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Tricky to use fiona from defaults #60

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ceball opened this issue May 28, 2018 · 1 comment
Closed

Tricky to use fiona from defaults #60

ceball opened this issue May 28, 2018 · 1 comment
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@msarahan

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@ceball
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ceball commented May 28, 2018 •
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I can't seem to import fiona from defaults (unless I constrain the version of poppler), whereas I can from conda-forge (as long as I make sure gdal is also from conda-forge).

defaults

$ conda create -n popplertest python=3.6
Solving environment: done

## Package Plan ##

  environment location: /cio/mc3/envs/popplertest

  added / updated specs: 
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2018.4.16          |           py36_0         142 KB

The following NEW packages will be INSTALLED:

    ca-certificates: 2018.03.07-0           
    certifi:         2018.4.16-py36_0       
    libedit:         3.1.20170329-h6b74fdf_2
    libffi:          3.2.1-hd88cf55_4       
    libgcc-ng:       7.2.0-hdf63c60_3       
    libstdcxx-ng:    7.2.0-hdf63c60_3       
    ncurses:         6.1-hf484d3e_0         
    openssl:         1.0.2o-h20670df_0      
    pip:             10.0.1-py36_0          
    python:          3.6.5-hc3d631a_2       
    readline:        7.0-ha6073c6_4         
    setuptools:      39.1.0-py36_0          
    sqlite:          3.23.1-he433501_0      
    tk:              8.6.7-hc745277_3       
    wheel:           0.31.1-py36_0          
    xz:              5.2.4-h14c3975_4       
    zlib:            1.2.11-ha838bed_2      

Proceed ([y]/n)? y


Downloading and Extracting Packages
certifi-2018.4.16    |  142 KB | : 100% 1.0/1 [00:00<00:00,  8.16it/s]               
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate popplertest
#
# To deactivate an active environment, use
#
#     $ conda deactivate

$ conda activate popplertest
(popplertest)$ conda install poppler fiona
Solving environment: done

## Package Plan ##

  environment location: /cio/mc3/envs/popplertest

  added / updated specs: 
    - fiona
    - poppler


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    poppler-data-0.4.9         |                0         3.5 MB
    click-plugins-1.0.3        |           py36_0           9 KB
    cligj-0.4.0                |           py36_0          14 KB
    ------------------------------------------------------------
                                           Total:         3.6 MB

The following NEW packages will be INSTALLED:

    blas:           1.0-mkl              
    bzip2:          1.0.6-h14c3975_5     
    cairo:          1.14.12-h8948797_3   
    click:          6.7-py36h5253387_0   
    click-plugins:  1.0.3-py36_0         
    cligj:          0.4.0-py36_0         
    curl:           7.60.0-h84994c4_0    
    expat:          2.2.5-he0dffb1_0     
    fiona:          1.7.10-py36h48a52f0_0
    fontconfig:     2.13.0-h9420a91_0    
    freetype:       2.9.1-h8a8886c_0     
    freexl:         1.0.5-h14c3975_0     
    gdal:           2.2.2-py36hc209d97_1 
    geos:           3.6.2-heeff764_2     
    giflib:         5.1.4-h26a3ec6_1     
    glib:           2.56.1-h000015b_0    
    hdf4:           4.2.13-h3ca952b_2    
    hdf5:           1.10.1-h9caa474_1    
    icu:            58.2-h9c2bf20_1      
    intel-openmp:   2018.0.0-8           
    jpeg:           9b-h024ee3a_2        
    json-c:         0.12.1-ha6a3662_2    
    kealib:         1.4.7-h79811e5_5     
    krb5:           1.16-h3f6afd0_6      
    libboost:       1.65.1-habcd387_4    
    libcurl:        7.60.0-h1ad7b7a_0    
    libdap4:        3.19.0-h5bd89bb_2    
    libgdal:        2.2.2-h804cdde_1     
    libgfortran-ng: 7.2.0-hdf63c60_3     
    libkml:         1.3.0-h9d32c78_3     
    libnetcdf:      4.4.1.1-h816af47_8   
    libpng:         1.6.34-hb9fc6fc_0    
    libpq:          10.3-h1ad7b7a_0      
    libspatialite:  4.3.0a-h72746d6_18   
    libssh2:        1.8.0-h9cfc8f7_4     
    libtiff:        4.0.9-he85c1e1_1     
    libuuid:        1.0.3-h1bed415_2     
    libxcb:         1.13-h1bed415_1      
    libxml2:        2.9.8-h26e45fe_1     
    mkl:            2018.0.2-1           
    mkl_fft:        1.0.1-py36h3010b51_0 
    mkl_random:     1.0.1-py36h629b387_0 
    munch:          2.3.2-py36_0         
    numpy:          1.14.3-py36hcd700cb_1
    numpy-base:     1.14.3-py36h9be14a7_1
    openjpeg:       2.3.0-h05c96fa_1     
    pcre:           8.42-h439df22_0      
    pixman:         0.34.0-hceecf20_3    
    poppler:        0.65.0-h581218d_1    
    poppler-data:   0.4.9-0              
    proj4:          4.9.3-hc8507d1_7     
    shapely:        1.6.4-py36h0c48222_0 
    six:            1.11.0-py36h372c433_1
    xerces-c:       3.2.1-hac72e42_0     

