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NCAR / pynio

PyNIO is a multi-format data I/O package with a NetCDF-style interface
http://www.pyngl.ucar.edu/Nio.shtml
Apache License 2.0
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Unable to install PyNIO and PyNGL in Debian Linux #23

Closed NJUlsg closed 6 years ago

NJUlsg commented 6 years ago

Hi, I try to install pynio and pyngl in Debian Linux (running in a virtual machine) by using "conda create --name pyn_env --channel conda-forge pynio pyngl", but it failed.

These are details:

UnsatisfiableError: The following specifications were found to be in conflict:

shigan@debian:~$ conda create --name pyn_env --channel conda-forge pyngl Fetching package metadata ............. Solving package specifications: .

UnsatisfiableError: The following specifications were found to be in conflict:

- conda list:

shigan@debian:~$ conda list

packages in environment at /home/shigan/miniconda2:

# cffi 1.9.1 py27_0 defaults conda 4.3.14 py27_0 defaults conda-env 2.6.0 0 defaults cryptography 1.7.1 py27_0 defaults enum34 1.1.6 py27_0 defaults idna 2.2 py27_0 defaults ipaddress 1.0.18 py27_0 defaults libffi 3.2.1 1 defaults openssl 1.0.2k 1 defaults pip 9.0.1 py27_1 defaults pyasn1 0.1.9 py27_0 defaults pycosat 0.6.1 py27_1 defaults pycparser 2.17 py27_0 defaults pyopenssl 16.2.0 py27_0 defaults python 2.7.13 0 defaults readline 6.2 2 defaults requests 2.12.4 py27_0 defaults ruamel_yaml 0.11.14 py27_1 defaults setuptools 27.2.0 py27_0 defaults six 1.10.0 py27_0 defaults sqlite 3.13.0 0 defaults tk 8.5.18 0 defaults wheel 0.29.0 py27_0 defaults yaml 0.1.6 0 defaults zlib 1.2.8 3 defaults

- conda info:

shigan@debian:~$ conda info Current conda install:

           platform : linux-64
      conda version : 4.3.14
   conda is private : False
  conda-env version : 4.3.14
conda-build version : not installed
     python version : 2.7.13.final.0
   requests version : 2.12.4
   root environment : /home/shigan/miniconda2  (writable)
default environment : /home/shigan/miniconda2
   envs directories : /home/shigan/miniconda2/envs
                      /home/shigan/.conda/envs
      package cache : /home/shigan/miniconda2/pkgs
                      /home/shigan/.conda/pkgs
       channel URLs : https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64
                      https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch
                      https://repo.continuum.io/pkgs/free/linux-64
                      https://repo.continuum.io/pkgs/free/noarch
                      https://repo.continuum.io/pkgs/r/linux-64
                      https://repo.continuum.io/pkgs/r/noarch
                      https://repo.continuum.io/pkgs/pro/linux-64
                      https://repo.continuum.io/pkgs/pro/noarch
        config file : /home/shigan/.condarc
       offline mode : False
         user-agent : conda/4.3.14 requests/2.12.4 CPython/2.7.13 Linux/4.9.0-7-amd64 debian/9.5 glibc/2.24
            UID:GID : 1000:1000
khallock commented 6 years ago

Hi @NJUlsg,

Thanks for reporting this issue. I tried to reproduce the problem on my own Debian 9 virtual machine, but found that the conda create ... command that caused problems for you seemed to work correctly for me. One thing that I noticed is that your conda info output above indicates that you're using conda v4.3.14; for comparison, I've got conda v4.5.4 on my virtual machine. Could you please try running conda update --all and then try re-running the conda create ... command?

NJUlsg commented 6 years ago

Thanks for the help! @khallock ,

PyNIO and PyNGL could be installed now. But it still some problems occurred when I tried importing PyNIO in pyn_env.

I used conda create --name pyn_env pynio pyngl to install them from Tsinghua Open Source Mirror (https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/) instead of conda create --name pyn_env --channel conda-forge pynio pyngl, because it is too slow for me to connect conda-forge.

NJUlsg commented 6 years ago

I found two versions of libpoppler in my Debian:

shigan@debian:~$ ls /usr/lib/ | grep libpoppler
libpoppler.so.18
libpoppler.so.71
NJUlsg commented 6 years ago

Hi @khallock ,

I created two environments, one contains pynio and ncl which is called pynio_ncl_env, the other contains pyngl and ncl which is called pyngl_ncl_env. I find that pynio and ncl could run normally in pynio_ncl_env. But in pyngl_ncl_env only pyngl could run without problem.

Here are details:

pyngl_ncl_env

NCL could not run.

(pyngl_ncl_env) shigan@debian:~$ ncl
ncl: error while loading shared libraries: libpoppler.so.71: cannot open shared object file: No such file or directory

Ngl could be imported.

