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<p style="margin-top:0;margin-bottom:0">Hi Kevin, </p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"></p>
<div>(spc_out) [vgensini@atlas cfsr]$ conda list -n spc_out</div>
<div># packages in environment at /home/vgensini/Programs/anaconda2/envs/spc_out:</div>
<div>#</div>
<div>backports 1.0 py27_1 conda-forge</div>
<div>backports.functools_lru_cache 1.5 py27_0 conda-forge</div>
<div>backports_abc 0.5 py27_0 conda-forge</div>
<div>basemap 1.1.0 py27_4 conda-forge</div>
<div>blas 1.1 openblas conda-forge</div>
<div>boost 1.66.0 py27_1 conda-forge</div>
<div>boost-cpp 1.66.0 1 conda-forge</div>
<div>bzip2 1.0.6 1 conda-forge</div>
<div>ca-certificates 2017.08.26 h1d4fec5_0</div>
<div>cairo 1.14.12 h77bcde2_0</div>
<div>certifi 2018.1.18 py27_0</div>
<div>curl 7.55.1 0 conda-forge</div>
<div>cycler 0.10.0 py27_0 conda-forge</div>
<div>dbus 1.10.22 0 conda-forge</div>
<div>expat 2.2.5 0 conda-forge</div>
<div>fontconfig 2.12.6 0 conda-forge</div>
<div>freetype 2.8.1 0 conda-forge</div>
<div>freexl 1.0.4 0 conda-forge</div>
<div>functools32 3.2.3.2 py27_2 conda-forge</div>
<div>g2clib 1.6.0 5 conda-forge</div>
<div>geos 3.6.2 1 conda-forge</div>
<div>giflib 5.1.4 0 conda-forge</div>
<div>glib 2.53.6 h5d9569c_2</div>
<div>gst-plugins-base 1.12.4 h33fb286_0</div>
<div>gstreamer 1.12.4 hb53b477_0</div>
<div>hdf4 4.2.13 0 conda-forge</div>
<div>hdf5 1.10.1 2 conda-forge</div>
<div>hdfeos2 2.19.1 8 conda-forge</div>
<div>hdfeos5 5.1.16 0 conda-forge</div>
<div>icu 58.2 0 conda-forge</div>
<div>jasper 1.900.1 4 conda-forge</div>
<div>jpeg 9b 2 conda-forge</div>
<div>json-c 0.12.1 0 conda-forge</div>
<div>kealib 1.4.7 4 conda-forge</div>
<div>kiwisolver 1.0.1 py27_1 conda-forge</div>
<div>krb5 1.14.2 0 conda-forge</div>
<div>libdap4 3.19.2 1 conda-forge</div>
<div>libedit 3.1 heed3624_0</div>
<div>libffi 3.2.1 hd88cf55_4</div>
<div>libgcc-ng 7.2.0 h7cc24e2_2</div>
<div>libgdal 2.2.2 h804cdde_1</div>
<div>libgfortran 3.0.0 1</div>
<div>libiconv 1.15 0 conda-forge</div>
<div>libkml 1.3.0 6 conda-forge</div>
<div>libnetcdf 4.4.1.1 10 conda-forge</div>
<div>libpng 1.6.34 0 conda-forge</div>
<div>libpq 9.6.6 h4e02ad2_0</div>
<div>libspatialite 4.3.0a h72746d6_18</div>
<div>libssh2 1.8.0 2 conda-forge</div>
<div>libstdcxx-ng 7.2.0 h7a57d05_2</div>
<div>libtiff 4.0.9 0 conda-forge</div>
<div>libxcb 1.12 1 conda-forge</div>
<div>libxml2 2.9.7 0 conda-forge</div>
<div>matplotlib 2.2.0 py27_0 conda-forge</div>
<div>ncurses 6.0 h9df7e31_2</div>
<div>numpy 1.14.1 py27_blas_openblas_200 [blas_openblas] conda-forge</div>
<div>openblas 0.2.20 7 conda-forge</div>
<div>openjpeg 2.3.0 2 conda-forge</div>
<div>openssl 1.0.2n hb7f436b_0</div>
<div>pcre 8.39 0 conda-forge</div>
<div>pip 9.0.1 py27_5</div>
<div>pixman 0.34.0 1 conda-forge</div>
<div>poppler 0.60.1 hc909a00_0</div>
<div>poppler-data 0.4.8 0 conda-forge</div>
<div>proj4 4.9.3 5 conda-forge</div>
<div>pynio 1.5.0 py27_3 conda-forge</div>
<div>pyparsing 2.2.0 py27_0 conda-forge</div>
<div>pyproj 1.9.5.1 py27_0 conda-forge</div>
<div>pyqt 5.6.0 py27_4 conda-forge</div>
<div>pyshp 1.2.12 py_0 conda-forge</div>
<div>python 2.7.14 h1571d57_29</div>
<div>python-dateutil 2.6.1 py27_0 conda-forge</div>
<div>pytz 2018.3 py_0 conda-forge</div>
<div>qt 5.6.2 h974d657_12</div>
<div>readline 7.0 ha6073c6_4</div>
<div>setuptools 38.5.1 py27_0</div>
<div>singledispatch 3.4.0.3 py27_0 conda-forge</div>
<div>sip 4.18 py27_1 conda-forge</div>
<div>six 1.11.0 py27_1 conda-forge</div>
