[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:
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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
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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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