system() command does not return git output

[shinyrhino]

Hi, I am generating a markdown page in a shiny app to document the version of the code I am using:

remote.url <- system("git config --get remote.origin.url", intern=TRUE)
cat("GIT Repository (public):\n", remote.url, "\n")

which previously worked perfectly. However, the output I get now is:

## Warning in system("git config --get remote.origin.url", intern = TRUE):
## running command 'git config --get remote.origin.url' had status 1

However, when I run the git command "git config --get remote.origin.url" in the bash terminal in the folder of the shiny server (/srv/shiny-server/dhub/), I get the expected output:

git config --get remote.origin.url
Bitbucket

The only recent change was an upgrade to R version 4.4.1 from some previous 4.x.x version.

Any advice to get the correct output via the system command in R?

Kr, Shiny

[pieterjanvc]

Hi,

My first guess would be that during execution the working directory is not the project root folder and thus the git project cannot be found.

Maybe try and use system("git -C <path> config --get remote.origin.url", intern=TRUE) and provide the project folder path where git is.

Hope this helps,
PJ

[shinyrhino]

Dear @pieterjanvc ,

thanks, your advice was half of the solution! I had to set the correct working directory as you suggested because the markdown file was in a sub-directory.

However, it seems that there was also an issue with dubious ownership. Since I run git commands in the shiny app (ie as "shiny" user), but I cloned the repo as a different user , eg "devusr", git chokes.

I could replicate the error by logging in as "shiny" user with sudo su shiny and executing the git commands.

Git itself noted the problem and suggested as a solution to add an exception:

"git config --global --add safe.directory /srv/shiny-server/dhub"

However, this did not fix the problem either.

Following, this advice [1], I tried:

git config --system --add safe.directory '*'

which finally fixed the problem!

However, I am not 100% sure what the security implications are and whether there is a better solution.

Comments welcome!

Kr, Shiny

Refs:
[1] https://community.atlassian.com/t5/Bitbucket-questions/Getting-code-128-fatal-detected-dubious-ownership-in-repository/qaq-p/2373506