiles/tag-atom/atom ~/.atom
Or if you have rcm installed:
$ rcup
Now go to another machine, and install Atom and package sync. Update your dotfiles repo, and then Open your Atom command pallete and type: sync
Now your Atom settings will get synced and integrated with the RCM dotilfe management system.
This is the files in my ~/.atom folder that get synced:
I recently built a package that syncs automatically your Atom settings and packages across multiple computers. A little bit like the bookmark synchronization mechanism in Google Chrome. It's called atom-package-sync. Maybe it could fit your needs.
You can sync your packages via package-list.txt file and a simple shell script.
Create the package-list.txt file
apm list --installed --bare > package-list.txt
Install missing packages on another host
BASEDIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
INSTALLEd_PKGS=$(apm list --installed --bare)
for PKG in $(cut -f1 -d# $BASEDIR/package-list.txt); do
grep -q $PKG <<< $INSTALLEd_PKGS || apm install $PKG
done
The .atom folder contains the packages folder, which can be rather huge. Unfortunately OneDrive doesn't allow you to exclude folders, so I went with a git option.
I excluded the packages from git and instead I committed a text file containing my packages (my-packages.txt).
To re-install packages I need to run: apm install --packages-file my-packages.txt.
To generate the my-packages.txt, I need something like this on a Bash shell: ls packages | xargs -n 1 echo | cut -d/ -f1 > my-packages.txt
I sync my Atom settings between Windows, macOS, and Linux machines using Resilio Sync Home. It is free and the files are not saved on the "cloud" (like Dropbox or Gists), but it requires that, at least, two machines are online in order to sync the current settings.
I do not want to sync caches, installation specific settings, et al., I update the .sync/IgnoreList file that is created in the synced directory (i.e., the ~/.atom directory). Unfortunately, you will have to update this on each machine that you sync (ironically, the IgnoreList file is not synced). By default, the file specifies various temporary files to be omitted from syncing, so you'll need to add the following:
## Atom-specific
/packages/node-debugger/debugger.log
\packages\node-debugger\debugger.log
/.apm
\.apm
/.node-gyp
\.node-gyp
/.npm
\.npm
/blob-store
\blob-store
/compile-cache
\compile-cache
/dev
\dev
/recovery
\recovery
/split-diff
\split-diff
/storage
\storage
Some of the omitted directories are package-specific (e.g., split-diff). Because Windows has different path delimiters than other platforms, I need to specify both(!!)
Install Resilio Sync Home on your first machine
Add the .atom directory to Resilio to be synced.
Update its IgnoreList file, as shown above. Save this file for the other machines you want to sync with.
Send a Resilio "Read & Write" link of that folder to the other machines you want to sync with or copy the "Read & Write" key to be used on the other machines. To do this, in Resilio's folder view, click on the .atom folder's menu (vertical dots on the right edge) and select "Copy Read & Write key". Save it for later.
Then on your other machines,
Install Resilio Sync Home
Create .atom/.sync
Copy the IgnoreList from your first machine to that directory
Add the .atom directory to be synced with the other machine. You should add the folder using "Enter key or link," then enter the key you copyed, above.
Wait until syncing is done before opening Atom. The first time will may take a few minutes.
Now I don't need to go around installing/removing packages on every machine, separately!
FYI: Changes to files and directories are saved in .sync/Archive, for some period of time, if you should need to recover them.
When attempting to run R, I get this error:
Fatal error: cannot mkdir R_TempDir
I found two possible fixes for this problem by googling around. The first was to ensure my tmp directory didn't contain a load of subdirectories - it doesn't and it's virtually empty. The second fix was to ensure that TMP, TMPDIR, and R_USER in my environment weren't set to non-existent paths - I didn't even have these set. Therefore, I created a tmp directory in my home directory and added it's path to TMP in my environment. I was able to run R once and then I got the fatal error again. Nothing was in the TMP directory that I set in my environment. Does anyone know what else I can try? Thanks.
