I got the same issue on julia-0.4.3-win64. It's a problem with windows git 
not dealing with files that have unix file permissions set to 755.

First, you might need to switch to ~/.julia/v0.4/METADATA and abort the 
rebase (git rebase --abort). 

Then, the following patch applied to the METADATA git repo will do the 
trick.

diff --git a/FixedEffectModels/versions/0.1.0/requires 
b/FixedEffectModels/versions/0.1.0/requires
old mode 100755
new mode 100644
diff --git a/FixedEffectModels/versions/0.1.1/requires 
b/FixedEffectModels/versions/0.1.1/requires
old mode 100755
new mode 100644
diff --git a/FixedEffectModels/versions/0.2.0/requires 
b/FixedEffectModels/versions/0.2.0/requires
old mode 100755
new mode 100644
diff --git a/FixedEffectModels/versions/0.2.1/requires 
b/FixedEffectModels/versions/0.2.1/requires
old mode 100755
new mode 100644
diff --git a/FixedEffectModels/versions/0.2.2/requires 
b/FixedEffectModels/versions/0.2.2/requires
old mode 100755
new mode 100644

Cheers,
Alex

On Saturday, February 20, 2016 at 4:56:29 AM UTC+11, Hua Chai wrote:
>
> You're right. 'git diff' does show old mode and new mode. But 'chmod' 
> still didn't work with the old mode number. 
> Looks like the problem is rooted in the fact that Juno currently doesn't 
> support Julia 0.4 (I noticed that from Junolab.org). I downloaded the 
> bundle from Junolab.org instead of Julialang.org and also installed the 
> command line version of Julia. The Pkg.update() problem didn't appear after 
> installation. But now my Julia is only v0.3.
> Hope the next Juno update will support Julia 0.4.
>
> On Fri, Feb 19, 2016 at 10:42 AM, Tony Kelman <[email protected] 
> <javascript:>> wrote:
>
>> When you do "git diff" it should be showing something to the effect of 
>> "old mode," that's what you should try to use for chmod. Check git diff 
>> before and after, and aim to make git diff not say anything.
>>
>> I don't know what's responsible for this but it seems like it may be 
>> specific to Juno somehow?
>
>
>

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