And it looks like for some reasons the content for Babel is not synced:
fbissey@Mirage ~/Gentoo $ ll usr/portage/dev-python/babel
total 20K
drwxr-xr-x    5 fbissey staff  170 Jun  5 10:17 .
drwxr-xr-x 1409 fbissey staff  47K May 31 00:01 ..
-rw-r--r--    1 fbissey staff 8.4K Jun  4 19:33 ChangeLog
-rw-r--r--    1 fbissey staff 2.9K Jun  4 19:33 Manifest
-rw-r--r--    1 fbissey staff  617 Jun  4 19:33 metadata.xml

scp-ing the stuff from a regular box is temporarily fixing the 
problem. We’ll see what happens next time I synced.

François

> On 5/06/2015, at 12:50, Francois Bissey <[email protected]> 
> wrote:
> 
> It looks like it is just the dev-python/Babel ebuild as far as I can see.
> I used to be happy on a case insensitive file system myself but
> I have the above as a dependency of something else and this is fun:
> 
> fbissey@Mirage ~/Gentoo $ emerge -puDNv dev-python/babel
> 
> These are the packages that would be merged, in order:
> 
> Calculating dependencies... done!
> 
> emerge: there are no ebuilds to satisfy "dev-python/babel".
> 
> emerge: searching for similar names...
> emerge: Maybe you meant any of these: dev-python/Babel, dev-python/babelfish, 
> dev-python/blz?
> fbissey@Mirage ~/Gentoo $ emerge -puDNv dev-python/Babel
> 
> These are the packages that would be merged, in order:
> 
> Calculating dependencies... done!
> 
> emerge: there are no ebuilds to satisfy "dev-python/Babel".
> 
> emerge: searching for similar names...
> emerge: Maybe you meant any of these: dev-python/babelfish, dev-python/blz, 
> dev-python/tablib?
> 
> There is a loose policy, as far as I remember to avoid capital in
> package names as much as possible (stuff like dev-lang/R being case 
> where you usually want capital). I am not entirely clear what it is in
> Babel that breaks things though, there must be something more than
> capitalisation.
> 
> François
> 
>> On 19/05/2015, at 12:03, Gibson, John <[email protected]> wrote:
>> 
>> On May 18, 2015, at 19:07, yegle <[email protected]> wrote:
>>> 
>>> On Mon, May 18, 2015 at 2:13 AM, Konstantin Tokarev <[email protected]> 
>>> wrote:
>>>> You should create case-sensitive partition and move your prefix there.
>>> 
>>> If this is a requirement of using Gentoo Prefix then yes I should
>>> start with a case-sensitive partition. But looks like this is not the
>>> case, at least I cannot find it in the bootstrap guide etc.
>>> 
>>> I've been using Gentoo Prefix on a case-insensitive FS (blame Apple
>>> for the default) for 5 years without a problem, and the rsync problem
>>> appeared in recent weeks.
>>> 
>>> So I'm looking for anyone who can confirm that there's a problem
>>> syncing and the problem tie to a case-insensitive FS. Then, either
>>> declare that Gentoo Prefix require a case-sensitive FS and everyone
>>> should migrate their existing prefix, or fix the problem by
>>> remove/rename the offending file in portage tree.
>>> 
>>> -- 
>>> yegle
>>> http://about.me/yegle
>>> 
>> 
>> I've been using Prefix since at least 2008 and it does require a 
>> case-sensitive file system, however as Fabian said way back then:
>>> I'm running on case-insensitive filesystem too, and the problems
>>> currently are very very very limited.  So just go for it and forget
>>> about it, until you start to hit weird errors ;)
>>> 
>> See this thread for details:
>> 
>> https://www.mail-archive.com/gentoo-alt%40lists.gentoo.org/msg03694.html
>> 
>> Changing the tree to support case-insensitve file systems may not be 
>> possible. AFAIK that the Prefix tree is really just the main Gentoo tree at 
>> this point, and because the main tree originated on Linux it assumes case 
>> sensitivity.
>> 
>> I run my prefix out of a case-insensitive sparse bundle and haven't seen the 
>> problem.
>> 
>> John
>> 
> 

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