What steps will reproduce the problem?

stone@skynet ~/annex $ git init
Initialized empty Git repository in /home/stone/annex/.git/
stone@skynet ~/annex $ git annex init "work"
init work 
*** Please tell me who you are.

Run

  git config --global user.email "you@example.com"
  git config --global user.name "Your Name"

to set your account's default identity.
Omit --global to set the identity only in this repository.

fatal: empty ident name (for <stone@skynet>) not allowed
git-annex: git ["--git-dir=/home/stone/annex/.git","--work-tree=/home/stone/annex","commit-tree","4b825dc652cb6eb9a060e64bf8d69288fbee4904"] exited 128
stone@skynet ~/annex $ git config -l
user.email=stone@nospam.hu
user.name=Stone
core.editor=nano
color.ui=auto
core.repositoryformatversion=0
core.filemode=true
core.bare=false
core.logallrefupdates=true
annex.uuid=499fb545-0b98-4bfc-816c-fb3704f3aaa0
stone@skynet ~/annex $ cat ~/.gitconfig 
[user]
    email = stone@nospam.hu
    name = Stone
[core]
    editor = nano
[color]
    ui = auto
stone@skynet ~/annex $ 

What is the expected output? What do you see instead?

What version of git-annex are you using? On what operating system?

commit 56c037c69e75def74d6ea90de8aa8a1954c52178 Arch Linux

Please provide any additional information below.

done by adding name to the user, in /etc/passwd. --Stone

Actually, done by avoiding clobbering HOME when running some git commands. --Joey

This is an error message from git. Git faq. I don't understand why git is doing it given the configuration shown, but I suppose it would do the same thing if you run git commit by hand.
Comment by http://joeyh.name/ Fri Aug 31 15:04:09 2012

I use git on the same machine nearly every day, it does not complain on commit.

(On the same session after "git annex init" failed...)

stone@skynet ~/annex $ echo stone > bu
stone@skynet ~/annex $ git add bu 
stone@skynet ~/annex $ git commit -a
[master (root-commit) ae5d41f] ds
 1 file changed, 1 insertion(+)
 create mode 100644 bu
stone@skynet ~/annex $ git log
commit ae5d41fdd0b7082740633cf7931bb5a07be0fc5e
Author: Stone <stone@nospam.hu>
Date:   Fri Aug 31 20:26:45 2012 +0200

    ds
stone@skynet ~/annex $ 

Why don't you try the identical command that git-annex is running that fails:

git --git-dir=/home/stone/annex/.git --work-tree=/home/stone/annex commit-tree 4b825dc652cb6eb9a060e64bf8d69288fbee4904

Comment by http://joeyh.name/ Fri Aug 31 18:52:53 2012

Finally I managed to get it working.

My use on the computer didn't had name, so the 5th colum of my /etc/password file was empty. After I filled in my name everything worked like charm.

Interesting that not my user's name from /etc/passwd get into the git log but the one that was in my ~/.gitconfig.

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