[pyngl-talk] missing shared library for PyNIO
Kevin Hallock
hallock at ucar.edu
Wed Feb 8 17:06:28 MST 2017
Hi Marcia,
The conda-forge automated build system is currently having issues building a new version of PyNGL, although PyNIO was successfully rebuilt yesterday. The problem now is that certain packages that both PyNIO and PyNGL depend on have been updated.
I have tried to create an environment containing both PyNIO and PyNGL using older dependencies, but I have not been able to find a working combination of dependencies (although I am certain one exists).
PyNIO is currently working if you do not also install PyNGL, and I have been working with conda-forge to get the new version of PyNGL released as soon as possible.
If you still have access to the conda environment that worked for you several weeks ago, you could try the following (an example from “conda list --help”):
Save packages for future use:
conda list --export > package-list.txt
Reinstall packages from an export file:
conda create -n myenv --file package-list.txt
I have no experience using “conda list” and “conda create” like this, but it might allow you to duplicate the environment you had before.
I’m sorry for the inconvenience, hopefully we’ll have PyNGL working again shortly.
Kevin
> On Feb 8, 2017, at 1:31 PM, Marcia Branstetter <branstetterm at ornl.gov> wrote:
>
> Hi Kevin,
>
> Here is the output:
> [mbranst at or-condo-login02 ~]$ conda list -n pyn_test
> # packages in environment at /home/mbranst/miniconda2/envs/pyn_test:
> #
> bzip2 1.0.6 3
> ca-certificates 2016.9.26 0 conda-forge
> cairo 1.14.6 0 conda-forge
> certifi 2016.2.28 py27_0
> curl 7.52.1 0
> expat 2.1.0 0
> fontconfig 2.11.1 6 conda-forge
> freetype 2.6.3 1 conda-forge
> freexl 1.0.2 1 conda-forge
> g2clib 1.6.0 2 conda-forge
> gdal 2.1.3 np111py27_1 conda-forge
> geos 3.5.0 0
> giflib 5.1.4 0 conda-forge
> gsl 2.2.1 0
> hdf4 4.2.11 0
> hdf5 1.8.17 1
> hdfeos2 2.19.1 7 conda-forge
> hdfeos5 5.1.15 6 conda-forge
> icu 56.1 4 conda-forge
> jasper 1.900.1 4 conda-forge
> jbig 2.1 0
> jpeg 9b 0
> json-c 0.12 0 conda-forge
> kealib 1.4.6 0
> libdap4 3.18.3 2 conda-forge
> libgcc 5.2.0 0
> libgfortran 3.0.0 1
> libiconv 1.14 0
> libnetcdf 4.4.1.1 2 conda-forge
> libpng 1.6.28 0 conda-forge
> libpq 9.5.4 0
> libspatialite 4.3.0a 14 conda-forge
> libtiff 4.0.6 3
> libxml2 2.9.4 0
> mkl 2017.0.1 0
> ncl 6.3.0 2 conda-forge
> ncurses 5.9 10
> numpy 1.11.3 py27_0
> openjpeg 2.1.2 2 conda-forge
> openssl 1.0.2k 0
> pcre 8.39 1
> pip 9.0.1 py27_1
> pixman 0.34.0 0
> pkg-config 0.28 1
> proj4 4.9.3 2 conda-forge
> pyngl 1.5.0_beta20161122 np111py27_1 conda-forge
> pynio 1.5.0_beta20160623 np111py27_14 conda-forge
> python 2.7.13 0
> readline 6.2 2
> setuptools 27.2.0 py27_0
> sqlite 3.13.0 0
> tk 8.5.18 0
> udunits2 2.2.23 0 conda-forge
> util-linux 2.21 0
> wheel 0.29.0 py27_0
> xerces-c 3.1.4 0
> xz 5.2.2 1
> zlib 1.2.8 3
>
> Thanks,
> Marcia
>
>
> On Tue, 7 Feb 2017, Kevin Hallock wrote:
>
>> Hi Marcia,
>>
>> Could you please run “conda list -n pyn_test” and reply with the output?
>>
>> The conda-forge project has been rebuilding packages the past few days to address issues with libicu like what you’ve experienced.
>>
>> Thanks,
>> Kevin
>>
>>> On Feb 7, 2017, at 1:23 PM, Marcia Branstetter <branstetterm at ornl.gov> wrote:
>>>
>>> Hi,
>>>
>>> I installed PyNIO and PyNGL on a computer:
>>> Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016 x86_64
>>> x86_64 x86_64 GNU/Linux
>>> today, using
>>> conda create --name pyn_test --channel conda-forge pynio
>>> pyngl
>>>
>>> but after I activate pyn_test, go into python and then try to import Nio,
>>> I get an error message:
>>>>>> import Nio
>>> Traceback (most recent call last):
>>> File "<stdin>", line 1, in <module>
>>> File
>>> "/home/mbranst/miniconda2/envs/pyn_test/lib/python2.7/site-packages/PyNIO/Nio.py",
>>> line 83, in <module>
>>> from nio import *
>>> ImportError: libicui18n.so.58: cannot open shared object file: No such
>>> file or directory
>>>>>> import Ngl
>>> Segmentation fault (core dumped)
>>>
>>> If I import Ngl first, and print the version, I get
>>>>>> import Ngl
>>>>>> print Ngl.__version__
>>> 1.5.0_beta20161122
>>>
>>> A few weeks ago, I installed PyNIO and PyNGL in the same way on another
>>> linux machine, and it's been working fine.
>>>
>>> I tried installing on a linux virtual machine today and got the same
>>> errors.
>>>
>>> Thanks,
>>> Marcia Branstetter
>>>
>>>
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>>
>>
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