[yt-users] yt installation crash

Tue Sep 17 09:30:37 PDT 2013

Hello,

I am getting the error while running $ bash install_script.sh
It appears that the ZeroMQ is causing trouble, here are the lines printed
in the terminal Installing distribute
Installing pip
Installing ZeroMQ
********************************************
        FAILURE REPORT:
********************************************

make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
Making install in tests
  CXX    test_disconnect_inproc.o
test_disconnect_inproc.cpp: In function ‘int main(int, char**)’:
test_disconnect_inproc.cpp:48: error: ‘strndup’ was not declared in this
scope
test_disconnect_inproc.cpp:52: error: ‘strndup’ was not declared in this
scope
test_disconnect_inproc.cpp:72: error: ‘strndup’ was not declared in this
scope
make[1]: *** [test_disconnect_inproc.o] Error 1
make: *** [install-recursive] Error 1

********************************************
********************************************
Failure.  Check /Users/tplaton/yt-i386/yt_install.log.  The last 10 lines
are above.

I had difficulties uploading the log file as it was to big.

Thank you,
Tudor

On Mon, Sep 16, 2013 at 2:58 PM, Nathan Goldbaum <nathan12343 at gmail.com>wrote:

> Hi all,
>
> I think the issue is with the ZeroMQ library provided by yt.  As indicated
> in the macports discussion originally linked to, you can fix this yourself
> by manually editing the offending file to not use the strndup function
>
> If you don't want ZeroMQ (needed to get the IPython notebook working
> properly) you can set INST_ZMQ=0 in the install script.  That should get
> past the error you're seeing.  You should be able to get a working zeroMQ
> in the end by installing pyzmq via pip, which can optionally install a
> bundled version of ZeroMQ.  To do this, run the following command when the
> install script finishes:
>
> $ pip install pyzmq
>
> I don't know whether you'll run into the same strndup issue, but it's
> certainly worth a try!  Like I said above, you can fix the original issue
> yourself by manually editing the ZeroMQ source as indicated in the macports
> discussion thread.
>
> The ZeroMQ issue is already fixed in the development version of ZeroMQ,
> but unfortunately there isn't a stable version of ZeroMQ available yet that
> includes the fix. Once such a version is released, we'll update the install
> script to build the new version.
>
> Sorry to hear you're having trouble.  Unfortunately this is an issue with
> an upstream package that we depend on so we wouldn't have caught it during
> yt's development cycle unless one of the developers was running 10.6 and
> tried to rebuild ZeroMQ.  It's very difficult for us to test the install
> script on a variety of OS and OS versions before doing releases, so issues
> like this can slip through the cracks.
>
> -Nathan
>
>
> On Mon, Sep 16, 2013 at 11:48 AM, j s oishi <jsoishi at gmail.com> wrote:
>
>> Tudor,
>>
>> The error seems to be with ZeroMQ, which yt depends on. It appears that
>> the version of ZeroMQ you are attempting to compile will not build on OS
>> 10.6.8; at least, that is what the link you provided indicates. I am not a
>>  Mac user, so I can't speak from experience on that, though.
>>
>> However, it's hard for us to tell if this is the version we ship with yt,
>> since you haven't provided very much context for the error you're getting.
>> Could you please set along the yt_install.log, so we can see if the problem
>> is with the yt provided ZeroMQ? In the future, we'll be able to provide
>> better help if we can get full error logs.
>>
>> thanks,
>>
>> Jeff
>>
>>
>> On Mon, Sep 16, 2013 at 2:42 PM, Britton Smith <brittonsmith at gmail.com>wrote:
>>
>>> Hi Tudor,
>>>
>>> Are you seeing that error when running that line?  If so, you can also
>>> try using wget instead of curl, if you have that installed from something
>>> like macports.  If that's not what's happening, can you be more specific
>>> about what you're doing and when you see that error?
>>>
>>> Britton
>>>
>>>
>>> On Mon, Sep 16, 2013 at 5:07 PM, Platon, Tudor <tplaton at cfa.harvard.edu>wrote:
>>>
>>>> Hello Britton,
>>>>
>>>> I am actually following the procedure on the yt-project.org. I am
>>>> using $ curl -O
>>>> http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh<http://hg.yt-project.org/yt/src/stable/doc/install_script.sh>
>>>> Do you have any other suggestions?
>>>>
>>>> Regards,
>>>> Tudor
>>>>
>>>>
>>>> On Mon, Sep 16, 2013 at 10:41 AM, Britton Smith <brittonsmith at gmail.com
>>>> > wrote:
>>>>
>>>>> Hi Tudor,
>>>>>
>>>>> It looks like you're trying to install yt from macports.  Is that
>>>>> right?  If so, I'm not sure who is in charge of the yt module in macports
>>>>> or if they are even following this list.  It seems that the latest yt
>>>>> version on macports is 2.3, which is from quite a while ago.  I recommend
>>>>> using the install script available at yt-project.org under the "Get
>>>>> yt" section.
>>>>>
>>>>> Britton
>>>>>
>>>>>
>>>>> On Fri, Sep 13, 2013 at 6:06 PM, Platon, Tudor <
>>>>> tplaton at cfa.harvard.edu> wrote:
>>>>>
>>>>>> Hello everyone,
>>>>>>
>>>>>> I am trying to install the current stable version of yt on a Mac,
>>>>>> running Mac OS X ver 10.6.8 and I get the following errors:
>>>>>> test_disconnect_inproc.cpp:48: error: ‘strndup’ was not declared in
>>>>>> this scope
>>>>>> test_disconnect_inproc.cpp:52: error: ‘strndup’ was not declared in
>>>>>> this scope
>>>>>> test_disconnect_inproc.cpp:72: error: ‘strndup’ was not declared in
>>>>>> this scope
>>>>>> The Xcode 3.2.6/iOS SDK bundle is already installed. A similar error
>>>>>> is reported on the following webpage:
>>>>>> http://trac.macports.org/ticket/39122?cversion=0&cnum_hist=8
>>>>>> Does anyone have a solution for this?
>>>>>>
>>>>>> Regards,
>>>>>> Tudor
>>>>>>
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>>>>>>
>>>>>>
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