[pyngl-talk] pyngl-talk Digest, Vol 145, Issue 6
Kevin Hallock
hallock at ucar.edu
Thu Mar 1 16:55:55 MST 2018
Hi Victor,
I just tried creating a fresh conda environment on both Mac and Linux using the command “conda install -c conda-forge -n pynio pynio” and was unable to reproduce your error.
Could you please run “conda list -n spc_out” and reply with the output?
Thanks,
Kevin
> On Feb 27, 2018, at 9:34 PM, Victor Gensini <vgensini at niu.edu> wrote:
>
> Hi Kevin,
>
> I just grabbed a fresh pynio conda install from the conda-forge channel and am getting a library error upon import:
>
> Python 2.7.14 |Anaconda, Inc.| (default, Dec 7 2017, 17:05:42)
> [GCC 7.2.0] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import Nio
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "/home/vgensini/Programs/anaconda2/envs/spc_out/lib/python2.7/site-packages/PyNIO/Nio.py", line 83, in <module>
> from nio import *
> ImportError: /home/vgensini/Programs/anaconda2/envs/spc_out/lib/python2.7/site-packages/PyNIO/../../../libgdal.so.20: undefined symbol: _ZN11xercesc_3_211InputSource11setEncodingEPKDs
>
>
> Best,
>
> ---------------------------------------
> Dr. Vittorio (Victor) A. Gensini
> Assistant Professor
> Department of Geographic and Atmospheric Sciences
> Northern Illinois University
> Davis Hall (DH), Room 118
> DeKalb, IL 60115
> http://wcs.niu.edu <http://wcs.niu.edu/>
> From: Kevin Hallock <hallock at ucar.edu>
> Sent: Monday, December 18, 2017 3:33:14 PM
> To: Paul Madden; Victor Gensini
> Cc: pyngl-talk at ucar.edu talk
> Subject: Re: [pyngl-talk] pyngl-talk Digest, Vol 145, Issue 6
>
> Hi Paul and Victor,
>
> This is an issue that we are aware of. As Paul mentioned below, a solution to the existing issue with NCL should solve the problem for PyNGL as well.
>
> The conda-forge project recently upgraded certain dependency packages; in particular, we’ve experienced problems getting the newest version of the HDF5 library to play nicely with a current-but-several-years-old HDFEOS5 library.
>
> We will try to get a fix for this onto conda-forge as soon as possible, but unfortunately some conda-forge compatibility/dependency issues are out of our (NCAR’s) control.
>
> I’m sorry for the inconvenience,
> Kevin
>
>> On Dec 17, 2017, at 12:13 PM, Paul Madden <maddenp at colorado.edu <mailto:maddenp at colorado.edu>> wrote:
>>
>> Hi Victor,
>>
>> I reported the same issue on this mailing list two days ago. I believe the problem is that the PyNGL conda package depends on the NCL package, which is currently broken. I opened an issue with the NCL package maintainers here: https://github.com/conda-forge/ncl-feedstock/issues/26 <https://github.com/conda-forge/ncl-feedstock/issues/26>. You might like to follow that issue because, I think, the PyNGL install will work again when the NCL package is fixed.
>>
>> paul
>>
>> On Sun, Dec 17, 2017 at 12:00 PM, <pyngl-talk-request at ucar.edu <mailto:pyngl-talk-request at ucar.edu>> wrote:
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>> 1. PyNGL install failure with Anaconda (Victor Gensini)
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>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Sun, 17 Dec 2017 02:46:20 +0000
>> From: Victor Gensini <vgensini at niu.edu <mailto:vgensini at niu.edu>>
>> To: "pyngl-talk at ucar.edu <mailto:pyngl-talk at ucar.edu>" <pyngl-talk at ucar.edu <mailto:pyngl-talk at ucar.edu>>
>> Subject: [pyngl-talk] PyNGL install failure with Anaconda
>> Message-ID:
>> <DM2PR04MB18682B90FB10902E36141905D5090 at DM2PR04MB1868.namprd04.prod.outlook.com <mailto:DM2PR04MB18682B90FB10902E36141905D5090 at DM2PR04MB1868.namprd04.prod.outlook.com>>
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>>
>> PyNGL users,
>>
>>
>> I've had good luck in the past using conda to install pynio and pyngl to isolated environments.
>>
>>
>> However, with the latest version of anaconda (5.0.1):
>>
>>
>> [vgensini at atlas ~]$ conda create -n ngl -c conda-forge pyngl
>> Fetching package metadata .............
>> Solving package specifications: .
>>
>> UnsatisfiableError: The following specifications were found to be in conflict:
>> - pyngl
>>
>>
>> Running CentOS 7 3.10.0-693.5.2.el7.x86_64 GNU/Linux
>>
>>
>> Running the same create env command for pynio results in a successful installation.
>>
>>
>> Best,
>>
>> ---------------------------------------
>>
>> Dr. Vittorio (Victor) A. Gensini
>>
>> Assistant Professor
>>
>> Department of Geographic and Atmospheric Sciences
>>
>> Northern Illinois University
>>
>> Davis Hall (DH), Room 118
>>
>> DeKalb, IL 60115
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