Corruption of branch?

Corruption of branch?

[Thomas Nyberg]

Hello,

I have a repository (which I unfortunately cannot provide access to) 
which is having some odd things happening with one (and only one) of its 
branches. This workflow repeats the issue (here `bad_branch` is one of 
the remotes branches; i.e. `origin/bad_branch`):

(1) clone the repository
(2) git checkout `bad_branch`

Basically nothing happens. Nothing is printed and I stay on the master 
branch. I also checked $? and there is no error code that is set. If I 
choose any of other branches, it correctly creates a local branch, sets 
it to track the remote and then switches to the local branch.

It seems like there could be some sort of weird bug in the checkout or 
possibly somehow some corruption in the actual object tree. From my 
vantage point, however, the data appears totally fine. For example, in 
`.git/packed-refs` everything appears normal and if I explicitly 
checkout the commit IDs directly (i.e. just copy the commit 
corresponding to refs/remotes/origin/bad_branch and checkout $commit) it 
checks out fine. If I do this with the bad_branch I get a detached HEAD 
as expected and git log lists the commits that it should.

This seems a bit odd to me. There's certainly some sort of error 
somewhere, but it's passing silently. I'm not really sure how to debug 
this and it's too bad I can't actually link the actual repository. I 
presume if I have the time I could try compiling git from source and 
seeing if it still shows up. I tested it on the following two versions 
of git get the same error:

* 1.9.1 (installed as a package from Linux Mint 17.2 Rafaela)
* 2.1.4 (installed as a package from Debian Jessie 8.2)

Also I should note that the original repository is hosted on Github.

Thanks for any help. Hopefully the fact that I can't provide enough 
information for others to reproduce the issue isn't too large a bother...

Cheers,
Thomas Nyberg

Re: Corruption of branch?

[Stefan Beller]

On Mon, Dec 14, 2015 at 9:40 AM, Thomas Nyberg <tomnyberg@gmail.com> wrote:
> Hello,
>
> I have a repository (which I unfortunately cannot provide access to) which
> is having some odd things happening with one (and only one) of its branches.
> This workflow repeats the issue (here `bad_branch` is one of the remotes
> branches; i.e. `origin/bad_branch`):
>
> (1) clone the repository
> (2) git checkout `bad_branch`
>
> Basically nothing happens. Nothing is printed and I stay on the master
> branch. I also checked $? and there is no error code that is set. If I
> choose any of other branches, it correctly creates a local branch, sets it
> to track the remote and then switches to the local branch.

Does that branch have a funny name? (i.e. is it ASCII only? Or is it
also utf8 characters?
Does it have some special characters in it like points, colons,
question marks etc)

Does it happen only with a single sha1 or can you apply commits on top
of that branch
and the error condition persists?

>
> It seems like there could be some sort of weird bug in the checkout or
> possibly somehow some corruption in the actual object tree. From my vantage
> point, however, the data appears totally fine. For example, in
> `.git/packed-refs` everything appears normal and if I explicitly checkout
> the commit IDs directly (i.e. just copy the commit corresponding to
> refs/remotes/origin/bad_branch and checkout $commit) it checks out fine. If
> I do this with the bad_branch I get a detached HEAD as expected and git log
> lists the commits that it should.
>
> This seems a bit odd to me. There's certainly some sort of error somewhere,
> but it's passing silently. I'm not really sure how to debug this and it's
> too bad I can't actually link the actual repository. I presume if I have the
> time I could try compiling git from source and seeing if it still shows up.
> I tested it on the following two versions of git get the same error:
>
> * 1.9.1 (installed as a package from Linux Mint 17.2 Rafaela)
> * 2.1.4 (installed as a package from Debian Jessie 8.2)

The refs handling code is in flux at the moment. (starting mid of last
year actually)
I cc'd people who did work recently on the file refs.c

So I think trying with a new version of Git would be a valuable datapoint!

>
> Also I should note that the original repository is hosted on Github.
>
> Thanks for any help. Hopefully the fact that I can't provide enough
> information for others to reproduce the issue isn't too large a bother...
>
> Cheers,
> Thomas Nyberg
> --
> To unsubscribe from this list: send the line "unsubscribe git" in
> the body of a message to majordomo@vger.kernel.org
> More majordomo info at  http://vger.kernel.org/majordomo-info.html

Re: Corruption of branch?