Proceed ([y]/n)? y


Downloading and Extracting Packages
poppler-data-0.4.9   |  3.5 MB | : 100% 1.0/1 [00:00<00:00,  1.06it/s]               
click-plugins-1.0.3  |    9 KB | : 100% 1.0/1 [00:00<00:00, 31.51it/s]
cligj-0.4.0          |   14 KB | : 100% 1.0/1 [00:00<00:00, 26.03it/s]
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(popplertest)$ python -c "import fiona"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/cio/mc3/envs/popplertest/lib/python3.6/site-packages/fiona/__init__.py", line 69, in <module>
    from fiona.collection import Collection, BytesCollection, vsi_path
  File "/cio/mc3/envs/popplertest/lib/python3.6/site-packages/fiona/collection.py", line 9, in <module>
    from fiona.ogrext import Iterator, ItemsIterator, KeysIterator
ImportError: libpoppler.so.71: cannot open shared object file: No such file or directory
(popplertest)$ ls -l /cio/mc3/envs/popplertest/lib/*poppler*
lrwxrwxrwx 1 ceball ceball      23 May 28 15:39 /cio/mc3/envs/popplertest/lib/libpoppler-cpp.so -> libpoppler-cpp.so.0.5.0
lrwxrwxrwx 1 ceball ceball      23 May 28 15:39 /cio/mc3/envs/popplertest/lib/libpoppler-cpp.so.0 -> libpoppler-cpp.so.0.5.0
-rwxrwxr-x 2 ceball ceball  123312 May 25 16:17 /cio/mc3/envs/popplertest/lib/libpoppler-cpp.so.0.5.0
lrwxrwxrwx 1 ceball ceball      24 May 28 15:39 /cio/mc3/envs/popplertest/lib/libpoppler-glib.so -> libpoppler-glib.so.8.9.0
lrwxrwxrwx 1 ceball ceball      24 May 28 15:39 /cio/mc3/envs/popplertest/lib/libpoppler-glib.so.8 -> libpoppler-glib.so.8.9.0
-rwxrwxr-x 2 ceball ceball  488400 May 25 16:17 /cio/mc3/envs/popplertest/lib/libpoppler-glib.so.8.9.0
lrwxrwxrwx 1 ceball ceball      20 May 28 15:39 /cio/mc3/envs/popplertest/lib/libpoppler.so -> libpoppler.so.76.0.0
lrwxrwxrwx 1 ceball ceball      20 May 28 15:39 /cio/mc3/envs/popplertest/lib/libpoppler.so.76 -> libpoppler.so.76.0.0
-rwxrwxr-x 1 ceball ceball 3056976 May 28 15:38 /cio/mc3/envs/popplertest/lib/libpoppler.so.76.0.0
(popplertest)$ conda deactivate

If I install an older version of poppler, things seem to be ok:

(popplertest)$ conda install "poppler<=0.60.1"
Solving environment: done

## Package Plan ##

  environment location: /cio/mc3/envs/popplertest

  added / updated specs:
    - poppler[version='<=0.60.1']


The following packages will be DOWNGRADED:

    cairo:      1.14.12-h8948797_3 --> 1.14.12-h77bcde2_0
    fontconfig: 2.13.0-h9420a91_0  --> 2.12.6-h49f89f6_0
    freetype:   2.9.1-h8a8886c_0   --> 2.8-hab7d2ae_1
    glib:       2.56.1-h000015b_0  --> 2.53.6-h5d9569c_2
    poppler:    0.65.0-h581218d_1  --> 0.60.1-hc909a00_0

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(popplertest)$ python -c "import fiona"
(popplertest)$

conda-forge

$ conda create -c conda-forge -n cfpopplertest python=3.6
Solving environment: done

## Package Plan ##

  environment location: /cio/mc3/envs/cfpopplertest

  added / updated specs: 
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2018.4.16          |           py36_0         142 KB  conda-forge

The following NEW packages will be INSTALLED:

    ca-certificates: 2018.4.16-0       conda-forge
    certifi:         2018.4.16-py36_0  conda-forge
    libgcc-ng:       7.2.0-hdf63c60_3             
    ncurses:         5.9-10            conda-forge
    openssl:         1.0.2o-0          conda-forge
    pip:             9.0.3-py36_0      conda-forge
    python:          3.6.5-1           conda-forge
    readline:        7.0-0             conda-forge
    setuptools:      39.2.0-py36_0     conda-forge
    sqlite:          3.20.1-2          conda-forge
    tk:              8.6.7-0           conda-forge
    wheel:           0.31.0-py36_0     conda-forge
    xz:              5.2.3-0           conda-forge
    zlib:            1.2.11-h470a237_2 conda-forge

Proceed ([y]/n)? y


Downloading and Extracting Packages
certifi-2018.4.16    |  142 KB | : 100% 1.0/1 [00:01<00:00,  1.25s/it]               
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate cfpopplertest
#
# To deactivate an active environment, use
#
#     $ conda deactivate

$ conda activate cfpopplertest
(cfpopplertest)$ conda install -c conda-forge poppler fiona gdal
Solving environment: done

## Package Plan ##

  environment location: /cio/mc3/envs/cfpopplertest

  added / updated specs: 
    - fiona
    - gdal
    - poppler


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    cligj-0.4.0                |           py36_0          12 KB  conda-forge
    poppler-data-0.4.9         |                0         3.5 MB  conda-forge
    click-plugins-1.0.3        |           py36_0           7 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         3.6 MB

The following NEW packages will be INSTALLED:

