sci-visus/OpenVisus

Cannot initialize submodule idx2

rahatzamancse opened this issue · 11 comments

rahatzamancse commented

While recursively cloning this repo, or initializing Libs/idx2 submodule later, I get the following error:

Cloning into 'OpenVisus'...
remote: Enumerating objects: 27627, done.
remote: Counting objects: 100% (3969/3969), done.
remote: Compressing objects: 100% (1498/1498), done.
remote: Total 27627 (delta 2443), reused 3746 (delta 2310), pack-reused 23658
Receiving objects: 100% (27627/27627), 127.49 MiB | 4.41 MiB/s, done.
Resolving deltas: 100% (18591/18591), done.
Submodule 'Libs/IDX2' (git@github.com:sci-visus/IDX2.git) registered for path 'Libs/IDX2'
Cloning into '/home/insane/Utah/ksdjf/OpenVisus/Libs/IDX2'...
git@github.com: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
fatal: clone of 'git@github.com:sci-visus/IDX2.git' into submodule path '/home/insane/Utah/ksdjf/OpenVisus/Libs/IDX2' failed
Failed to clone 'Libs/IDX2'. Retry scheduled
Cloning into '/home/insane/Utah/ksdjf/OpenVisus/Libs/IDX2'...
git@github.com: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
fatal: clone of 'git@github.com:sci-visus/IDX2.git' into submodule path '/home/insane/Utah/ksdjf/OpenVisus/Libs/IDX2' failed
Failed to clone 'Libs/IDX2' a second time, aborting

I think it is because a wrong branch of idx2 named abdbc8daa1 is used, but there exists no such branch in origin. Should I create a PR with relinking idx2 with the master branch?

amygooch commented
rahatzamancse commented

@amygooch I don't think it is related to my GitHub account token. I am just using git (not github cli: gh) and just cloning a public repo. Also, I can clone many other public repos with submodules in them.

rahatzamancse commented

Another thing I have noticed is that Binder is also not working. I think it is for the very same reason that Binder cannot properly clone the repo due to not being able to find the HEAD. Here's Binder's log:

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockerta6ikfxa'...
Updating files: 100% (3493/3493), done.
HEAD is now at 3cf04d6e Fixing python3.9 for windows
Submodule 'Libs/IDX2' (git@github.com:sci-visus/IDX2.git) registered for path 'Libs/IDX2'
Cloning into '/tmp/repo2dockerta6ikfxa/Libs/IDX2'...
error: cannot run ssh: No such file or directory
fatal: unable to fork
fatal: clone of 'git@github.com:sci-visus/IDX2.git' into submodule path '/tmp/repo2dockerta6ikfxa/Libs/IDX2' failed
Failed to clone 'Libs/IDX2'. Retry scheduled
Cloning into '/tmp/repo2dockerta6ikfxa/Libs/IDX2'...
error: cannot run ssh: No such file or directory
fatal: unable to fork
fatal: clone of 'git@github.com:sci-visus/IDX2.git' into submodule path '/tmp/repo2dockerta6ikfxa/Libs/IDX2' failed
Failed to clone 'Libs/IDX2' a second time, aborting
Error during build: Command '['git', 'submodule', 'update', '--init', '--recursive']' returned non-zero exit status 1.
scrgiorgio commented
rahatzamancse commented

Nope having save error.

I did not receive any invitation though. Did you send it to this GitHub account (rahatzamancse@gmail.com or @rahatzamancse)?

And as I said, I do not think it is related to my account (as all these repos are public).

Does the recursive cloning work on your end? @scrgiorgio @amygooch

git clone --recursive https://github.com/sci-visus/OpenVisus.git

please try now (I've sent you an invitation to join sci repositories as a "writer")
…
On Thu, Sep 15, 2022 at 9:58 AM Rahat Zaman @.> wrote: Another thing I have noticed is that Binder is also not working. I think it is for the very same reason that Binder cannot properly clone the repo due to not being able to find the HEAD. Here's Binder's log: Waiting for build to start... Picked Git content provider. Cloning into '/tmp/repo2dockerta6ikfxa'... Updating files: 100% (3493/3493), done. HEAD is now at 3cf04d6 Fixing python3.9 for windows Submodule 'Libs/IDX2' @.:sci-visus/IDX2.git) registered for path 'Libs/IDX2' Cloning into '/tmp/repo2dockerta6ikfxa/Libs/IDX2'... error: cannot run ssh: No such file or directory fatal: unable to fork fatal: clone of @.:sci-visus/IDX2.git' into submodule path '/tmp/repo2dockerta6ikfxa/Libs/IDX2' failed Failed to clone 'Libs/IDX2'. Retry scheduled Cloning into '/tmp/repo2dockerta6ikfxa/Libs/IDX2'... error: cannot run ssh: No such file or directory fatal: unable to fork fatal: clone of @.:sci-visus/IDX2.git' into submodule path '/tmp/repo2dockerta6ikfxa/Libs/IDX2' failed Failed to clone 'Libs/IDX2' a second time, aborting Error during build: Command '['git', 'submodule', 'update', '--init', '--recursive']' returned non-zero exit status 1. — Reply to this email directly, view it on GitHub <#196 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTZP6CGNNEGIQ3LBWAEUTV6NBRJANCNFSM6AAAAAAQNQS33E . You are receiving this because you are subscribed to this thread.Message ID: @.***>
-- Giorgio Scorzelli Director of Software Development - Center for Extreme Data Management, Analysis and Visualization (CEDMAV) Director of Software Development - National Science Data Fabric (NSDF)

scrgiorgio commented
amygooch commented
rahatzamancse commented

Ok, I figured out the problem. It was because the idx2 origin was set to the ssh link (not the HTTPS link) in .gitmodules file. So either I had to have an unexpired ssh token setup to GitHub, or change the URL of idx2 submodule in .gitmodules. Then it works!

rahatzamancse commented

Although this issue is solved, but I would still recommend to use HTTPS link for submodules so that Binder can work.

scrgiorgio commented
rahatzamancse commented

This solved the git cloning issue of binder. But the conda installation issue persists. Maybe I will create a new issue for conda installation problem later.