[Thomas Nyberg]

Hi Stefan thanks for much for the response! So I compiled release 
version 2.6.4 as well as the current master branch on the git git 
repository (2.7.0.rc0.20.g4b9ab0e) and the problem persists on both.

To answer your questions, there are no weird characters. The name of the 
bad_branch is "frus". There is another branch called 
"frus_body_cleaning" that is totally fine.

As to whether the error continues after commits, the answer is no which 
is good. I.e. if I run `git checkout -b frus origin/frus` that works 
fine. I then decided to checkout a new branch (so as to not mess with 
the original branch and possibly turning this into a Heisenbug) and add 
a test commit which I pushed upstream. I then recloned the repository 
and was able to checkout this new branch just fine, but I still couldn't 
check out the original frus branch using the simplified command.

So of course on the practical side, I have a fix which is to just use 
`git checkout -b frus origin/frus` (apparently only this one time) and 
then be on my merry way (in fact I had only just broken myself of the 
habit typing it this older way after many versions of the newer simpler 
syntax), but it seems like it could be good to sort out what's going on 
here...

Thanks again for the response!

Cheers,
Thomas

On 12/14/2015 12:51 PM, Stefan Beller wrote:
> On Mon, Dec 14, 2015 at 9:40 AM, Thomas Nyberg <tomnyberg@gmail.com> wrote:
>> Hello,
>>
>> I have a repository (which I unfortunately cannot provide access to) which
>> is having some odd things happening with one (and only one) of its branches.
>> This workflow repeats the issue (here `bad_branch` is one of the remotes
>> branches; i.e. `origin/bad_branch`):
>>
>> (1) clone the repository
>> (2) git checkout `bad_branch`
>>
>> Basically nothing happens. Nothing is printed and I stay on the master
>> branch. I also checked $? and there is no error code that is set. If I
>> choose any of other branches, it correctly creates a local branch, sets it
>> to track the remote and then switches to the local branch.
>
> Does that branch have a funny name? (i.e. is it ASCII only? Or is it
> also utf8 characters?
> Does it have some special characters in it like points, colons,
> question marks etc)
>
> Does it happen only with a single sha1 or can you apply commits on top
> of that branch
> and the error condition persists?
>
>>
>> It seems like there could be some sort of weird bug in the checkout or
>> possibly somehow some corruption in the actual object tree. From my vantage
>> point, however, the data appears totally fine. For example, in
>> `.git/packed-refs` everything appears normal and if I explicitly checkout
>> the commit IDs directly (i.e. just copy the commit corresponding to
>> refs/remotes/origin/bad_branch and checkout $commit) it checks out fine. If
>> I do this with the bad_branch I get a detached HEAD as expected and git log
>> lists the commits that it should.
>>
>> This seems a bit odd to me. There's certainly some sort of error somewhere,
>> but it's passing silently. I'm not really sure how to debug this and it's
>> too bad I can't actually link the actual repository. I presume if I have the
>> time I could try compiling git from source and seeing if it still shows up.
>> I tested it on the following two versions of git get the same error:
>>
>> * 1.9.1 (installed as a package from Linux Mint 17.2 Rafaela)
>> * 2.1.4 (installed as a package from Debian Jessie 8.2)
>
> The refs handling code is in flux at the moment. (starting mid of last
> year actually)
> I cc'd people who did work recently on the file refs.c
>
> So I think trying with a new version of Git would be a valuable datapoint!
>
>>
>> Also I should note that the original repository is hosted on Github.
>>
>> Thanks for any help. Hopefully the fact that I can't provide enough
>> information for others to reproduce the issue isn't too large a bother...
>>
>> Cheers,
>> Thomas Nyberg
>> --
>> To unsubscribe from this list: send the line "unsubscribe git" in
>> the body of a message to majordomo@vger.kernel.org
>> More majordomo info at  http://vger.kernel.org/majordomo-info.html

Re: Corruption of branch?

