date:20121026

Re: [Pytables-users] PyTables broke in Ubuntu 12.10

2012-10-26 Thread Jason Moore

I just tried installing python-tables on a clean install of 12.10 on a
different machine and all went fine. So I've got something corrupted on my
machine...just a localized bug.

Jason

On Fri, Oct 26, 2012 at 2:40 PM, Jason Moore  wrote:

> I've posted a bug report here:
> https://bugs.launchpad.net/ubuntu/+source/pytables/+bug/1071918
>
> Maybe others could see if it is reproducible in Ubuntu 12.10.
>
> Thanks,
>
> Jason
>
>
> On Fri, Oct 26, 2012 at 2:09 PM, Jason Moore  wrote:
>
>> The simlink is a workaround for Ubuntu 12.10. It is certainly not the
>> long term solution, but I don't see why it is a bad idea. python-tables in
>> the Ubuntu 12.10 repos cannot find the HDF5 library because it is looking
>> for libhdf5.so.6 on the path but there is only libhdf5.so.7 (which is a
>> simlink to libhdf5.so.7.0.2). This must be hard coded in the
>> utilsExtensions.so binary that is include with PyTables. Seems like that
>> these need to be recompiled for the distribution or something.
>>
>> Jason
>>
>>
>> On Fri, Oct 26, 2012 at 1:12 PM, Antonio Valentino <
>> antonio.valent...@tiscali.it> wrote:
>>
>>> Hi Jason,
>>>
>>> Il 26/10/2012 21:59, Jason Moore ha scritto:
>>> > Solution was simple once I found it. Here is the workaround:
>>> >
>>> > https://bugs.launchpad.net/ubuntu/+source/octave/+bug/1005243
>>> >
>>> > Just make a symlink to the new file.
>>> >
>>> > Jason
>>>
>>> Honestly I don't think it is a good idea.
>>>
>>>
>>> ciao
>>>
>>> --
>>> Antonio Valentino
>>>
>>>
>>> --
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>>>
>>
>>
>>
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>>
>>
>>
>
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>
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Re: [Pytables-users] PyTables broke in Ubuntu 12.10

2012-10-26 Thread Jason Moore

I've posted a bug report here:
https://bugs.launchpad.net/ubuntu/+source/pytables/+bug/1071918

Maybe others could see if it is reproducible in Ubuntu 12.10.

Thanks,

Jason

On Fri, Oct 26, 2012 at 2:09 PM, Jason Moore  wrote:

> The simlink is a workaround for Ubuntu 12.10. It is certainly not the long
> term solution, but I don't see why it is a bad idea. python-tables in the
> Ubuntu 12.10 repos cannot find the HDF5 library because it is looking for
> libhdf5.so.6 on the path but there is only libhdf5.so.7 (which is a simlink
> to libhdf5.so.7.0.2). This must be hard coded in the utilsExtensions.so
> binary that is include with PyTables. Seems like that these need to be
> recompiled for the distribution or something.
>
> Jason
>
>
> On Fri, Oct 26, 2012 at 1:12 PM, Antonio Valentino <
> antonio.valent...@tiscali.it> wrote:
>
>> Hi Jason,
>>
>> Il 26/10/2012 21:59, Jason Moore ha scritto:
>> > Solution was simple once I found it. Here is the workaround:
>> >
>> > https://bugs.launchpad.net/ubuntu/+source/octave/+bug/1005243
>> >
>> > Just make a symlink to the new file.
>> >
>> > Jason
>>
>> Honestly I don't think it is a good idea.
>>
>>
>> ciao
>>
>> --
>> Antonio Valentino
>>
>>
>> --
>> WINDOWS 8 is here.
>> Millions of people.  Your app in 30 days.
>> Visit The Windows 8 Center at Sourceforge for all your go to resources.
>> http://windows8center.sourceforge.net/
>> join-generation-app-and-make-money-coding-fast/
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>> https://lists.sourceforge.net/lists/listinfo/pytables-users
>>
>
>
>
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> Davis, CA
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>
>
>
>