<div>sqlite 3.22.0 h1bed415_0</div>
<div>ssl_match_hostname 3.5.0.1 py27_1 conda-forge</div>
<div>subprocess32 3.2.7 py27_0 conda-forge</div>
<div>tk 8.6.7 hc745277_3</div>
<div>tornado 4.5.3 py27_0 conda-forge</div>
<div>util-linux 2.21 0</div>
<div>wheel 0.30.0 py27h2bc6bb2_1</div>
<div>xerces-c 3.2.0 0 conda-forge</div>
<div>xorg-libxau 1.0.8 3 conda-forge</div>
<div>xorg-libxdmcp 1.1.2 3 conda-forge</div>
<div>xz 5.2.3 0 conda-forge</div>
<div>zlib 1.2.11 ha838bed_2</div>
<div><br>
</div>
<br>
<p></p>
<p style="margin-top:0;margin-bottom:0">-----------------</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"></p>
<div>(spc_out) [vgensini@atlas cfsr]$ python</div>
<div>Python 2.7.14 |Anaconda, Inc.| (default, Dec 7 2017, 17:05:42)</div>
<div>[GCC 7.2.0] on linux2</div>
<div>Type "help", "copyright", "credits" or "license" for more information.</div>
<div>>>> import Nio</div>
<div>Traceback (most recent call last):</div>
<div> File "<stdin>", line 1, in <module></div>
<div> File "/home/vgensini/Programs/anaconda2/envs/spc_out/lib/python2.7/site-packages/PyNIO/Nio.py", line 83, in <module></div>
<div> from nio import *</div>
<div>ImportError: /home/vgensini/Programs/anaconda2/envs/spc_out/lib/python2.7/site-packages/PyNIO/../../../libgdal.so.20: undefined symbol: _ZN11xercesc_3_211InputSource11setEncodingEPKDs</div>
<br>
<p></p>
<div id="Signature">
<div id="divtagdefaultwrapper" dir="ltr" style="font-size:12pt; color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols">
<p><span style="font-family:Garamond,Georgia,serif; font-size:11pt">---------------------------------------</span></p>
<span style="font-size:11pt"></span><span style="font-family:Garamond,Georgia,serif; font-size:11pt"></span><span style="font-size:11pt"></span>
<p><span style="font-family:Garamond,Georgia,serif; font-size:11pt">Dr. Vittorio (Victor) A. Gensini</span></p>
<span style="font-size:11pt"></span><span style="font-family:Garamond,Georgia,serif; font-size:11pt"></span><span style="font-size:11pt"></span>
<p><span style="font-family:Garamond,Georgia,serif; font-size:11pt">Assistant Professor</span></p>
<span style="font-size:11pt"></span><span style="font-family:Garamond,Georgia,serif; font-size:11pt"></span><span style="font-size:11pt"></span>
<p><span style="font-family:Garamond,Georgia,serif; font-size:11pt">Department of Geographic and Atmospheric Sciences</span></p>
<span style="font-size:11pt"></span><span style="font-family:Garamond,Georgia,serif; font-size:11pt"></span><span style="font-size:11pt"></span>
<p><span style="font-family:Garamond,Georgia,serif; font-size:11pt">Northern Illinois University</span></p>
<p><span style="font-family:Garamond,Georgia,serif; font-size:11pt">Davis Hall (DH), Room 118</span></p>
<p><span style="font-family:Garamond,Georgia,serif; font-size:11pt">DeKalb, IL 60115</span></p>
<p><span style="font-family:Garamond,Georgia,serif; font-size:11pt"><a href="http://atlas.niu.edu" class="OWAAutoLink" id="LPNoLP">http://atlas.niu.edu</a><br>
</span></p>
<p><span style="font-family:Garamond,Georgia,serif; font-size:11pt"><a href="http://a" class="OWAAutoLink" id="LPNoLP"></a><a href="http://atlas.niu.edu" class="OWAAutoLink" id="LPNoLP"></a></span></p>
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<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Kevin Hallock <hallock@ucar.edu><br>
<b>Sent:</b> Thursday, March 1, 2018 5:55:55 PM<br>
<b>To:</b> Victor Gensini<br>
<b>Cc:</b> pyngl-talk@ucar.edu talk<br>