[David Turner]

On Mon, 2015-12-14 at 13:08 -0500, Thomas Nyberg wrote:
> Hi Stefan thanks for much for the response! So I compiled release 
> version 2.6.4 as well as the current master branch on the git git 
> repository (2.7.0.rc0.20.g4b9ab0e) and the problem persists on both.
> 
> To answer your questions, there are no weird characters. The name of the 
> bad_branch is "frus". There is another branch called 
> "frus_body_cleaning" that is totally fine.

What's in .git/config under [branch "frus"] (if anything)?

What does "grep refs/heads/frus .git/packed-refs" say?  What about
find .git -name frus ?

Sorry for the possibly-stupid questions, but I'm really baffled by this
one.

Re: Corruption of branch?

[Thomas Nyberg]

In the .git/config there is no [branch "frus"] section. At first this is 
expected (i.e. cleaning cloning), but nothing changes when I execute 
`git checkout frus`. When I execute `git checkout frus_body_cleaning` 
that gets added to .git/config as expected.

.git/refs/heads contains two files "master" and "frus_body_cleaning" 
pointing to their respective commits, but there is nothing else there. 
here's the other command

$ grep frus packed-refs
3a1dbe48299f6eda1cc4b69cab35284c0f0355eb refs/remotes/origin/frus
1750cba5a94b3fe6041aaf49de430a558a3b9bc8 
refs/remotes/origin/frus_body_cleaning

So here frus actually is showing up. The find command isn't working 
either. I changed it to add the * but only shows the frus_body_cleaning 
branch:

$ find .git -name 'frus*'
.git/logs/refs/heads/frus_body_cleaning
.git/refs/heads/frus_body_cleaning

So yeah this is pretty weird. I'm guessing you're looking for name 
collisions of some kind? I had the idea that the problem might that too 
and used git show-index to look for all objects, but none of them have 
frus in them (I thought that maybe if the sha of one of them started 
with "frus" that would explain it but no dice). Since the command `git 
checkout -b frus origin/frus` works, it seems to me like somehow git is 
getting confused going from the `git checkout frus` command to that 
expanded one.

It is pretty baffling.

On 12/14/2015 02:20 PM, David Turner wrote:
> On Mon, 2015-12-14 at 13:08 -0500, Thomas Nyberg wrote:
>> Hi Stefan thanks for much for the response! So I compiled release
>> version 2.6.4 as well as the current master branch on the git git
>> repository (2.7.0.rc0.20.g4b9ab0e) and the problem persists on both.
>>
>> To answer your questions, there are no weird characters. The name of the
>> bad_branch is "frus". There is another branch called
>> "frus_body_cleaning" that is totally fine.
>
> What's in .git/config under [branch "frus"] (if anything)?
>
> What does "grep refs/heads/frus .git/packed-refs" say?  What about
> find .git -name frus ?
>
> Sorry for the possibly-stupid questions, but I'm really baffled by this
> one.
>

Re: Corruption of branch?

[Dennis Kaarsemaker]

On ma, 2015-12-14 at 14:59 -0500, Thomas Nyberg wrote:
> I'm guessing you're looking for namecollisions of some kind?

I was thinking the same. Can you share the (sanitised) output of 

git for-each-ref?

-- 
Dennis Kaarsemaker
www.kaarsemaker.net

Re: Corruption of branch?

[Thomas Nyberg]

What exactly are you looking for? Here's the results of the following 
command:

$ git for-each-ref | grep frus
1750cba5a94b3fe6041aaf49de430a558a3b9bc8 commit 
refs/heads/frus_body_cleaning
3a1dbe48299f6eda1cc4b69cab35284c0f0355eb commit	refs/remotes/origin/frus
1750cba5a94b3fe6041aaf49de430a558a3b9bc8 commit 
refs/remotes/origin/frus_body_cleaning

Sorry if this isn't what you're looking for. I'm actually not very 
familiar with these different internal git commands...

Regardless this looks to me exactly like what I'd expect given the 
current situation...it's as if I never checked out the "frus" branch at 
all (which I suppose is true since this is a fresh copy and "git 
checkout frus" didn't do anything).

Btw after checking out explicitly with `git checkout -b frus 
origin/frus`, things look as I'd expect.