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Re: [Pytables-users] PyTables broke in Ubuntu 12.10

2012-10-26 Thread Jason Moore

The simlink is a workaround for Ubuntu 12.10. It is certainly not the long
term solution, but I don't see why it is a bad idea. python-tables in the
Ubuntu 12.10 repos cannot find the HDF5 library because it is looking for
libhdf5.so.6 on the path but there is only libhdf5.so.7 (which is a simlink
to libhdf5.so.7.0.2). This must be hard coded in the utilsExtensions.so
binary that is include with PyTables. Seems like that these need to be
recompiled for the distribution or something.

Jason

On Fri, Oct 26, 2012 at 1:12 PM, Antonio Valentino <
antonio.valent...@tiscali.it> wrote:

> Hi Jason,
>
> Il 26/10/2012 21:59, Jason Moore ha scritto:
> > Solution was simple once I found it. Here is the workaround:
> >
> > https://bugs.launchpad.net/ubuntu/+source/octave/+bug/1005243
> >
> > Just make a symlink to the new file.
> >
> > Jason
>
> Honestly I don't think it is a good idea.
>
>
> ciao
>
> --
> Antonio Valentino
>
>
> --
> WINDOWS 8 is here.
> Millions of people.  Your app in 30 days.
> Visit The Windows 8 Center at Sourceforge for all your go to resources.
> http://windows8center.sourceforge.net/
> join-generation-app-and-make-money-coding-fast/
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> https://lists.sourceforge.net/lists/listinfo/pytables-users
>



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Re: [Pytables-users] PyTables broke in Ubuntu 12.10

2012-10-26 Thread Antonio Valentino

Hi Jason,

Il 26/10/2012 21:59, Jason Moore ha scritto:
> Solution was simple once I found it. Here is the workaround:
>
> https://bugs.launchpad.net/ubuntu/+source/octave/+bug/1005243
>
> Just make a symlink to the new file.
>
> Jason

Honestly I don't think it is a good idea.


ciao

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Re: [Pytables-users] PyTables broke in Ubuntu 12.10

2012-10-26 Thread Antonio Valentino

Hi Jason,

Il 26/10/2012 21:37, Jason Moore ha scritto:
> I'll post the bug report, but I'd like to get this working on my system.
> I've always had trouble compiling pytables from source due to the
> dependencies. Right now I just need to get this working because I can no
> longer use my software now that PyTabes is broken.
>

If you use ubuntu 12.04 you can install build dependencies as follows:

$ sudo apt-get install libhdf5-dev python-dev cython python-numexpr 
libbz2-dev zlib1g-dev, liblzo2-dev

or simply

$ sudo apt-get build-dep pytables

Then you can build pytables typing

python setup.py build


> Question 1:
>
> What are the exact command for installing for source (including all flags)?
> I can't find this explicitly in the documentation especially how to use the
> --hdf5 flag and other flags to point to where the dependencies are
> installed. I'm trying:
>
> sudo python setup.py build_ext --inplace --hdf5=/usr/lib/libhdf5.so.7
>
> But having little luck. It still can't find my hdf5 library.
>

The use of the --hdf5 flag is explained in [1], anyway you should not 
need it on ubuntu.

[1] http://pytables.github.com/usersguide/installation.html


> Question 2:
>
> I tried your pytables2.4 ppa but it also can't find the hdf5 library. How
> can I install the old /usr/lib/lbhdf5.so.6 file? I also remember it being
> painful to install the HDF5 libraries from source. Is this file available
> in the Ubuntu repositories?
>

This is very strange.
It seems to me a misconfiguration of the apt system.
Are you sure that all you apt sources point to quantal?
Maybe some of them still points to precise


cheers

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Re: [Pytables-users] PyTables broke in Ubuntu 12.10

2012-10-26 Thread Jason Moore

Solution was simple once I found it. Here is the workaround:

https://bugs.launchpad.net/ubuntu/+source/octave/+bug/1005243

Just make a symlink to the new file.