<b>Subject:</b> Re: [pyngl-talk] pyngl-talk Digest, Vol 145, Issue 6</font>
<div> </div>
</div>
<div class="" style="word-wrap:break-word">Hi Victor,
<div class=""><br class="">
</div>
<div class="">I just tried creating a fresh conda environment on both Mac and Linux using the command “<font face="Menlo" class="">conda install -c conda-forge -n pynio pynio</font>” and was unable to reproduce your error.</div>
<div class=""><br class="">
</div>
<div class="">Could you please run “<font face="Menlo" class="">conda list -n spc_out</font>” and reply with the output?</div>
<div class=""><br class="">
</div>
<div class="">Thanks,</div>
<div class="">Kevin</div>
<div class=""><br class="">
</div>
<div class="">
<div>
<blockquote type="cite" class="">
<div class="">On Feb 27, 2018, at 9:34 PM, Victor Gensini <<a href="mailto:vgensini@niu.edu" class="">vgensini@niu.edu</a>> wrote:</div>
<br class="x_Apple-interchange-newline">
<div class="">
<div id="x_divtagdefaultwrapper" dir="ltr" class="" style="font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; font-size:12pt; font-family:Garamond,Georgia,serif">
<div class="" style="margin-top:0px; margin-bottom:0px">Hi Kevin, </div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px">I just grabbed a fresh pynio conda install from the conda-forge channel and am getting a library error upon import:</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<p class="" style="margin-top:0px; margin-bottom:0px"></p>
<div class="">Python 2.7.14 |Anaconda, Inc.| (default, Dec 7 2017, 17:05:42)</div>
<div class="">[GCC 7.2.0] on linux2</div>
<div class="">Type "help", "copyright", "credits" or "license" for more information.</div>
<div class="">>>> import Nio</div>
<div class="">Traceback (most recent call last):</div>
<div class=""> File "<stdin>", line 1, in <module></div>
<div class=""> File "/home/vgensini/Programs/anaconda2/envs/spc_out/lib/python2.7/site-packages/PyNIO/Nio.py", line 83, in <module></div>
<div class=""> from nio import *</div>
<div class="">ImportError: /home/vgensini/Programs/anaconda2/envs/spc_out/lib/python2.7/site-packages/PyNIO/../../../<span class="" style="background-color:rgb(255,255,0)">libgdal.so.20: undefined symbol: _ZN11xercesc_3_211InputSource11setEncodingEPKDs</span></div>
<div class=""><br class="">
</div>
<br class="">
<p class="" style="margin-top:0px; margin-bottom:0px"></p>
<div class="" style="margin-top:0px; margin-bottom:0px">Best, </div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div id="x_Signature" class="">
<div id="x_divtagdefaultwrapper" dir="ltr" class="" style="font-size:12pt; font-family:Calibri,Helvetica,sans-serif,EmojiFont,'Apple Color Emoji','Segoe UI Emoji',NotoColorEmoji,'Segoe UI Symbol','Android Emoji',EmojiSymbols,EmojiFont,'Apple Color Emoji','Segoe UI Emoji',NotoColorEmoji,'Segoe UI Symbol','Android Emoji',EmojiSymbols,EmojiFont,'Apple Color Emoji','Segoe UI Emoji',NotoColorEmoji,'Segoe UI Symbol','Android Emoji',EmojiSymbols">
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-family:Garamond,Georgia,serif; font-size:11pt">---------------------------------------</span></div>
<span class="" style="font-size:11pt"></span><span class="" style="font-family:Garamond,Georgia,serif; font-size:11pt"></span><span class="" style="font-size:11pt"></span>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-family:Garamond,Georgia,serif; font-size:11pt">Dr. Vittorio (Victor) A. Gensini</span></div>