$ git for-each-ref | grep frus
3a1dbe48299f6eda1cc4b69cab35284c0f0355eb commit	refs/heads/frus
1750cba5a94b3fe6041aaf49de430a558a3b9bc8 commit 
refs/heads/frus_body_cleaning
3a1dbe48299f6eda1cc4b69cab35284c0f0355eb commit	refs/remotes/origin/frus
1750cba5a94b3fe6041aaf49de430a558a3b9bc8 commit 
refs/remotes/origin/frus_body_cleaning

Btw just to test things a little more I deleted both the frus and 
frus_body_cleaning branches and tried to recheck them out, but the 
problem still persists.

Cheers,
Thomas

On 12/14/2015 03:18 PM, Dennis Kaarsemaker wrote:
> On ma, 2015-12-14 at 14:59 -0500, Thomas Nyberg wrote:
>> I'm guessing you're looking for namecollisions of some kind?
>
> I was thinking the same. Can you share the (sanitised) output of
>
> git for-each-ref?
>

Re: Corruption of branch?

[Dennis Kaarsemaker]

On ma, 2015-12-14 at 15:33 -0500, Thomas Nyberg wrote:
> What exactly are you looking for? Here's the results of the following
> command:
> 
> $ git for-each-ref | grep frus
> 1750cba5a94b3fe6041aaf49de430a558a3b9bc8 commit 
> refs/heads/frus_body_cleaning
> 3a1dbe48299f6eda1cc4b69cab35284c0f0355eb commit	refs/remotes/o
> rigin/frus
> 1750cba5a94b3fe6041aaf49de430a558a3b9bc8 commit 
> refs/remotes/origin/frus_body_cleaning
> 
> Sorry if this isn't what you're looking for. I'm actually not very 
> familiar with these different internal git commands...

This is what I was looking for. Unfortunately it doesn't show any of
the smoking guns I had hoped for.

That leaves only one option: you also have a file or directory named
'frus' in the root of your repository. In this case 'git checkout frus'
does the same as 'git checkout -- frus' instead of DWIM'ing 'git
checkout frus' to 'git checkout -b frus origin/frus'

-- 
Dennis Kaarsemaker
www.kaarsemaker.net

Re: Corruption of branch?

[Junio C Hamano]

Dennis Kaarsemaker <dennis@kaarsemaker.net> writes:

> That leaves only one option: you also have a file or directory named
> 'frus' in the root of your repository. In this case 'git checkout frus'
> does the same as 'git checkout -- frus' instead of DWIM'ing 'git
> checkout frus' to 'git checkout -b frus origin/frus'

;-)  That would be my guess.

Re: Corruption of branch?

[Thomas Nyberg]

wow right on the button. yeah i have the "frus" folder in the root of my 
repository. i never knew that git checkout also searches the root of the 
repository like that. it appears i'm a fool who doesn't read 
documentation...

i learned something knew and can move this from the "bizarre index 
corruption" category to the "user error" category. thanks so much everyone!

On 12/14/2015 03:40 PM, Dennis Kaarsemaker wrote:
> On ma, 2015-12-14 at 15:33 -0500, Thomas Nyberg wrote:
>> What exactly are you looking for? Here's the results of the following
>> command:
>>
>> $ git for-each-ref | grep frus
>> 1750cba5a94b3fe6041aaf49de430a558a3b9bc8 commit
>> refs/heads/frus_body_cleaning
>> 3a1dbe48299f6eda1cc4b69cab35284c0f0355eb commit	refs/remotes/o
>> rigin/frus
>> 1750cba5a94b3fe6041aaf49de430a558a3b9bc8 commit
>> refs/remotes/origin/frus_body_cleaning
>>
>> Sorry if this isn't what you're looking for. I'm actually not very
>> familiar with these different internal git commands...
>
> This is what I was looking for. Unfortunately it doesn't show any of
> the smoking guns I had hoped for.
>
> That leaves only one option: you also have a file or directory named
> 'frus' in the root of your repository. In this case 'git checkout frus'
> does the same as 'git checkout -- frus' instead of DWIM'ing 'git
> checkout frus' to 'git checkout -b frus origin/frus'
>