Jason

On Fri, Oct 26, 2012 at 12:37 PM, Jason Moore  wrote:

> I'll post the bug report, but I'd like to get this working on my system.
> I've always had trouble compiling pytables from source due to the
> dependencies. Right now I just need to get this working because I can no
> longer use my software now that PyTabes is broken.
>
> Question 1:
>
> What are the exact command for installing for source (including all
> flags)? I can't find this explicitly in the documentation especially how to
> use the --hdf5 flag and other flags to point to where the dependencies are
> installed. I'm trying:
>
> sudo python setup.py build_ext --inplace --hdf5=/usr/lib/libhdf5.so.7
>
> But having little luck. It still can't find my hdf5 library.
>
> Question 2:
>
> I tried your pytables2.4 ppa but it also can't find the hdf5 library. How
> can I install the old /usr/lib/lbhdf5.so.6 file? I also remember it being
> painful to install the HDF5 libraries from source. Is this file available
> in the Ubuntu repositories?
>
> Jason
>
>
> On Fri, Oct 26, 2012 at 10:16 AM, Antonio Valentino <
> antonio.valent...@tiscali.it> wrote:
>
>> Hi Jason,
>>
>> Il 26/10/2012 18:44, Jason Moore ha scritto:
>> > Where exactly do I submit the bug report? There doesn't seem to be a bug
>> > option here:
>> https://launchpad.net/ubuntu/quantal/+package/python-tables
>> >
>> > Jason
>>
>> of course you need a launchpad account, than you can follow instruction
>> of the ReportingBugs page on the ubuntu wiki [1]
>>
>> [1] https://help.ubuntu.com/community/ReportingBugs
>>
>>
>> ciao
>>
>> > On Thu, Oct 25, 2012 at 11:27 PM, Antonio Valentino <
>> > antonio.valent...@tiscali.it> wrote:
>> >
>> >> Hi Jason,
>> >>
>> >> Il giorno 26/ott/2012, alle ore 07:28, Jason Moore <
>> moorepa...@gmail.com>
>> >> ha scritto:
>> >>
>> >>> So it looks like python-tables in Ubuntu 12.10 requires libhdf5-7 and
>> >> libhdf5-7 has /usr/lib/libhdf5.so.7 not libhdf5.so.6.
>> >>
>> >> Correct, the hdf5 package has been updated in ubuntu 12.10.
>> >> If you use the standard python-tables package from ubuntu repositories
>> >> please file a bug report on launchpad.
>> >>
>> >>
>> >>> Jason
>> >>>
>> >>> On Thu, Oct 25, 2012 at 4:10 PM, Aquil Abdullah <
>> >> aquil.abdul...@gmail.com> wrote:
>> >>> Can you check to see if libhdf5.so is in your path? If not, you can
>> add
>> >> it to the path where it resides to your PATH variable.
>> >>>
>> >>> Hopefully, that helps.
>> >>>
>> >>> Aquil H. Abdullah
>> >>>
>> >>> On Oct 25, 2012, at 18:42, Jason Moore  wrote:
>> >>>
>>  I just updated to Ubuntu 12.10 and my pytables install is broken. I
>> >> reinstalled and it seems like I have hdf5 1.8.4 installed but I get
>> this
>> >> error:
>> 
>>  moorepants@moorepants-LT:BicycleDataProcessor(master)$ vitables
>> >> InstrumentedBicycleData.h5
>>  Traceback (most recent call last):
>> File "/usr/bin/vitables", line 105, in 
>>   main(sys.argv)
>> File "/usr/bin/vitables", line 48, in main
>>   from vitables.vtapp import VTApp
>> File "/usr/share/vitables/vitables/vtapp.py", line 35, in 
>>   import tables
>> File "/usr/local/lib/python2.7/dist-packages/tables/__init__.py",
>> >> line 30, in 
>>   from tables.utilsExtension import getPyTablesVersion,
>> getHDF5Version
>>  ImportError: libhdf5.so.6: cannot open shared object file: No such
>> file
>> >> or directory
>> 
>>  What am I missing?
>> 
>>  Jason
>> >>
>> >>
>> >> Anyway you can also use the eotools PPA [1] that has a more updated
>> >> version of pytables: 2.4 against 2.3.1 of the official universe repo.
>> >>
>> >> [1]
>> >>
>> https://launchpad.net/~a.valentino/+archive/eotools?field.series_filter=quantal
>> >>
>> >> best regards
>> >>
>> >>
>> >> --
>> >> Antonio Valentino
>>
>>
>>
>> --
>> Antonio Valentino
>>
>>
>> --
>> The Windows 8 Center
>> In partnership with Sourceforge
>> Your idea - your app - 30 days. Get started!
>> http://windows8center.sourceforge.net/
>> what-html-developers-need-to-know-about-coding-windows-8-metro-style-apps/
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>> https://lists.sourceforge.net/lists/listinfo/pytables-users
>>
>
>
>
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>
>
>
>


