Re: [AMBER] Error while trying to upgrade AmberTools 15

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 8 Jun 2016 06:31:16 -0400

The connection to the Internet timed out.

This means one of a few things:

1. You don't have internet on your computer or you connect through a proxy and haven't set up your proxy settings yet.

In this case, you either need to get Internet or provide your proxy settings and try again.

2. Your connection to the Amber server is bad (either because the Amber server is down or the connection is just bad for you either permanently or temporarily).

In this case, either wait for the connection to improve and try again if it's temporary, or increase the timeout that update_amber will wait.

So check that you can navigate to http://ambermd.org and see the bug fixes page, and try again if that works.

HTH,
Jason 

--
Jason M. Swails
> On Jun 8, 2016, at 5:48 AM, Nikolay N. Kuzmich <nnkuzmich.gmail.com> wrote:
> 
> Dear Amber users,
> 
> I launched the update_amber script
> and the upgrade process presumably wasn't successful:
> 
> nikolay/amber14% $AMBERHOME/update_amber --update
> Preparing to apply updates... please wait.
> Traceback (most recent call last):
>  File "/home/nikolay/amber14/update_amber", line 23, in <module>
>    app.mainloop()
>  File "/home/nikolay/amber14/updateutils/main.py", line 489, in mainloop
>    self.update()
>  File "/home/nikolay/amber14/updateutils/main.py", line 43, in newfcn
>    fcn(self, *args, **kwargs)
>  File "/home/nikolay/amber14/updateutils/main.py", line 317, in update
>    self._update_ambertools()
>  File "/home/nikolay/amber14/updateutils/main.py", line 43, in newfcn
>    fcn(self, *args, **kwargs)
>  File "/home/nikolay/amber14/updateutils/main.py", line 212, in
> _update_ambertools
>    last)
>  File "/home/nikolay/amber14/updateutils/main.py", line 43, in newfcn
>    fcn(self, *args, **kwargs)
>  File "/home/nikolay/amber14/updateutils/main.py", line 187, in
> _update_tree
>    last = remote.last()
>  File "/home/nikolay/amber14/updateutils/repos.py", line 289, in last
>    self.fill_list()
>  File "/home/nikolay/amber14/updateutils/downloader.py", line 104, in
> new_fcn
>    return fcn(*args, **kwargs)
>  File "/home/nikolay/amber14/updateutils/repos.py", line 204, in fill_list
>    p = urlopen(url)
>  File "/usr/lib64/python2.7/urllib2.py", line 127, in
> urlopen
> 
>    return _opener.open(url, data,
> timeout)
> 
>  File "/usr/lib64/python2.7/urllib2.py", line 410, in
> open
> 
>    response = meth(req,
> response)
> 
>  File "/usr/lib64/python2.7/urllib2.py", line 523, in
> http_response
> 
>    'http', request, response, code, msg,
> hdrs)
> 
>  File "/usr/lib64/python2.7/urllib2.py", line 442, in
> error
> 
>    result =
> self._call_chain(*args)
> 
>  File "/usr/lib64/python2.7/urllib2.py", line 382, in
> _call_chain
> 
>    result =
> func(*args)
> 
>  File "/usr/lib64/python2.7/urllib2.py", line 629, in
> http_error_302
> 
>    return self.parent.open(new,
> timeout=req.timeout)
> 
>  File "/usr/lib64/python2.7/urllib2.py", line 404, in
> open
> 
>    response = self._open(req,
> data)
> 
>  File "/usr/lib64/python2.7/urllib2.py", line 422, in
> _open
> 
>    '_open', req)
>  File "/usr/lib64/python2.7/urllib2.py", line 382, in _call_chain
>    result = func(*args)
>  File "/usr/lib64/python2.7/urllib2.py", line 1214, in http_open
>    return self.do_open(httplib.HTTPConnection, req)
>  File "/usr/lib64/python2.7/urllib2.py", line 1187, in do_open
>    r = h.getresponse(buffering=True)
>  File "/usr/lib64/python2.7/httplib.py", line 1067, in getresponse
>    response.begin()
>  File "/usr/lib64/python2.7/httplib.py", line 409, in begin
>    version, status, reason = self._read_status()
>  File "/usr/lib64/python2.7/httplib.py", line 365, in _read_status
>    line = self.fp.readline(_MAXLINE + 1)
>  File "/usr/lib64/python2.7/socket.py", line 476, in readline
>    data = self._sock.recv(self._rbufsize)
> socket.timeout: timed out
> nikolay/amber14%
> 
> Could you please give me an advice how to fix it?
> Thank you in advance.
> 
> Kind regards,
> Nick
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Jun 08 2016 - 04:00:02 PDT
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