    boost:          1.66.0-py36_1         conda-forge
    boost-cpp:      1.66.0-1              conda-forge
    bzip2:          1.0.6-1               conda-forge
    cairo:          1.14.10-0             conda-forge
    click:          6.7-py_1              conda-forge
    click-plugins:  1.0.3-py36_0          conda-forge
    cligj:          0.4.0-py36_0          conda-forge
    curl:           7.60.0-0              conda-forge
    expat:          2.2.5-0               conda-forge
    fiona:          1.7.11-py36_3         conda-forge
    fontconfig:     2.12.6-0              conda-forge
    freetype:       2.8.1-0               conda-forge
    freexl:         1.0.5-0               conda-forge
    gdal:           2.2.4-py36_0          conda-forge
    geos:           3.6.2-1               conda-forge
    geotiff:        1.4.2-1               conda-forge
    gettext:        0.19.8.1-0            conda-forge
    giflib:         5.1.4-0               conda-forge
    glib:           2.55.0-0              conda-forge
    hdf4:           4.2.13-0              conda-forge
    hdf5:           1.10.1-2              conda-forge
    icu:            58.2-0                conda-forge
    jpeg:           9b-2                  conda-forge
    json-c:         0.12.1-0              conda-forge
    kealib:         1.4.7-4               conda-forge
    krb5:           1.14.6-0              conda-forge
    libdap4:        3.18.3-2              conda-forge
    libffi:         3.2.1-3               conda-forge
    libgdal:        2.2.4-2               conda-forge
    libgfortran:    3.0.0-1                          
    libgfortran-ng: 7.2.0-hdf63c60_3                 
    libiconv:       1.15-0                conda-forge
    libkml:         1.3.0-6               conda-forge
    libnetcdf:      4.6.1-2               conda-forge
    libopenblas:    0.2.20-h9ac9557_4                
    libpng:         1.6.34-0              conda-forge
    libpq:          9.6.3-0               conda-forge
    libspatialite:  4.3.0a-19             conda-forge
    libssh2:        1.8.0-2               conda-forge
    libtiff:        4.0.9-0               conda-forge
    libxml2:        2.9.8-0               conda-forge
    munch:          2.3.2-py_0            conda-forge
    numpy:          1.14.3-py36h28100ab_1            
    numpy-base:     1.14.3-py36h0ea5e3f_1            
    openjpeg:       2.3.0-2               conda-forge
    pcre:           8.41-1                conda-forge
    pixman:         0.34.0-2              conda-forge
    poppler:        0.61.1-3              conda-forge
    poppler-data:   0.4.9-0               conda-forge
    proj4:          4.9.3-5               conda-forge
    shapely:        1.6.4-py36_0          conda-forge
    six:            1.11.0-py36_1         conda-forge
    util-linux:     2.21-0                           
    xerces-c:       3.2.0-0               conda-forge

Proceed ([y]/n)? y


Downloading and Extracting Packages
cligj-0.4.0          |   12 KB | : 100% 1.0/1 [00:00<00:00,  1.14it/s] 
poppler-data-0.4.9   |  3.5 MB | : 100% 1.0/1 [00:02<00:00,  2.38s/it]               
click-plugins-1.0.3  |    7 KB | : 100% 1.0/1 [00:00<00:00,  1.81it/s] 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(cfpopplertest)$ python -c "import fiona"
(cfpopplertest)$

If I don't specify gdal, it ends up coming from defaults, so same problem:

$ conda create -c conda-forge -n cfpopplertest2 python=3.6
Solving environment: done

## Package Plan ##

  environment location: /cio/mc3/envs/cfpopplertest2

  added / updated specs: 
    - python=3.6


The following NEW packages will be INSTALLED:

    ca-certificates: 2018.4.16-0       conda-forge
    certifi:         2018.4.16-py36_0  conda-forge
    libgcc-ng:       7.2.0-hdf63c60_3             
    ncurses:         5.9-10            conda-forge
    openssl:         1.0.2o-0          conda-forge
    pip:             9.0.3-py36_0      conda-forge
    python:          3.6.5-1           conda-forge
    readline:        7.0-0             conda-forge
    setuptools:      39.2.0-py36_0     conda-forge
    sqlite:          3.20.1-2          conda-forge
    tk:              8.6.7-0           conda-forge
    wheel:           0.31.0-py36_0     conda-forge
    xz:              5.2.3-0           conda-forge
    zlib:            1.2.11-h470a237_2 conda-forge

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate cfpopplertest2
#
# To deactivate an active environment, use
#
#     $ conda deactivate

$ conda activate cfpopplertest2
(cfpopplertest2)$ conda install -c conda-forge poppler fiona
Solving environment: done

## Package Plan ##

  environment location: /cio/mc3/envs/cfpopplertest2

  added / updated specs: 
    - fiona
    - poppler


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    xerces-c-3.2.1             |                0         3.9 MB  conda-forge