Dirk is right, but misses a point: If /tmp is full, you can't create subdirectories there. Try
df /tmp
I just hit this on a shared server, where /tmp is mounted on it's own partition, and is shared by many users. In this particular case, you can't really see who's fault it is, because permissions restrict you seeing who is filling up the tmp partition. Basically have to ask the sys admins to figure it out.
Your default temporary directory appears to have the wrong permissions. Here I have
$ ls -ld /tmp
drwxrwxrwt 22 root root 4096 2011-06-10 09:17 /tmp
The key part is 'everybody' can read or write. You need that too. It certainly can contain subdirectories.
Are you running something like AppArmor or SE Linux?
Edit 2011-07-21: As someone just deemed it necessary to downvote this answer -- help(tempfile) is very clear on what values tmpdir (the default directory for temporary files or directories) tries:
By default, 'tmpdir' will be the directory given by 'tempdir()'. This
will be a subdirectory of the temporary directory found by the
following rule. The environment variables 'TMPDIR', 'TMP' and 'TEMP'
are checked in turn and the first found which points to a writable
directory is used: if none succeeds '/tmp' is used.
So my money is on checking those three environment variables. But AppArmor and SELinux have shown to be an issue too on some distributions.
Go to your user directory and create a file called .Renviron and add the following line, save it and reopen RStudio or Rgui or Rterm
TMP = '<path to folder where Everyone has full control>'
This worked with me on Windows 7
If you are running one of the rocker docker images (e.g., rocker/verse), you need to map a local directory to the /tmp directory in the container. For example,
docker run --rm -v ${PWD}/tmp:/tmp -p 8787:8787 -e PASSWORD=password rocker/verse:4.0.4
where ${PWD} for me is ~/devProjs/r, and I created a /tmp directory inside it, so that the container's /tmp is mapped to my ~/devProjs/r/tmp directory.
Just had this issue and finally solved it. Simply a windows permission issue. Go to environment variables and find the location of the temp folders. Then right click on the folder > properties > security > advanced > change everyone to full control > tick "replace all child object permission entries with inheritable permission entries from this object" > Ok > ok.
This will also happen when your computer is completely, utterly out of space. Currently, my Mac has 0 kb free and it's causing this error. Freeing up some space solved the problem.
Check for the user account with which you are launching the RStudio with. Now u check the TMP(System Environment variable) for its location. If the user who is launching RStudio has Write access for those directories you will not face this issue. Being said that you are facing this issue, all you have to do is to change the permissions for that user to have write access on those directories.
Running R on CentOS system and had the same issue. I had to remove all R folders from the tmp directory. Usually all R folders will be in the form of /tmp/Rtmp*****
so i tried to delete the folders from /tmp by running the below.
CD into /tmp directory and run rm -rf Rtmp*
R shell Worked for me afterwards
I had this issue, solution was slightly different. I run R on a linux server - it turned out for me R had made a whole load of tempdirs when running jobs with cron that had hung and not been cleaned up, clogging up the root /tmp directory with ~300 RtmpXXXXXX folders.
Using terminal access, I navigated to the /tmp folder did a recursive find/rm - deleting all of them using this command:
find . -type d -name 'Rtmp*' -exec rm -r -v {} \;
After this, Rstudio took a while to load up, but was once again happy and my scripts began to run again.
You will need the appropriate admin rights for this solution. And always be careful when running rm -r, especially with a find command, as it's easy to remove things unexpectedly.
When it comes to deleting tmp files, make sure that the tmp files are in the server or in local.
If its in the remote, 1st check for the df /tmp in the server or in the remote to see who uses more storage.
Then use rm(file_name)` to remove the files which cause the blocking.
If its in the remote, then use rm /tmp/(file_name)..
MOreover, you can also refer to https://support.rstudio.com/hc/en-us/articles/218730228-Resetting-a-user-s-state-on-RStudio-Server