[pyngl-talk] missing shared library for PyNIO

Marcia Branstetter branstetterm at ornl.gov
Thu Feb 9 12:41:54 MST 2017


Hi Kevin,

I tried this, but got an error message when I tried to create the new 
myenv2:

[mbranst at or-condo-login02 ~]$ conda create -n myenv2 --file 
package-list.txt
Fetching package metadata .........


PackageNotFoundError: Package not found: '' Package missing in current 
linux-64 channels:
   - ca-certificates 2016.9.26 0

You can search for packages on anaconda.org with

     anaconda search -t conda ca-certificates

You may need to install the anaconda-client command line client with

     conda install anaconda-client
-------------------------------------------------
I tried those suggestions, but still kept getting the same error.

Thanks,
Marcia

On Wed, 8 Feb 2017, Kevin Hallock wrote:

> 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/N
>             io.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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