(pyngl_ncl_env) shigan@debian:~$ python
Python 2.7.15 | packaged by conda-forge | (default, Jul 27 2018, 10:26:36) 
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Ngl
>>> 
>>> Ngl.__version__
'1.5.0'
>>> exit()

Variable: x Type: integer Total Size: 4 bytes 1 values Number of Dimensions: 1 Dimensions and sizes: [1] Coordinates: (0) 1 ncl 2> exit (pynio_ncl_env) shigan@debian:~$ python Python 3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:53:17) [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux Type "help", "copyright", "credits" or "license" for more information.

import Nio Nio.version '1.5.1'

- conda list:

(pynio_ncl_env) shigan@debian:~$ conda list

packages in environment at /home/shigan/miniconda2/envs/pynio_ncl_env:

#

Name Version Build Channel

blas 1.1 openblas https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge boost-cpp 1.67.0 h3a22d5f_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge bzip2 1.0.6 h470a237_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge ca-certificates 2018.4.16 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge cairo 1.14.12 he56eebe_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge certifi 2018.8.13 py36_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge curl 7.61.0 h93b3f91_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge esmf 7.1.0r ha678704_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge expat 2.2.5 hfc679d8_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge fontconfig 2.13.0 hd36ec8e_5 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge freetype 2.8.1 hfa320df_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge freexl 1.0.5 hf837533_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge g2clib 1.6.0 5 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge geos 3.6.2 hfc679d8_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge geotiff 1.4.2 hb54a4aa_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge gettext 0.19.8.1 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge giflib 5.1.4 h470a237_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge glib 2.55.0 h464dc38_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge gsl 2.2.1 blas_openblas_4 [blas_openblas] https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge hdf4 4.2.13 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge hdf5 1.10.2 hc401514_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge hdfeos2 2.19.1 8 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge hdfeos5 5.1.16 h647bee3_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge icu 58.2 hfc679d8_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge jasper 1.900.1 4 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge jpeg 9c h470a237_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge json-c 0.12.1 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge kealib 1.4.9 h0bee7d0_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge krb5 1.14.6 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libffi 3.2.1 hfc679d8_4 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libgcc-ng 7.2.0 hdf63c60_3 defaults libgdal 2.2.4 h25f9fa3_7 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libgfortran 3.0.0 1 defaults libiconv 1.15 h470a237_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libkml 1.3.0 hccc92b1_8 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libnetcdf 4.6.1 he6cff42_5 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libpng 1.6.34 ha92aebf_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libpq 9.6.3 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libspatialite 4.3.0a hdfcc80b_21 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libssh2 1.8.0 h5b517e9_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libstdcxx-ng 7.2.0 hdf63c60_3 defaults libtiff 4.0.9 he6b73bb_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libuuid 2.32.1 h470a237_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libxcb 1.13 h470a237_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libxml2 2.9.8 h422b904_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge mpi 1.0 mpich https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge mpich 3.2.1 h26a2512_4 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge ncl 6.5.0 blas_openblashe663f49_0 [blas_openblas] https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge ncurses 6.1 hfc679d8_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge netcdf-fortran 4.4.4 h4363f12_8 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge numpy 1.15.0 py36_blas_openblashd3ea46f_200 [blas_openblas] https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge openblas 0.2.20 8 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge openjpeg 2.3.0 h0e734dc_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge openssl 1.0.2o h470a237_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge pcre 8.41 h470a237_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge pip 18.0 py36_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge pixman 0.34.0 2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge poppler 0.61.1 3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge poppler-data 0.4.9 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge proj4 4.9.3 5 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge pthread-stubs 0.4 h470a237_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge pynio 1.5.1 py36h36f4ed2_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge python 3.6.6 h5001a0f_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge readline 7.0 haf1bffa_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge setuptools 40.0.0 py36_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge sqlite 3.24.0 h2f33b56_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge tk 8.6.8 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge udunits2 2.2.27.6 h3a4f0e9_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge util-linux 2.21 0 defaults wheel 0.31.1 py36_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xerces-c 3.2.0 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-imake 1.0.7 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-kbproto 1.0.7 h470a237_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libice 1.0.9 h470a237_4 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libsm 1.2.2 h8c8a85c_6 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libx11 1.6.5 h470a237_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libxau 1.0.8 h470a237_6 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libxaw 1.0.13 h470a237_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libxdmcp 1.1.2 h470a237_7 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libxext 1.3.3 h470a237_4 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libxmu 1.1.2 h470a237_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libxpm 3.5.12 h470a237_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libxrender 0.9.10 h470a237_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-libxt 1.1.5 h470a237_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-makedepend 1.0.5 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-renderproto 0.11.1 h470a237_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-xextproto 7.3.0 h470a237_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xorg-xproto 7.0.31 h470a237_7 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge xz 5.2.4 h470a237_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge zlib 1.2.11 h470a237_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge

ocefpaf commented 6 years ago

@NJUlsg and @khallock the situation with conda is broken at the moment due to https://github.com/conda/conda/issues/7626

(please help us by make some noise there :wink:)

A workaround is to remove one of the channel completely. Because the packages here are only available on conda-forge you have to remove defaults (from your .condarc and env specification).

Let me know if that works for you.

ocefpaf commented 6 years ago

BTW @NJUlsg your old conda error was better than the broken env that newer conda gives us :unamused:

khallock commented 6 years ago

Thanks for all of the information, @NJUlsg!

I believe this issue should now be fixed. New builds of NCL, PyNIO, and PyNGL have all been created today.

NJUlsg commented 6 years ago

Thank you for the help @khallock @ocefpaf , PyNIO, PyNGL and NCL work well now!

@ocefpaf, firstly I removed all the channels before, then I added conda-forge channel from USTC Open Source Software Mirror and installed these packages successfully. Maybe there is something wrong with Tsinghua Open Source Mirror. 😉

ocefpaf commented 6 years ago

@ocefpaf, firstly I removed all the channels before, then I added conda-forge channel from USTC Open Source Software Mirror and installed these packages successfully.

Could be but it took a while for us to re-build them, so maybe you got us in the middle of the rebuild.

BTW, :+1: on this issue are welcomed. It is aimed at fixing this for good in conda itself.