git_clone: error authenticating: failed connecting with agent

[pat-s]

OS: Arch Linux

Using git2r in usethis::create_from_github():

Error in git2r::clone(origin_url, normalizePath(repo_path, mustWork = FALSE),  : 
  Error in 'git2r_clone': error authenticating: failed connecting with agent

However, when specifying the credentials explicitly, everything works:

cred <- git2r::cred_ssh_key(
     publickey = "~/.ssh/id_rsa.pub",
     privatekey = "~/.ssh/id_rsa"
usethis::create_from_github("<repo>", destdir = "~/git", credentials = cred)

My ssh-agent is running and I've added the ssh key to the agent.

ssh-agent
SSH_AUTH_SOCK=/tmp/ssh-BAHgeA39uy66/agent.6961; export SSH_AUTH_SOCK;
SSH_AGENT_PID=6962; export SSH_AGENT_PID;
echo Agent pid 6962;

[pat-s]

Update:

I specifically set $USERPROFILE as recommended in http://happygitwithr.com/ssh-keys.html#git2r-or-some-other-tool-cant-find-ssh-keys-on-windows. It was empty before.

Now I see:

as.list(Sys.getenv(
+     c("HOME", "USERPROFILE")
+ ))
$HOME
[1] "/home/pjs"

$USERPROFILE
[1] "/home/pjs"

list.files(
+     Sys.getenv("USERPROFILE"),
+     pattern = "ssh|git",
+     include.dirs = TRUE,
+     all.files = TRUE
+ )
[1] ".clusterssh" ".gitconfig"  ".ssh"        "git" 

but it still does not work.

[jennybc]

I don't think USERPROFILE will have any effect on Linux.

Is your SSH key protected by a passphrase?

[pat-s]

Hi Jenny,
No protection of my keys. They have the standard 600 permission value for ssh keys.

_{Sent with GitHawk}

[pat-s]

@jennybc I just tackled this issue again and came across a solution that worked for me on Arch.

So while you propose that credentials = NULL triggers a search for the default running ssh-agent, I found that

cred_ssh_key()
$publickey
[1] "/home/pjs/.ssh/id_rsa.pub"

$privatekey
[1] "/home/pjs/.ssh/id_rsa"

$passphrase
character(0)

attr(,"class")
[1] "cred_ssh_key"

does its job as expected. As you state in #357 we do not really know what lib2git really does in the background? So why not just rely on cred_ssh_key() and if that function returns the correct ssh paths, everythings fine?

If create_from_github() would use credentials = cred_ssh_key() instead of credentials = NULL, everything would work perfectly for me.

Now ofc I do not know if this also helps in Windows or on any other OS but for Arch (maybe Linux in general?) it looks like a valid approach.

[jennybc]

So why not just rely on cred_ssh_key() and if that function returns the correct ssh paths, everythings fine?

This aspect of git2r has been changing a lot, as a result of all this credential-finding pain, and what I said in March does not necessarily hold today. And, as you say, it varies by OS. Last I checked, my ssh keys still aren't found on Windows.

[pat-s]

But if they will be found one day, cred_ssh_key() will probably also return them correctly.

So for now, cred_ssh_key() seems to work on Arch (maybe other Linux or even UNIX OS) while credentials = NULL does not. So changing from credentials = NULL to credentials = cred_ssh_key() could solve some issues for users, even if behavior may change again.

Is there a point that would speak against this change?

[jennybc]

Is there a point that would speak against this change?

I've just tested that on Windows and Mac. I think this will come down to whether people have a passphrase-protected SSH key. On Windows, I do not and the current behaviour of git2r::cred_ssh_key() does seem to find my keys, for the first time ever 🎉. On Mac, though, I do have a passphrase and the ssh agent is configured to manage it. So an explicit call to git2r::cred_ssh_key() results in a passphrase challenge, which is a drag.

We'll also need to think through the workflow for someone using https, i.e. make sure there is no attempt to call git2r::cred_ssh_key(). But I agree that the hope of having the git2r bits of usethis "just work" is looking brighter.

[pat-s]

Great! Looking forward to future enhancements. I love create_from_github() and other usethis funtions so much. Thanks!

[pat-s]

After all this time, it seems that I finally managed to set up the SSH stuff the right way so the SSH keys are automatically recognized.

For Linux, specifically Arch Linux, I am now using the keychain library.

Surely this more of a niche user group but maybe its worth adding it as a quick link/note somewhere in "Happy Gith with R" or elsewhere.

Setup:

1. Install keychain
2. Put the respective line for your shell into .bashrc/fish.config/etc (see below)

From man keychain:

 This snippet should work in most shells to load two ssh keys and one gpg key:

           eval `keychain --eval id_rsa id_dsa 0123ABCD`

       For the fish shell, use the following format:

           if status --is-interactive
               keychain --eval --quiet -Q id_rsa | source
           end

       If you have trouble with that in csh:

           setenv SHELL /bin/csh
           eval `keychain --eval id_rsa id_dsa 0123ABCD`

       This is equivalent for Bourne shells (including bash and zsh) but doesn't use keychain's
       --eval feature:

           keychain id_rsa id_dsa 0123ABCD
           [ -z "$HOSTNAME" ] && HOSTNAME=`uname -n`
           [ -f $HOME/.keychain/$HOSTNAME-sh ] && \
                   . $HOME/.keychain/$HOSTNAME-sh
           [ -f $HOME/.keychain/$HOSTNAME-sh-gpg ] && \
                   . $HOME/.keychain/$HOSTNAME-sh-gpg