#673 Avogadro Squared: openbabel reference is not a tree



I've tried to build Avogadro on a Scientific Linux 6 machine with git, cmake,... installed using "Avogadro Squared", as there are no binaries for SL. During the basic cloning process

git clone --recursive git://github.com/cryos/avogadro-squared.git

I stumble upon the following error:

Initialized empty Git repository in /home/pvme/src/avogadro-squared/openbabel/.git/
remote: Counting objects: 39465, done.
remote: Compressing objects: 100% (7176/7176), done.
remote: Total 39465 (delta 32101), reused 39394 (delta 32060)
Receiving objects: 100% (39465/39465), 30.25 MiB | 211 KiB/s, done.
Resolving deltas: 100% (32101/32101), done.
fatal: reference is not a tree: 2d41e95c6c94d8eab39ddc3459f990b47fcf2e51
Unable to checkout '2d41e95c6c94d8eab39ddc3459f990b47fcf2e51' in submodule path 'openbabel'

If I interpret the error correctly, the outer repository has a reference to a commit in the submodule that someone did not push up yet.

Can someone give me a hint, if I messed something up, or simply push up the commit?

Thanks in advance,


  • Geoff Hutchison

    Geoff Hutchison - 2013-09-21
    • assigned_to: Marcus D. Hanwell
  • Geoff Hutchison

    Geoff Hutchison - 2013-09-21

    Marcus, can you comment on this? I suspect avogadro-squared and similar repos need to point at the new openbabel/openbabel git repository.

  • Anonymous - 2013-10-26

    This is still a problem. I just had this same problem on a CentOS 5.10 machine.


  • Anonymous - 2014-01-15

    i am having the same problem. may i know if this has been resolved? thank you

  • Debanjan Basu

    Debanjan Basu - 2014-03-14

    I tried to clone avogadro-squared and saw the same problem. This ticket should have been closed by now!

  • Geoff Hutchison

    Geoff Hutchison - 2016-04-26
    • status: open --> closed


Cancel  Add attachments

Get latest updates about Open Source Projects, Conferences and News.

Sign up for the SourceForge newsletter:

No, thanks