[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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