<span class="" style="font-size:11pt"></span><span class="" style="font-family:Garamond,Georgia,serif; font-size:11pt"></span><span class="" style="font-size:11pt"></span>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-family:Garamond,Georgia,serif; font-size:11pt">Assistant Professor</span></div>
<span class="" style="font-size:11pt"></span><span class="" style="font-family:Garamond,Georgia,serif; font-size:11pt"></span><span class="" style="font-size:11pt"></span>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-family:Garamond,Georgia,serif; font-size:11pt">Department of Geographic and Atmospheric Sciences</span></div>
<span class="" style="font-size:11pt"></span><span class="" style="font-family:Garamond,Georgia,serif; font-size:11pt"></span><span class="" style="font-size:11pt"></span>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-family:Garamond,Georgia,serif; font-size:11pt">Northern Illinois University</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-family:Garamond,Georgia,serif; font-size:11pt">Davis Hall (DH), Room 118</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-family:Garamond,Georgia,serif; font-size:11pt">DeKalb, IL 60115</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-family:Garamond,Georgia,serif; font-size:11pt"><a href="http://wcs.niu.edu/" class="x_OWAAutoLink" id="LPNoLP">http://wcs.niu.edu</a></span></div>
</div>
</div>
</div>
<hr tabindex="-1" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; display:inline-block; width:862.390625px">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; float:none; display:inline!important"></span>
<div id="x_divRplyFwdMsg" dir="ltr" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px">
<font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="x_Apple-converted-space"> </span>Kevin Hallock <<a href="mailto:hallock@ucar.edu" class="">hallock@ucar.edu</a>><br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Monday, December 18, 2017 3:33:14 PM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>Paul Madden; Victor Gensini<br class="">
<b class="">Cc:</b><span class="x_Apple-converted-space"> </span><a href="mailto:pyngl-talk@ucar.edu" class="">pyngl-talk@ucar.edu</a> talk<br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: [pyngl-talk] pyngl-talk Digest, Vol 145, Issue 6</font>
<div class=""> </div>
</div>
<div class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; word-wrap:break-word">
Hi Paul and Victor,
<div class=""><br class="">
</div>
<div class="">This is an issue that we are aware of. As Paul mentioned below, a solution to the existing issue with NCL<span class="x_Apple-converted-space"> </span><i class="">should</i> solve the problem for PyNGL as well.</div>
<div class=""><br class="">
</div>
<div class="">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.</div>
<div class=""><br class="">
</div>
<div class="">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.</div>
<div class="">
<div class=""><br class="">
</div>
<div class="">I’m sorry for the inconvenience,</div>
</div>
<div class="">Kevin</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On Dec 17, 2017, at 12:13 PM, Paul Madden <<a href="mailto:maddenp@colorado.edu" class="">maddenp@colorado.edu</a>> wrote:</div>
<br class="x_x_Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi Victor,
<div class=""><br class="">
</div>
<div class="">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: <a href="https://github.com/conda-forge/ncl-feedstock/issues/26" class="">https://github.com/conda-forge/ncl-feedstock/issues/26</a>.
