[yt-users] Error on installation of yt on system python
trobolo dinni
trobolo.trobolo.dinni5 at gmail.com
Sun Feb 24 17:36:43 PST 2013
Just one last thing, since the command line is different from the one
suggested in the website (
http://yt-project.org/doc/advanced/installing.html#manual-installation)
maybe it could be useful to the users to update it.
Thanks,
Roberto
On 25 February 2013 12:29, trobolo dinni
<trobolo.trobolo.dinni5 at gmail.com>wrote:
> Hi all,
>
> sorry for the delay in replying and thanks for the help! :)
>
> @ Kacper
> If I run the command you suggested in the YT egg directory i get:
> *cthulhu at 42828678:/usr/local/bin/yt-hg$ find . -name
> "data_point_utilities.*"*
> *./yt/utilities/data_point_utilities.c*
> *./build/lib.linux-x86_64-2.7/yt/utilities/data_point_utilities.so*
> *./build/temp.linux-x86_64-2.7/yt/utilities/data_point_utilities.o*
>
> Also, I attached the build log as "output.txt", I am using Ubuntu release
> 12.10.
>
>
> @Michael
> Okay by just doing 'sudo add-apt-repository ppa:kuhlen/ppa', then going
> into python and typing 'from yt.mods import *' seems to work fine. I still
> didn't test yt anyway, I will let you know if something goes wrong again!
>
> Thank you very much for the help again,
> Roberto
>
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>
> On 21 February 2013 07:47, Michael Kuhlen <mqk at astro.berkeley.edu> wrote:
>
>> Yeah, I did figure out the problem. It's that the debian/ubuntu packaging
>> program dpkg-source doesn't include newly created empty files into the diff
>> that it uses to build the updated package:
>>
>> dpkg-source: warning: newly created empty file
>> 'yt/frontends/_skeleton/misc.py' will not be represented in diff
>> dpkg-source: warning: newly created empty file
>> 'yt/frontends/_skeleton/definitions.py' will not be represented in diff
>> dpkg-source: warning: newly created empty file
>> 'yt/frontends/athena/misc.py' will not be represented in diff
>> dpkg-source: warning: newly created empty file
>> 'yt/frontends/athena/__init__.py' will not be represented in diff
>>
>> The last one is the culprit, because as a result the athena/__init__.py
>> file doesn't make it into the package, and hence the import fails. Arrgh.
>>
>> For the life of me I couldn't figure out how to force dpkg-source to
>> include those newly created empty files, and so in the end I opted for the
>> slightly hackish fix of adding a comment ("### comment to allow inclusion
>> in dpkg-source diff file.") to those files. Now the package works, and I've
>> just uploaded it to my PPA. Should be available in a few hours, once it's
>> built.
>>
>> Cheers,
>>
>> Mike
>>
>>
>> On Wed, Feb 20, 2013 at 11:25 AM, Matthew Turk <matthewturk at gmail.com>wrote:
>>
>>> Hey Mike,
>>>
>>> I just verified, and in stable we *do* add Athena as a subpackage, so
>>> I think this should be working. Any ideas as to what might be
>>> different between the install and the deb?
>>>
>>> -MAtt
>>>
>>> On Wed, Feb 20, 2013 at 2:23 PM, Michael Kuhlen <mqk at astro.berkeley.edu>
>>> wrote:
>>> > OK, the updated Ubuntu packages are available. I just tried them out
>>> on my
>>> > ubuntu 12.04.2 LTS and yt-devel works great. With the stable version
>>> (yt) I
>>> > get an import error:
>>> >
>>> > In [1]: from yt.mods import *
>>> >
>>> ---------------------------------------------------------------------------
>>> > ImportError Traceback (most recent call
>>> last)
>>> > <ipython-input-1-c31905f7fc2e> in <module>()
>>> > ----> 1 from yt.mods import *
>>> >
>>> > /usr/lib/pymodules/python2.7/yt/mods.py in <module>()
>>> > 97 GDFStaticOutput, GDFFieldInfo, add_gdf_field
>>> > 98
>>> > ---> 99 from yt.frontends.athena.api import \
>>> > 100 AthenaStaticOutput, AthenaFieldInfo, add_athena_field
>>> > 101
>>> >
>>> > ImportError: No module named athena.api
>>> >
>>> >
>>> > This is weird, because when I install that exact same changeset
>>> > (329d11eeff22) from source (with python ./setup.py develop
>>> > --prefix=$HOME/local) it works just fine. I'll have to investigate.
>>> But if
>>> > you're ok with using the development package (yt-devel), then you
>>> should be
>>> > good to go.