The following NEW packages will be INSTALLED:

    boost:          1.66.0-py36_1         conda-forge
    boost-cpp:      1.66.0-1              conda-forge
    bzip2:          1.0.6-1               conda-forge
    cairo:          1.14.10-0             conda-forge
    click:          6.7-py_1              conda-forge
    click-plugins:  1.0.3-py36_0          conda-forge
    cligj:          0.4.0-py36_0          conda-forge
    curl:           7.60.0-0              conda-forge
    expat:          2.2.5-0               conda-forge
    fiona:          1.7.11-py36_3         conda-forge
    fontconfig:     2.12.6-0              conda-forge
    freetype:       2.8.1-0               conda-forge
    freexl:         1.0.5-0               conda-forge
    gdal:           2.2.2-py36hc209d97_1             
    geos:           3.6.2-1               conda-forge
    gettext:        0.19.8.1-0            conda-forge
    giflib:         5.1.4-0               conda-forge
    glib:           2.55.0-0              conda-forge
    hdf4:           4.2.13-0              conda-forge
    hdf5:           1.10.1-2              conda-forge
    icu:            58.2-0                conda-forge
    jpeg:           9b-2                  conda-forge
    json-c:         0.12.1-0              conda-forge
    kealib:         1.4.7-4               conda-forge
    krb5:           1.14.6-0              conda-forge
    libdap4:        3.19.2-1              conda-forge
    libffi:         3.2.1-3               conda-forge
    libgdal:        2.2.2-h804cdde_1                 
    libgfortran:    3.0.0-1                          
    libgfortran-ng: 7.2.0-hdf63c60_3                 
    libiconv:       1.15-0                conda-forge
    libkml:         1.3.0-6               conda-forge
    libnetcdf:      4.4.1.1-10            conda-forge
    libopenblas:    0.2.20-h9ac9557_4                
    libpng:         1.6.34-0              conda-forge
    libpq:          9.6.6-h4e02ad2_0                 
    libspatialite:  4.3.0a-19             conda-forge
    libssh2:        1.8.0-2               conda-forge
    libstdcxx-ng:   7.2.0-hdf63c60_3                 
    libtiff:        4.0.9-0               conda-forge
    libxml2:        2.9.8-0               conda-forge
    munch:          2.3.2-py_0            conda-forge
    numpy:          1.14.3-py36h28100ab_1            
    numpy-base:     1.14.3-py36h0ea5e3f_1            
    openjpeg:       2.3.0-2               conda-forge
    pcre:           8.41-1                conda-forge
    pixman:         0.34.0-2              conda-forge
    poppler:        0.64.0-0              conda-forge
    poppler-data:   0.4.9-0               conda-forge
    proj4:          4.9.3-5               conda-forge
    shapely:        1.6.4-py36_0          conda-forge
    six:            1.11.0-py36_1         conda-forge
    util-linux:     2.21-0                           
    xerces-c:       3.2.1-0               conda-forge

Proceed ([y]/n)? y


Downloading and Extracting Packages
xerces-c-3.2.1       |  3.9 MB | : 100% 1.0/1 [00:26<00:00, 26.17s/it]              
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(cfpopplertest2)$ python -c "import fiona"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/cio/mc3/envs/cfpopplertest2/lib/python3.6/site-packages/fiona/__init__.py", line 69, in <module>
    from fiona.collection import Collection, BytesCollection, vsi_path
  File "/cio/mc3/envs/cfpopplertest2/lib/python3.6/site-packages/fiona/collection.py", line 9, in <module>
    from fiona.ogrext import Iterator, ItemsIterator, KeysIterator
ImportError: libpoppler.so.71: cannot open shared object file: No such file or directory

conda info:


     active environment : popplertest
    active env location : /cio/mc3/envs/popplertest
            shell level : 1
       user config file : /home/ceball/.condarc
 populated config files :
          conda version : 4.5.4
    conda-build version : 3.10.1
         python version : 3.6.4.final.0
       base environment : /cio/mc3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /cio/mc3/pkgs
                          /home/ceball/.conda/pkgs
       envs directories : /cio/mc3/envs
                          /home/ceball/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.4 requests/2.18.4 CPython/3.6.4 Linux/3.16.0-4-amd64 debian/8 glibc/2.19
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False
@ceball ceball mentioned this issue May 28, 2018
Closed
3 tasks
@jjhelmus
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This is the same issue as ContinuumIO/anaconda-issues#9449. @msarahan is working on a fix.

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@ceball @msarahan @jjhelmus