On 08/11/2010 04:40 AM, samrat wrote:
> # sage -upgrade ask
>
> Downloading packages from http://www.sagemath.org//spkg
> Reading package lists...
> Traceback (most recent call last):
> File "/usr/local/pkgs/sage_4.5/local/bin/sage-update", line 357, in
> <module>
> do_update()
> File "/usr/local/pkgs/sage_4.5/local/bin/sage-update", line 266, in
> do_update
> packages = spkg_list('standard')
> File "/usr/local/pkgs/sage_4.5/local/bin/sage-update", line 202, in
> spkg_list
> urllib.urlretrieve(web_url, file, reporthook)
> File "/usr/local/pkgs/sage_4.5/local/lib/python/urllib.py", line 94,
> in urlretrieve
> return _urlopener.retrieve(url, filename, reporthook, data)
> File "/usr/local/pkgs/sage_4.5/local/lib/python/urllib.py", line
> 238, in retrieve
> fp = self.open(url, data)
> File "/usr/local/pkgs/sage_4.5/local/lib/python/urllib.py", line
> 206, in open
> return getattr(self, name)(url)
> File "/usr/local/pkgs/sage_4.5/local/lib/python/urllib.py", line
> 345, in open_http
> h.endheaders()
> File "/usr/local/pkgs/sage_4.5/local/lib/python/httplib.py", line
> 892, in endheaders
> self._send_output()
> File "/usr/local/pkgs/sage_4.5/local/lib/python/httplib.py", line
> 764, in _send_output
> self.send(msg)
> File "/usr/local/pkgs/sage_4.5/local/lib/python/httplib.py", line
> 723, in send
> self.connect()
> File "/usr/local/pkgs/sage_4.5/local/lib/python/httplib.py", line
> 704, in connect
> self.timeout)
> File "/usr/local/pkgs/sage_4.5/local/lib/python/socket.py", line
> 516, in create_connection
> raise error, msg
> IOError: [Errno socket error] timed out
> Error getting new packages!
> Double checking that all packages have been installed.
> Downloading packages from http://www.sagemath.org//spkg
> Reading package lists...
> Traceback (most recent call last):
> File "/usr/local/pkgs/sage_4.5/local/bin/sage-update", line 357, in
> <module>
> do_update()
> File "/usr/local/pkgs/sage_4.5/local/bin/sage-update", line 266, in
> do_update
> packages = spkg_list('standard')
> File "/usr/local/pkgs/sage_4.5/local/bin/sage-update", line 202, in
> spkg_list
> urllib.urlretrieve(web_url, file, reporthook)
> File "/usr/local/pkgs/sage_4.5/local/lib/python/urllib.py", line 94,
> in urlretrieve
> return _urlopener.retrieve(url, filename, reporthook, data)
> File "/usr/local/pkgs/sage_4.5/local/lib/python/urllib.py", line
> 238, in retrieve
> fp = self.open(url, data)
> File "/usr/local/pkgs/sage_4.5/local/lib/python/urllib.py", line
> 206, in open
> return getattr(self, name)(url)
> File "/usr/local/pkgs/sage_4.5/local/lib/python/urllib.py", line
> 345, in open_http
> h.endheaders()
> File "/usr/local/pkgs/sage_4.5/local/lib/python/httplib.py", line
> 892, in endheaders
> self._send_output()
> File "/usr/local/pkgs/sage_4.5/local/lib/python/httplib.py", line
> 764, in _send_output
> self.send(msg)
> File "/usr/local/pkgs/sage_4.5/local/lib/python/httplib.py", line
> 723, in send
> self.connect()
> File "/usr/local/pkgs/sage_4.5/local/lib/python/httplib.py", line
> 704, in connect
> self.timeout)
> File "/usr/local/pkgs/sage_4.5/local/lib/python/socket.py", line
> 516, in create_connection
> raise error, msg
> IOError: [Errno socket error] timed out
> Error getting new packages!
>
> ---> SELinux in in 'enforcing' mode. Initially (after installing) i
> had some problem with SELinux and so as root i had run: chcon -t
> textrel_shlib_t /usr/local/pkgs/sage_4.5/local/lib/libpari-gmp.so.2.
> After this i could invoke sage as non-root user. But i am upgrading as
> root. Does this help?
What happens if you completely disable SELinux, at least temporarily,
and try again? On Fedora 12, at least, I can disable it with
echo 0 >| /selinux/enforce
and renable it with
echo 0 >| /selinux/enforce
By the way, this is what I see when I try upgrading from 4.5.1 on
sage.math.washington.edu:
sage-4.5.1$ ./sage -upgrade
Testing mirrors...
[2 ] boxen.math.washington.edu 49 [ms]
[16] www.cecm.sfu.ca 57 [ms]
[13] modular.math.jmu.edu 160 [ms]
[12] modular.fas.harvard.edu 171 [ms]
[4 ] ftp.kaist.ac.kr 253 [ms]
[3 ] echidna.maths.usyd.edu.au 295 [ms]
[6 ] ftp.sh.cvut.cz 357 [ms]
[8 ] mirror.aarnet.edu.au 357 [ms]
[9 ] mirror.switch.ch 371 [ms]
[17] www.mirrorservice.org 387 [ms]
[11] mirrors.fe.up.pt 430 [ms]
[14] sagemath.c3sl.ufpr.br 500 [ms]
[15] sunsite.rediris.es 547 [ms]
[5 ] ftp.leg.uct.ac.za 846 [ms]
[10] mirror.yandex.ru 1229 [ms]
[7 ] mira.sunsite.utk.edu 1780 [ms]
Automatically selected server www.cecm.sfu.ca (http://www.cecm.sfu.ca/sage/)
Downloading packages from http://www.cecm.sfu.ca/sage//spkg
Reading package lists.......... Done!