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Re: [Pytables-users] PyTables broke in Ubuntu 12.10

2012-10-26 Thread Jason Moore

I'll post the bug report, but I'd like to get this working on my system.
I've always had trouble compiling pytables from source due to the
dependencies. Right now I just need to get this working because I can no
longer use my software now that PyTabes is broken.

Question 1:

What are the exact command for installing for source (including all flags)?
I can't find this explicitly in the documentation especially how to use the
--hdf5 flag and other flags to point to where the dependencies are
installed. I'm trying:

sudo python setup.py build_ext --inplace --hdf5=/usr/lib/libhdf5.so.7

But having little luck. It still can't find my hdf5 library.

Question 2:

I tried your pytables2.4 ppa but it also can't find the hdf5 library. How
can I install the old /usr/lib/lbhdf5.so.6 file? I also remember it being
painful to install the HDF5 libraries from source. Is this file available
in the Ubuntu repositories?

Jason

On Fri, Oct 26, 2012 at 10:16 AM, Antonio Valentino <
antonio.valent...@tiscali.it> wrote:

> Hi Jason,
>
> Il 26/10/2012 18:44, Jason Moore ha scritto:
> > Where exactly do I submit the bug report? There doesn't seem to be a bug
> > option here: https://launchpad.net/ubuntu/quantal/+package/python-tables
> >
> > Jason
>
> of course you need a launchpad account, than you can follow instruction
> of the ReportingBugs page on the ubuntu wiki [1]
>
> [1] https://help.ubuntu.com/community/ReportingBugs
>
>
> ciao
>
> > On Thu, Oct 25, 2012 at 11:27 PM, Antonio Valentino <
> > antonio.valent...@tiscali.it> wrote:
> >
> >> Hi Jason,
> >>
> >> Il giorno 26/ott/2012, alle ore 07:28, Jason Moore <
> moorepa...@gmail.com>
> >> ha scritto:
> >>
> >>> So it looks like python-tables in Ubuntu 12.10 requires libhdf5-7 and
> >> libhdf5-7 has /usr/lib/libhdf5.so.7 not libhdf5.so.6.
> >>
> >> Correct, the hdf5 package has been updated in ubuntu 12.10.
> >> If you use the standard python-tables package from ubuntu repositories
> >> please file a bug report on launchpad.
> >>
> >>
> >>> Jason
> >>>
> >>> On Thu, Oct 25, 2012 at 4:10 PM, Aquil Abdullah <
> >> aquil.abdul...@gmail.com> wrote:
> >>> Can you check to see if libhdf5.so is in your path? If not, you can add
> >> it to the path where it resides to your PATH variable.
> >>>
> >>> Hopefully, that helps.
> >>>
> >>> Aquil H. Abdullah
> >>>
> >>> On Oct 25, 2012, at 18:42, Jason Moore  wrote:
> >>>
>  I just updated to Ubuntu 12.10 and my pytables install is broken. I
> >> reinstalled and it seems like I have hdf5 1.8.4 installed but I get this
> >> error:
> 
>  moorepants@moorepants-LT:BicycleDataProcessor(master)$ vitables
> >> InstrumentedBicycleData.h5
>  Traceback (most recent call last):
> File "/usr/bin/vitables", line 105, in 
>   main(sys.argv)
> File "/usr/bin/vitables", line 48, in main
>   from vitables.vtapp import VTApp
> File "/usr/share/vitables/vitables/vtapp.py", line 35, in 
>   import tables
> File "/usr/local/lib/python2.7/dist-packages/tables/__init__.py",
> >> line 30, in 
>   from tables.utilsExtension import getPyTablesVersion,
> getHDF5Version
>  ImportError: libhdf5.so.6: cannot open shared object file: No such
> file
> >> or directory
> 
>  What am I missing?
> 
>  Jason
> >>
> >>
> >> Anyway you can also use the eotools PPA [1] that has a more updated
> >> version of pytables: 2.4 against 2.3.1 of the official universe repo.
> >>
> >> [1]
> >>
> https://launchpad.net/~a.valentino/+archive/eotools?field.series_filter=quantal
> >>
> >> best regards
> >>
> >>
> >> --
> >> Antonio Valentino
>
>
>
> --
> Antonio Valentino
>
>
> --
> The Windows 8 Center
> In partnership with Sourceforge
> Your idea - your app - 30 days. Get started!
> http://windows8center.sourceforge.net/
> what-html-developers-need-to-know-about-coding-windows-8-metro-style-apps/
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Re: [Pytables-users] PyTables broke in Ubuntu 12.10

