I've also tried
git submodule foreach git pull
It's complaining
Entering 'AmberTools/src/ambertools-binary-build'
You are not currently on a branch. Please specify which
branch you want to merge with. See git-pull(1) for details.
git pull <remote> <branch>
Stopping at 'AmberTools/src/ambertools-binary-build'; script returned
non-zero status.
I can do git pull, again seeing that I'm already up-to-date, and git
checkout master, to see that I'm already on master. I can also go into
AmberTools/src/ambertools-binary-build/ and do
git clone
https://github.com/Amber-MD/ambertools-binary-build.git
to see if that helps. Still no luck. That gets me:
Permission denied (publickey).
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.
Unable to fetch in submodule path 'AmberTools/src/build-bot/ambertools-test'
which is a familiar error.
So, I suppose what I should be trying to do at this point is make a fresh
clone and get its submodules initialized, but I need a protocol for doing
that. What I'm trying to do at the moment is:
git clone gitosis.git.ambermd.org:/amber.git <new amber repo>
cd <new amber repo>/AmberTools/src/build-bot/
git clone
https://github.com/Amber-MD/ambertools-ci.git
cd <new amber repo>/AmberTools/src/ambertools-binary-build/
git clone
https://github.com/Amber-MD/ambertools-binary-build.git
cd <new amber repo>
git pull
git submodule update --init
But, this is not working for various errors shown above.
Dave
On Mon, Jun 12, 2017 at 11:55 AM, David Cerutti <dscerutti.gmail.com> wrote:
> Aha you were pointing me to github. I can clone that repo directly:
>
> git clone https://github.com/Amber-MD/ambertools-ci.git
>
> If I do that within AmberTools/src/build-bot/, I also get a directory
> ambertools-test/ with only a .git file for its contents. Then, if I go
> back to ${AMBERHOME} and do git pull (already up to date), git submodule
> update --init I get:
>
> fatal: Needed a single revision
> Unable to find current revision in submodule path
> 'AmberTools/src/build-bot/ambertools-test'
>
>
>
>
> On Mon, Jun 12, 2017 at 11:39 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>> On Mon, Jun 12, 2017 at 11:32 AM, David Cerutti <dscerutti.gmail.com>
>> wrote:
>>
>> > How should I clone just the one directory?
>>
>>
>> I don't know what you meant here.
>>
>> What's your git version? if it's old, I recommend to update it and retry.
>>
>> Hai
>>
>>
>> > I'm warying of doing a sparse
>> > checkout because all that I see online tends to revolve around cloning a
>> > clean repository with only portions of the original.
>> >
>> > On Mon, Jun 12, 2017 at 11:18 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>> >
>> > > I am not sure why, but that ambertools-test repo was renamed to
>> > > ambertools-ci (https://github.com/Amber-MD/ambertools-ci)
>> > >
>> > > Can you try git clone that repo directly to see if you got the denial?
>> > >
>> > > I will have a look tonight.
>> > > Meanwhile, you can safely ignore that repo to continue your work.
>> > >
>> > > Hai
>> > >
>> > > On Mon, Jun 12, 2017 at 11:08 AM, David Cerutti <dscerutti.gmail.com>
>> > > wrote:
>> > >
>> > > > Hello devs,
>> > > >
>> > > > Has anyone seen this problem? It looks like a git permissions
>> issue,
>> > but
>> > > > that is very odd since I can do a clean
>> > > >
>> > > > git clone gitosis.git.ambermd.org:/amber.git <amber install
>> directory>
>> > > >
>> > > > without problems. However, if I then do
>> > > >
>> > > > git pull
>> > > > git submodule update --init
>> > > >
>> > > > Submodule 'AmberTools/src/ambertools-binary-build' (
>> > > > https://github.com/Amber-MD/ambertools-binary-build) registered for
>> > path
>> > > > 'AmberTools/src/ambertools-binary-build'
>> > > > Submodule 'AmberTools/src/build-bot/ambertools-test'
>> > > > (git.github.com:Amber-MD/ambertools-test)
>> > > > registered for path 'AmberTools/src/build-bot/ambertools-test'
>> > > > Submodule 'AmberTools/src/build-bot/docker-amber-build-box'
>> > > > (git.github.com:Amber-MD/docker-amber-build-box)
>> > > > registered for path 'AmberTools/src/build-bot/dock
>> er-amber-build-box'
>> > > > Submodule 'AmberTools/src/cphstats' (git.github.com:/Amber-MD/
>> > > > cphstats.git)
>> > > > registered for path 'AmberTools/src/cphstats'
>> > > > Submodule 'AmberTools/src/cpptraj' (git.github.com:/Amber-MD/
>> > > cpptraj.git)
>> > > > registered for path 'AmberTools/src/cpptraj'
>> > > > Submodule 'AmberTools/src/parmed' (git.github.com:/ParmEd/ParmEd
>> .git)
>> > > > registered for path 'AmberTools/src/parmed'
>> > > > Submodule 'AmberTools/src/pdb4amber' (git.github.com:/Amber-MD/
>> > > pdb4amber)
>> > > > registered for path 'AmberTools/src/pdb4amber'
>> > > > Submodule 'AmberTools/src/pytraj' (git.github.com:/Amber-MD/
>> > pytraj.git)
>> > > > registered for path 'AmberTools/src/pytraj'
>> > > > Cloning into 'AmberTools/src/ambertools-binary-build'...
>> > > > remote: Counting objects: 1700, done.
>> > > > remote: Compressing objects: 100% (71/71), done.
>> > > > remote: Total 1700 (delta 60), reused 65 (delta 32), pack-reused
>> 1597
>> > > > Receiving objects: 100% (1700/1700), 246.98 KiB, done.
>> > > > Resolving deltas: 100% (1012/1012), done.
>> > > > Submodule path 'AmberTools/src/ambertools-binary-build': checked
>> out
>> > > > '18c419831a106b836ed60bf2296c241a44a4714e'
>> > > > Cloning into 'AmberTools/src/build-bot/ambertools-test'...
>> > > > Permission denied (publickey).
>> > > > fatal: Could not read from remote repository.
>> > > >
>> > > > Please make sure you have the correct access rights
>> > > > and the repository exists.
>> > > > Clone of 'git.github.com:Amber-MD/ambertools-test' into submodule
>> path
>> > > > 'AmberTools/src/build-bot/ambertools-test' failed
>> > > > [cerutti.casegroup1 amber3]$ ls AmberTools/src/build-bot/
>> > > >
>> > > > It looks like a permissions issue, but I'm not certain. The
>> directory
>> > > > AmberTools/src/build-bot/ certainly exists, and I'm assuming that it
>> > > wants
>> > > > to clone a new directory ambertools-test/ into that, but at present
>> I
>> > > don't
>> > > > see ambertools-test/. I've been trying to clone a new repo because
>> > I've
>> > > > been having this same problem when I try to update the current repo
>> > I've
>> > > > been working in. Am I missing something obvious?
>> > > >
>> > > > Thanks!
>> > > >
>> > > > Dave
>> > > > _______________________________________________
>> > > > AMBER-Developers mailing list
>> > > > AMBER-Developers.ambermd.org
>> > > > http://lists.ambermd.org/mailman/listinfo/amber-developers
>> > > >
>> > > _______________________________________________
>> > > AMBER-Developers mailing list
>> > > AMBER-Developers.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber-developers
>> > >
>> > _______________________________________________
>> > AMBER-Developers mailing list
>> > AMBER-Developers.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>> >
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
>
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Received on Mon Jun 12 2017 - 10:00:02 PDT