The following packages will be upgraded:
cvxopt-0.9.p9 examples-4.5.2 extcode-4.5.2 lcalc-20100428-1.23.p1
pari-2.3.5.p2 sage-4.5.2 sage_scripts-4.5.2 sagenb-0.8.2
** WARNING: This is a source-based upgrade, which could take hours,
** fail, and render your Sage install useless!!
Do you want to continue [y/N]?
I'm surprised that you don't see the mirror test, but the urllib problem
seems more fundamental. Could you also report what happens with
sage: import urllib
sage: urllib.urlretrieve('http://www.sagemath.org//spkg', 'test.html')
('test.html', <httplib.HTTPMessage instance at 0x47788c0>)
sage:
This should write a file test.html in the current directory.
Just to be sure, is http://www.sagemath.org//spkg accessible from a browser?
Thanks!
> On Aug 11, 2:27 pm, Mitesh Patel <[email protected]> wrote:
>> On 08/11/2010 12:37 AM, samrat wrote:
>>> Here is the output of the command sage -upgrade. I installed and am
>>> upgrading as root. I am using CentOS 5.5 as a single user.
>>
>>> # sage -upgrade
>>> Downloading packages fromhttp://www.sagemath.org//spkg
>>> Reading package lists...
>>> Traceback (most recent call last):
>>> File "/usr/local/pkgs/sage_4.5/local/bin/sage-update", line 357, in
>>> <module>
>>> do_update()
>>> File "/usr/local/pkgs/sage_4.5/local/bin/sage-update", line 266, in
>>> do_update
>>> packages = spkg_list('standard')
>>> File "/usr/local/pkgs/sage_4.5/local/bin/sage-update", line 202, in
>>> spkg_list
>>> urllib.urlretrieve(web_url, file, reporthook)
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/urllib.py", line 94,
>>> in urlretrieve
>>> return _urlopener.retrieve(url, filename, reporthook, data)
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/urllib.py", line
>>> 238, in retrieve
>>> fp = self.open(url, data)
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/urllib.py", line
>>> 206, in open
>>> return getattr(self, name)(url)
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/urllib.py", line
>>> 345, in open_http
>>> h.endheaders()
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/httplib.py", line
>>> 892, in endheaders
>>> self._send_output()
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/httplib.py", line
>>> 764, in _send_output
>>> self.send(msg)
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/httplib.py", line
>>> 723, in send
>>> self.connect()
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/httplib.py", line
>>> 704, in connect
>>> self.timeout)
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/socket.py", line
>>> 516, in create_connection
>>> raise error, msg
>>> IOError: [Errno socket error] timed out
>>> Error getting new packages!
>>> Double checking that all packages have been installed.
>>> Downloading packages fromhttp://www.sagemath.org//spkg
>>> Reading package lists...
>>> Traceback (most recent call last):
>>> File "/usr/local/pkgs/sage_4.5/local/bin/sage-update", line 357, in
>>> <module>
>>> do_update()
>>> File "/usr/local/pkgs/sage_4.5/local/bin/sage-update", line 266, in
>>> do_update
>>> packages = spkg_list('standard')
>>> File "/usr/local/pkgs/sage_4.5/local/bin/sage-update", line 202, in
>>> spkg_list
>>> urllib.urlretrieve(web_url, file, reporthook)
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/urllib.py", line 94,
>>> in urlretrieve
>>> return _urlopener.retrieve(url, filename, reporthook, data)
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/urllib.py", line
>>> 238, in retrieve
>>> fp = self.open(url, data)
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/urllib.py", line
>>> 206, in open
>>> return getattr(self, name)(url)
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/urllib.py", line
>>> 345, in open_http
>>> h.endheaders()
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/httplib.py", line
>>> 892, in endheaders
>>> self._send_output()
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/httplib.py", line
>>> 764, in _send_output
>>> self.send(msg)
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/httplib.py", line
>>> 723, in send
>>> self.connect()
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/httplib.py", line
>>> 704, in connect
>>> self.timeout)
>>> File "/usr/local/pkgs/sage_4.5/local/lib/python/socket.py", line
>>> 516, in create_connection
>>> raise error, msg
>>> IOError: [Errno socket error] timed out
>>> Error getting new packages!
>>
>> We should handle this exception, though I'm not sure about what exactly
>> is causing it. Could you try
>>
>> sage -upgrade ask
>>
>> ? Harald, do you happen to see what's going on?
>>
>>> On Aug 11, 2:27 am, Mitesh Patel <[email protected]> wrote:
>>>> On 08/10/2010 10:47 AM, Daniel Harris wrote:
>>>>> I just had the same error but a make clean and then make again solved
>>>>> the problem
>>>>> Dan
>>
>>>>> On Tue, Aug 10, 2010 at 10:06 AM, samrat <[email protected]
>>>>> <mailto:[email protected]>> wrote:
>>
>>>>> Hi,
>>
>>>>> I installed 4.5.1 from source. Now i am unable to upgrade from 4.5.1
>>>>> to 4.5.1. I ran the command: sage -upgrade
>>
>>>>> The last couple of lines of the error are:
>>
>>>>> IOError: [Errno socket error] timed out
>>>>> Error getting new packages!
>>
>>>>> Kindly advise. Thanks.
>>
>>>> Maybe the selected upgrade mirror did not later respond during package
>>>> download? If you still have it, could you paste the entire output of
>>>> 'sage -upgrade'? That could help to narrow the list of possibilities.
>
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