2012-10-26 Thread Antonio Valentino

Hi Jason,

Il 26/10/2012 18:44, Jason Moore ha scritto:
> Where exactly do I submit the bug report? There doesn't seem to be a bug
> option here: https://launchpad.net/ubuntu/quantal/+package/python-tables
>
> Jason

of course you need a launchpad account, than you can follow instruction 
of the ReportingBugs page on the ubuntu wiki [1]

[1] https://help.ubuntu.com/community/ReportingBugs


ciao

> On Thu, Oct 25, 2012 at 11:27 PM, Antonio Valentino <
> antonio.valent...@tiscali.it> wrote:
>
>> Hi Jason,
>>
>> Il giorno 26/ott/2012, alle ore 07:28, Jason Moore 
>> ha scritto:
>>
>>> So it looks like python-tables in Ubuntu 12.10 requires libhdf5-7 and
>> libhdf5-7 has /usr/lib/libhdf5.so.7 not libhdf5.so.6.
>>
>> Correct, the hdf5 package has been updated in ubuntu 12.10.
>> If you use the standard python-tables package from ubuntu repositories
>> please file a bug report on launchpad.
>>
>>
>>> Jason
>>>
>>> On Thu, Oct 25, 2012 at 4:10 PM, Aquil Abdullah <
>> aquil.abdul...@gmail.com> wrote:
>>> Can you check to see if libhdf5.so is in your path? If not, you can add
>> it to the path where it resides to your PATH variable.
>>>
>>> Hopefully, that helps.
>>>
>>> Aquil H. Abdullah
>>>
>>> On Oct 25, 2012, at 18:42, Jason Moore  wrote:
>>>
 I just updated to Ubuntu 12.10 and my pytables install is broken. I
>> reinstalled and it seems like I have hdf5 1.8.4 installed but I get this
>> error:

 moorepants@moorepants-LT:BicycleDataProcessor(master)$ vitables
>> InstrumentedBicycleData.h5
 Traceback (most recent call last):
File "/usr/bin/vitables", line 105, in 
  main(sys.argv)
File "/usr/bin/vitables", line 48, in main
  from vitables.vtapp import VTApp
File "/usr/share/vitables/vitables/vtapp.py", line 35, in 
  import tables
File "/usr/local/lib/python2.7/dist-packages/tables/__init__.py",
>> line 30, in 
  from tables.utilsExtension import getPyTablesVersion, getHDF5Version
 ImportError: libhdf5.so.6: cannot open shared object file: No such file
>> or directory

 What am I missing?

