[yt-users] yt installation crash

Nathan Goldbaum nathan12343 at gmail.com
Mon Sep 16 11:58:11 PDT 2013


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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