You might like to follow that issue because, I think, the PyNGL install will work again when the NCL package is fixed.</div>
<div class=""><br class="">
</div>
<div class="">paul</div>
</div>
<div class="x_x_gmail_extra"><br class="">
<div class="x_x_gmail_quote">On Sun, Dec 17, 2017 at 12:00 PM,<span class="x_Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:pyngl-talk-request@ucar.edu" target="_blank" class="">pyngl-talk-request@ucar.edu</a>></span><span class="x_Apple-converted-space"> </span>wrote:<br class="">
<blockquote class="x_x_gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left-width:1px; border-left-style:solid; border-left-color:rgb(204,204,204); padding-left:1ex">
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Today's Topics:<br class="">
<br class="">
1. PyNGL install failure with Anaconda (Victor Gensini)<br class="">
<br class="">
<br class="">
------------------------------<wbr class="">------------------------------<wbr class="">----------<br class="">
<br class="">
Message: 1<br class="">
Date: Sun, 17 Dec 2017 02:46:20 +0000<br class="">
From: Victor Gensini <<a href="mailto:vgensini@niu.edu" class="">vgensini@niu.edu</a>><br class="">
To: "<a href="mailto:pyngl-talk@ucar.edu" class="">pyngl-talk@ucar.edu</a>" <<a href="mailto:pyngl-talk@ucar.edu" class="">pyngl-talk@ucar.edu</a>><br class="">
Subject: [pyngl-talk] PyNGL install failure with Anaconda<br class="">
Message-ID:<br class="">
<<a href="mailto:DM2PR04MB18682B90FB10902E36141905D5090@DM2PR04MB1868.namprd04.prod.outlook.com" class="">DM2PR04MB18682B90FB10902E3614<wbr class="">1905D5090@DM2PR04MB1868.<wbr class="">namprd04.prod.outlook.com</a>><br class="">
<br class="">
Content-Type: text/plain; charset="iso-8859-1"<br class="">
<br class="">
PyNGL users,<br class="">
<br class="">
<br class="">
I've had good luck in the past using conda to install pynio and pyngl to isolated environments.<br class="">
<br class="">
<br class="">
However, with the latest version of anaconda (5.0.1):<br class="">
<br class="">
<br class="">
[vgensini@atlas ~]$ conda create -n ngl -c conda-forge pyngl<br class="">
Fetching package metadata .............<br class="">
Solving package specifications: .<br class="">
<br class="">
UnsatisfiableError: The following specifications were found to be in conflict:<br class="">
- pyngl<br class="">
<br class="">
<br class="">
Running CentOS 7 3.10.0-693.5.2.el7.x86_64 GNU/Linux<br class="">
<br class="">
<br class="">
Running the same create env command for pynio results in a successful installation.<br class="">
<br class="">
<br class="">
Best,<br class="">
<br class="">
------------------------------<wbr class="">---------<br class="">
<br class="">
Dr. Vittorio (Victor) A. Gensini<br class="">
<br class="">
Assistant Professor<br class="">
<br class="">
Department of Geographic and Atmospheric Sciences<br class="">
<br class="">
Northern Illinois University<br class="">
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