 Jason
>>
>>
>> Anyway you can also use the eotools PPA [1] that has a more updated
>> version of pytables: 2.4 against 2.3.1 of the official universe repo.
>>
>> [1]
>> https://launchpad.net/~a.valentino/+archive/eotools?field.series_filter=quantal
>>
>> best regards
>>
>>
>> --
>> Antonio Valentino



-- 
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Re: [Pytables-users] PyTables broke in Ubuntu 12.10

2012-10-26 Thread Jason Moore

Where exactly do I submit the bug report? There doesn't seem to be a bug
option here: https://launchpad.net/ubuntu/quantal/+package/python-tables

Jason

On Thu, Oct 25, 2012 at 11:27 PM, Antonio Valentino <
antonio.valent...@tiscali.it> wrote:

> Hi Jason,
>
> Il giorno 26/ott/2012, alle ore 07:28, Jason Moore 
> ha scritto:
>
> > So it looks like python-tables in Ubuntu 12.10 requires libhdf5-7 and
> libhdf5-7 has /usr/lib/libhdf5.so.7 not libhdf5.so.6.
>
> Correct, the hdf5 package has been updated in ubuntu 12.10.
> If you use the standard python-tables package from ubuntu repositories
> please file a bug report on launchpad.
>
>
> > Jason
> >
> > On Thu, Oct 25, 2012 at 4:10 PM, Aquil Abdullah <
> aquil.abdul...@gmail.com> wrote:
> > Can you check to see if libhdf5.so is in your path? If not, you can add
> it to the path where it resides to your PATH variable.
> >
> > Hopefully, that helps.
> >
> > Aquil H. Abdullah
> >
> > On Oct 25, 2012, at 18:42, Jason Moore  wrote:
> >
> >> I just updated to Ubuntu 12.10 and my pytables install is broken. I
> reinstalled and it seems like I have hdf5 1.8.4 installed but I get this
> error:
> >>
> >> moorepants@moorepants-LT:BicycleDataProcessor(master)$ vitables
> InstrumentedBicycleData.h5
> >> Traceback (most recent call last):
> >>   File "/usr/bin/vitables", line 105, in 
> >> main(sys.argv)
> >>   File "/usr/bin/vitables", line 48, in main
> >> from vitables.vtapp import VTApp
> >>   File "/usr/share/vitables/vitables/vtapp.py", line 35, in 
> >> import tables
> >>   File "/usr/local/lib/python2.7/dist-packages/tables/__init__.py",
> line 30, in 
> >> from tables.utilsExtension import getPyTablesVersion, getHDF5Version
> >> ImportError: libhdf5.so.6: cannot open shared object file: No such file
> or directory
> >>
> >> What am I missing?
> >>
> >> Jason
>
>
> Anyway you can also use the eotools PPA [1] that has a more updated
> version of pytables: 2.4 against 2.3.1 of the official universe repo.
>
> [1]
> https://launchpad.net/~a.valentino/+archive/eotools?field.series_filter=quantal
>
> best regards
>
>
> --
> Antonio Valentino
>
>
>
> --
> Everyone hates slow websites. So do we.
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Re: [Pytables-users] PyTables broke in Ubuntu 12.10

Re: [Pytables-users] PyTables broke in Ubuntu 12.10

Re: [Pytables-users] PyTables broke in Ubuntu 12.10

Re: [Pytables-users] PyTables broke in Ubuntu 12.10

Re: [Pytables-users] PyTables broke in Ubuntu 12.10

Re: [Pytables-users] PyTables broke in Ubuntu 12.10

Re: [Pytables-users] PyTables broke in Ubuntu 12.10

Re: [Pytables-users] PyTables broke in Ubuntu 12.10

Re: [Pytables-users] PyTables broke in Ubuntu 12.10

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