>>> >
>>> > Mike
>>> >
>>> >
>>> >
>>> >
>>> > On Wed, Feb 20, 2013 at 2:02 AM, Michael Kuhlen <
>>> mqk at astro.berkeley.edu>
>>> > wrote:
>>> >>
>>> >> Hi Roberto
>>> >>
>>> >> I'm the maintainer of that ubuntu PPA, sorry you're having trouble
>>> with
>>> >> it. I think maybe all you need to do is to run 'sudo
>>> add-apt-repository
>>> >> ppa:kuhlen/ppa'. Note the trailing '/ppa'. Can you give that a try?
>>> >>
>>> >> Otherwise, can you look under /etc/apt/sources.list.d/ and see if
>>> there's
>>> >> a file named 'kuhlen-ppa-precise.list'? If there is, what is its
>>> content?
>>> >>
>>> >> I've been a bit remiss in keeping these packages up-to-date, but
>>> spurned
>>> >> by your email I just re-packaged updates to the most recent versions
>>> (yt:
>>> >> 329d11eeff22, yt-devel: 09a0fd75818b). Should be available there some
>>> time
>>> >> tomorrow.
>>> >>
>>> >> Cheers,
>>> >> Mike
>>> >>
>>> >>
>>> >>
>>> >>
>>> >> On Tue, Feb 19, 2013 at 11:32 PM, Kacper Kowalik <
>>> xarthisius.kk at gmail.com>
>>> >> wrote:
>>> >>>
>>> >>> On 02/18/2013 12:58 AM, trobolo dinni wrote:
>>> >>> > Hi Nathan,
>>> >>> >
>>> >>> > sorry for the delay in replying.
>>> >>> >
>>> >>> > To install yt on the system python I followed the procedure you
>>> >>> > mentioned:
>>> >>> > entered the yt directory cloned from bitbucket, run "python
>>> setup.py
>>> >>> > install".
>>> >>> > I did that again to check another time but the error persists.
>>> >>> >
>>> >>> > As I said I just reinstalled the same Ubuntu version on the same
>>> >>> > computer
>>> >>> > where before yt was usually installed by following the procedure
>>> above
>>> >>> > and
>>> >>> > it was normally running.
>>> >>> >
>>> >>> > Could reinstall cython help to solve the problem?
>>> >>> >
>>> >>> > Thanks,
>>> >>> > Roberto
>>> >>>
>>> >>> Hi Roberto,
>>> >>> could you run the following command in your $YT_HG directory:
>>> >>>
>>> >>> find . -name "data_point_utilities.*"
>>> >>>
>>> >>> and post the output? Also if you could try installing again but
>>> provide
>>> >>> us with build.log.gz from:
>>> >>>
>>> >>> cd $YT_HG
>>> >>> bash ./clean.sh
>>> >>> python setup.py build | gzip --fast > build.log.gz
>>> >>>
>>> >>> What version of ubuntu are you using?
>>> >>> Cheers,
>>> >>> Kacper
>>> >>>
>>> >>>
>>> >>>
>>> >>> _______________________________________________
>>> >>> yt-users mailing list
>>> >>> yt-users at lists.spacepope.org
>>> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>> >>>
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> *********************************************************************
>>> >> * *
>>> >> * Dr. Michael Kuhlen Theoretical Astrophysics Center *
>>> >> * email: mqk at astro.berkeley.edu UC Berkeley *
>>> >> * cell phone: (831) 588-1468 B-116 Hearst Field Annex # 3411 *
>>> >> * skype username: mikekuhlen Berkeley, CA 94720 *
>>> >> * *
>>> >> *********************************************************************
>>> >
>>> >
>>> >
>>> >
>>> > --
>>> > *********************************************************************
>>> > * *
>>> > * Dr. Michael Kuhlen Theoretical Astrophysics Center *
>>> > * email: mqk at astro.berkeley.edu UC Berkeley *
>>> > * cell phone: (831) 588-1468 B-116 Hearst Field Annex # 3411 *
>>> > * skype username: mikekuhlen Berkeley, CA 94720 *
>>> > * *
>>> > *********************************************************************
>>> >
>>> > _______________________________________________
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>>> >
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>>
>>
>>
>> --
>> *********************************************************************
>> * *
>> * Dr. Michael Kuhlen Theoretical Astrophysics Center *
>> * email: mqk at astro.berkeley.edu UC Berkeley *
>> * cell phone: (831) 588-1468 B-116 Hearst Field Annex # 3411 *
>> * skype username: mikekuhlen Berkeley, CA 94720 *
>> * *
>> *********************************************************************
>>
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