[pyngl-talk] pyngl-talk Digest, Vol 145, Issue 6

Kevin Hallock hallock at ucar.edu
Fri Mar 16 10:47:44 MDT 2018


Hi Victor,

I’m sorry for the delay in responding.

With your “spc_out” environment activated, could you please try running “conda update --all -c conda-forge”? This should hopefully get all of the dependencies in sync.

Thanks,
Kevin

> On Mar 8, 2018, at 1:46 PM, Victor Gensini <vgensini at niu.edu> wrote:
> 
> Hi Kevin, 
> 
> (spc_out) [vgensini at atlas cfsr]$ conda list -n spc_out
> # packages in environment at /home/vgensini/Programs/anaconda2/envs/spc_out:
> #
> backports                 1.0                      py27_1    conda-forge
> backports.functools_lru_cache 1.5                      py27_0    conda-forge
> backports_abc             0.5                      py27_0    conda-forge
> basemap                   1.1.0                    py27_4    conda-forge
> blas                      1.1                    openblas    conda-forge
> boost                     1.66.0                   py27_1    conda-forge
> boost-cpp                 1.66.0                        1    conda-forge
> bzip2                     1.0.6                         1    conda-forge
> ca-certificates           2017.08.26           h1d4fec5_0
> cairo                     1.14.12              h77bcde2_0
> certifi                   2018.1.18                py27_0
> curl                      7.55.1                        0    conda-forge
> cycler                    0.10.0                   py27_0    conda-forge
> dbus                      1.10.22                       0    conda-forge
> expat                     2.2.5                         0    conda-forge
> fontconfig                2.12.6                        0    conda-forge
> freetype                  2.8.1                         0    conda-forge
> freexl                    1.0.4                         0    conda-forge
> functools32               3.2.3.2                  py27_2    conda-forge
> g2clib                    1.6.0                         5    conda-forge
> geos                      3.6.2                         1    conda-forge
> giflib                    5.1.4                         0    conda-forge
> glib                      2.53.6               h5d9569c_2
> gst-plugins-base          1.12.4               h33fb286_0
> gstreamer                 1.12.4               hb53b477_0
> hdf4                      4.2.13                        0    conda-forge
> hdf5                      1.10.1                        2    conda-forge
> hdfeos2                   2.19.1                        8    conda-forge
> hdfeos5                   5.1.16                        0    conda-forge
> icu                       58.2                          0    conda-forge
> jasper                    1.900.1                       4    conda-forge
> jpeg                      9b                            2    conda-forge
> json-c                    0.12.1                        0    conda-forge
> kealib                    1.4.7                         4    conda-forge
> kiwisolver                1.0.1                    py27_1    conda-forge
> krb5                      1.14.2                        0    conda-forge
> libdap4                   3.19.2                        1    conda-forge
> libedit                   3.1                  heed3624_0
> libffi                    3.2.1                hd88cf55_4
> libgcc-ng                 7.2.0                h7cc24e2_2
> libgdal                   2.2.2                h804cdde_1
> libgfortran               3.0.0                         1
> libiconv                  1.15                          0    conda-forge
> libkml                    1.3.0                         6    conda-forge
> libnetcdf                 4.4.1.1                      10    conda-forge
> libpng                    1.6.34                        0    conda-forge
> libpq                     9.6.6                h4e02ad2_0
> libspatialite             4.3.0a              h72746d6_18
> libssh2                   1.8.0                         2    conda-forge
> libstdcxx-ng              7.2.0                h7a57d05_2
> libtiff                   4.0.9                         0    conda-forge
> libxcb                    1.12                          1    conda-forge
> libxml2                   2.9.7                         0    conda-forge
> matplotlib                2.2.0                    py27_0    conda-forge
> ncurses                   6.0                  h9df7e31_2
> numpy                     1.14.1          py27_blas_openblas_200  [blas_openblas]  conda-forge
> openblas                  0.2.20                        7    conda-forge
> openjpeg                  2.3.0                         2    conda-forge
> openssl                   1.0.2n               hb7f436b_0
> pcre                      8.39                          0    conda-forge
> pip                       9.0.1                    py27_5
> pixman                    0.34.0                        1    conda-forge
> poppler                   0.60.1               hc909a00_0
> poppler-data              0.4.8                         0    conda-forge
> proj4                     4.9.3                         5    conda-forge
> pynio                     1.5.0                    py27_3    conda-forge
> pyparsing                 2.2.0                    py27_0    conda-forge
> pyproj                    1.9.5.1                  py27_0    conda-forge
> pyqt                      5.6.0                    py27_4    conda-forge
> pyshp                     1.2.12                     py_0    conda-forge
> python                    2.7.14              h1571d57_29
> python-dateutil           2.6.1                    py27_0    conda-forge
> pytz                      2018.3                     py_0    conda-forge
> qt                        5.6.2               h974d657_12
> readline                  7.0                  ha6073c6_4
> setuptools                38.5.1                   py27_0
> singledispatch            3.4.0.3                  py27_0    conda-forge
> sip                       4.18                     py27_1    conda-forge
> six                       1.11.0                   py27_1    conda-forge
> sqlite                    3.22.0               h1bed415_0
> ssl_match_hostname        3.5.0.1                  py27_1    conda-forge
> subprocess32              3.2.7                    py27_0    conda-forge
> tk                        8.6.7                hc745277_3
> tornado                   4.5.3                    py27_0    conda-forge
> util-linux                2.21                          0
> wheel                     0.30.0           py27h2bc6bb2_1
> xerces-c                  3.2.0                         0    conda-forge
> xorg-libxau               1.0.8                         3    conda-forge
> xorg-libxdmcp             1.1.2                         3    conda-forge
> xz                        5.2.3                         0    conda-forge
> zlib                      1.2.11               ha838bed_2
> 
> 
> -----------------
> 
> (spc_out) [vgensini at atlas cfsr]$ python
> 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
> 
> ---------------------------------------
> 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://atlas.niu.edu <http://atlas.niu.edu/>
>  <http://a/> <http://atlas.niu.edu/>
> From: Kevin Hallock <hallock at ucar.edu>
> Sent: Thursday, March 1, 2018 5:55:55 PM
> To: Victor Gensini
> Cc: pyngl-talk at ucar.edu talk
> Subject: Re: [pyngl-talk] pyngl-talk Digest, Vol 145, Issue 6
>  
> 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 <mailto: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 <mailto:hallock at ucar.edu>>
>> Sent: Monday, December 18, 2017 3:33:14 PM
>> To: Paul Madden; Victor Gensini
>> Cc: pyngl-talk at ucar.edu <mailto: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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>>> Today's Topics:
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>>>    1. PyNGL install failure with Anaconda (Victor Gensini)
>>> 
>>> 
>>> ----------------------------------------------------------------------
>>> 
>>> 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>>
>>> 
>>> Content-Type: text/plain; charset="iso-8859-1"
>>> 
>>> 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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