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

Victor Gensini vgensini at niu.edu
Fri Mar 16 18:49:02 MDT 2018


Fixed! Thank you!


---------------------------------------

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://a><http://atlas.niu.edu>

________________________________
From: Kevin Hallock <hallock at ucar.edu>
Sent: Friday, March 16, 2018 11:47:44 AM
To: Victor Gensini
Cc: pyngl-talk at ucar.edu talk
Subject: Re: [pyngl-talk] pyngl-talk Digest, Vol 145, Issue 6

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<mailto: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<mailto:hallock at ucar.edu>>
Sent: Thursday, March 1, 2018 5:55:55 PM
To: 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 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. 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:
Send pyngl-talk mailing list submissions to
        pyngl-talk at ucar.edu<mailto:pyngl-talk at ucar.edu>

To subscribe or unsubscribe via the World Wide Web, visit
        http://mailman.ucar.edu/mailman/listinfo/pyngl-talk
or, via email, send a message with subject or body 'help' to
        pyngl-talk-request at ucar.edu<mailto:pyngl-talk-request at ucar.edu>

You can reach the person managing the list at
        pyngl-talk-owner at ucar.edu<mailto:pyngl-talk-owner at ucar.edu>

When replying, please edit your Subject line so it is more specific
than "Re: Contents of pyngl-talk digest..."


Today's Topics:

   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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.ucar.edu/pipermail/pyngl-talk/attachments/20171217/a6042ab4/attachment-0001.html>

------------------------------

Subject: Digest Footer

_______________________________________________
pyngl-talk mailing list
pyngl-talk at ucar.edu<mailto:pyngl-talk at ucar.edu>
http://mailman.ucar.edu/mailman/listinfo/pyngl-talk


------------------------------

End of pyngl-talk Digest, Vol 145, Issue 6
******************************************

_______________________________________________
pyngl-talk mailing list
List instructions, subscriber options, unsubscribe:
http://mailman.ucar.edu/mailman/listinfo/pyngl-talk

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.ucar.edu/pipermail/pyngl-talk/attachments/20180317/92fd6d93/attachment-0001.html>


More information about the pyngl-talk mailing list