Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fiona install fails with libpoppler error #62

Closed
jorisvandenbossche opened this issue Nov 23, 2017 · 10 comments
Closed

Fiona install fails with libpoppler error #62

jorisvandenbossche opened this issue Nov 23, 2017 · 10 comments

Comments

@jorisvandenbossche
Copy link
Member

Our pandas CI where we test downstream packages including geopandas just started failing:

================================== FAILURES ===================================
________________________________ test_geopandas ________________________________
[gw1] linux -- Python 3.6.3 /home/travis/miniconda3/envs/pandas/bin/python
    def test_geopandas():
    
>       geopandas = import_module('geopandas')  # noqa
pandas/tests/test_downstream.py:97: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
pandas/tests/test_downstream.py:19: in import_module
    return importlib.import_module(name)
../../../miniconda3/envs/pandas/lib/python3.6/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:994: in _gcd_import
    ???
<frozen importlib._bootstrap>:971: in _find_and_load
   ???
<frozen importlib._bootstrap>:955: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:665: in _load_unlocked
    ???
<frozen importlib._bootstrap_external>:678: in exec_module
    ???
<frozen importlib._bootstrap>:219: in _call_with_frames_removed
    ???
../../../miniconda3/envs/pandas/lib/python3.6/site-packages/geopandas/__init__.py:4: in <module>
    from geopandas.io.file import read_file
../../../miniconda3/envs/pandas/lib/python3.6/site-packages/geopandas/io/file.py:3: in <module>
    import fiona
../../../miniconda3/envs/pandas/lib/python3.6/site-packages/fiona/__init__.py:69: in <module>
    from fiona.collection import Collection, BytesCollection, vsi_path
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
    import logging
    import os
    import warnings
    
    from fiona import compat
>   from fiona.ogrext import Iterator, ItemsIterator, KeysIterator
E   ImportError: libpoppler.so.66: cannot open shared object file: No such file or directory
../../../miniconda3/envs/pandas/lib/python3.6/site-packages/fiona/collection.py:9: ImportError

The logs are here: https://travis-ci.org/pandas-dev/pandas/jobs/306469511#L2019. You need to expand line 541 "$ ci/install_travis.sh" to see the install logs. As far as I can see, everything is coming from conda-forge, and there are no downgrades/changes that could mess things up after fiona and geopandas are installed.
@jorisvandenbossche jorisvandenbossche mentioned this issue Nov 23, 2017
Closed
@jorisvandenbossche
Copy link
Member Author

I can replicate this locally in a clean env:

joris@joris-XPS-13-9350:~/scipy$ conda create -n TEST python=3 geopandas -c conda-forge
Fetching package metadata ...............
Solving package specifications: .

Package plan for installation in environment /home/joris/miniconda3/envs/TEST:

The following NEW packages will be INSTALLED:

    backports:                     1.0-py36_1            conda-forge
    backports.functools_lru_cache: 1.4-py36_1            conda-forge
    ca-certificates:               2017.11.5-0           conda-forge
    cairo:                         1.14.6-5              conda-forge
    certifi:                       2017.11.5-py36_0      conda-forge
    click:                         6.7-py36_0            conda-forge
    click-plugins:                 1.0.3-py36_0          conda-forge
    cligj:                         0.4.0-py36_0          conda-forge
    curl:                          7.55.1-0              conda-forge
    cycler:                        0.10.0-py36_0         conda-forge
    dbus:                          1.10.22-0             conda-forge
    descartes:                     1.1.0-py36_0          conda-forge
    expat:                         2.1.0-3               conda-forge
    fiona:                         1.7.9-py36_0          conda-forge
    fontconfig:                    2.12.1-6              conda-forge
    freetype:                      2.7-2                 conda-forge
    freexl:                        1.0.4-0               conda-forge
    geopandas:                     0.3.0-py36_0          conda-forge
    geos:                          3.6.2-1               conda-forge
    geotiff:                       1.4.2-0               conda-forge
    gettext:                       0.19.7-1              conda-forge
    giflib:                        5.1.4-0               conda-forge
    glib:                          2.51.4-0              conda-forge
    gst-plugins-base:              1.8.0-0               conda-forge
    gstreamer:                     1.8.0-2               conda-forge
    hdf4:                          4.2.13-0              conda-forge
    hdf5:                          1.10.1-1              conda-forge
    icu:                           58.2-0                conda-forge
    intel-openmp:                  2018.0.0-hc7b2577_8              
    jpeg:                          9b-2                  conda-forge
    json-c:                        0.12.1-0              conda-forge
    kealib:                        1.4.7-4               conda-forge
    krb5:                          1.14.2-0              conda-forge
    libdap4:                       3.18.3-2              conda-forge
    libffi:                        3.2.1-3               conda-forge
    libgcc-ng:                     7.2.0-h7cc24e2_2                 
    libgdal:                       2.1.4-6               conda-forge
    libgfortran:                   3.0.0-1                          
    libgfortran-ng:                7.2.0-h9f7466a_2                 
    libiconv:                      1.15-0                conda-forge
    libkml:                        1.3.0-3               conda-forge
    libnetcdf:                     4.4.1.1-10            conda-forge
    libpng:                        1.6.28-2              conda-forge
    libpq:                         9.6.3-0               conda-forge
    libspatialindex:               1.8.5-1               conda-forge
    libspatialite:                 4.3.0a-17             conda-forge
    libssh2:                       1.8.0-2               conda-forge
    libstdcxx-ng:                  7.2.0-h7a57d05_2                 
    libtiff:                       4.0.7-1               conda-forge
    libxcb:                        1.12-1                conda-forge
    libxml2:                       2.9.5-2               conda-forge
    matplotlib:                    2.1.0-py36_1          conda-forge
    mkl:                           2018.0.1-h19d6760_4              
    munch:                         2.2.0-py36_0          conda-forge
    ncurses:                       5.9-10                conda-forge
    numpy:                         1.13.3-py36ha12f23b_0            
    openjpeg:                      2.3.0-1               conda-forge
    openssl:                       1.0.2l-0              conda-forge
    pandas:                        0.21.0-py36_0         conda-forge
    pcre:                          8.39-0                conda-forge
    pixman:                        0.34.0-0              conda-forge
    poppler:                       0.61.1-0              conda-forge
    poppler-data:                  0.4.8-0               conda-forge
    proj4:                         4.9.3-5               conda-forge
    psycopg2:                      2.7.3.2-py36_0        conda-forge
    pyparsing:                     2.2.0-py36_0          conda-forge
    pyproj:                        1.9.5.1-py36_0        conda-forge
    pyqt:                          5.6.0-py36_4          conda-forge
    pysal:                         1.14.3-py36_0         conda-forge
    python:                        3.6.3-1               conda-forge
    python-dateutil:               2.6.1-py36_0          conda-forge
    pytz:                          2017.3-py_2           conda-forge
    qt:                            5.6.2-6               conda-forge
    readline:                      6.2-0                 conda-forge
    rtree:                         0.8.3-py36_0          conda-forge
    scipy:                         1.0.0-py36hbf646e7_0             
    setuptools:                    36.7.2-py36_0         conda-forge
    shapely:                       1.6.2-py36_1          conda-forge
    sip:                           4.18-py36_1           conda-forge
    six:                           1.11.0-py36_1         conda-forge
    sqlalchemy:                    1.1.13-py36_0         conda-forge
    sqlite:                        3.13.0-1              conda-forge
    tk:                            8.5.19-2              conda-forge
    tornado:                       4.5.2-py36_0          conda-forge
    util-linux:                    2.21-0                           
    xerces-c:                      3.1.4-3               conda-forge
    xorg-libxau:                   1.0.8-3               conda-forge
    xorg-libxdmcp:                 1.1.2-3               conda-forge
    xz:                            5.2.3-0               conda-forge
    zlib:                          1.2.11-0              conda-forge

Proceed ([y]/n)? 

intel-openmp-2 100% |##############################################################################################################################################################################################| Time: 0:00:02 227.23 kB/s
libiconv-1.15- 100% |##############################################################################################################################################################################################| Time: 0:00:08 235.49 kB/s
poppler-data-0 100% |##############################################################################################################################################################################################| Time: 0:00:15 237.41 kB/s
freexl-1.0.4-0 100% |##############################################################################################################################################################################################| Time: 0:00:00 253.75 kB/s
libxml2-2.9.5- 100% |##############################################################################################################################################################################################| Time: 0:00:21 237.63 kB/s
mkl-2018.0.1-h 100% |##############################################################################################################################################################################################| Time: 0:16:48 192.07 kB/s
openjpeg-2.3.0 100% |##############################################################################################################################################################################################| Time: 0:00:01 222.28 kB/s
fontconfig-2.1 100% |##############################################################################################################################################################################################| Time: 0:00:04 220.86 kB/s
poppler-0.61.1 100% |##############################################################################################################################################################################################| Time: 0:00:28 236.84 kB/s
#
# To activate this environment, use:
# > source activate TEST
#
# To deactivate an active environment, use:
# > source deactivate
#

joris@joris-XPS-13-9350:~/scipy$ act TEST
(TEST) joris@joris-XPS-13-9350:~/scipy$ python
Python 3.6.3 | packaged by conda-forge | (default, Nov  4 2017, 10:10:56) 
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import geopandas
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/joris/miniconda3/envs/TEST/lib/python3.6/site-packages/geopandas/__init__.py", line 4, in <module>
    from geopandas.io.file import read_file
  File "/home/joris/miniconda3/envs/TEST/lib/python3.6/site-packages/geopandas/io/file.py", line 3, in <module>
    import fiona
  File "/home/joris/miniconda3/envs/TEST/lib/python3.6/site-packages/fiona/__init__.py", line 69, in <module>
    from fiona.collection import Collection, BytesCollection, vsi_path
  File "/home/joris/miniconda3/envs/TEST/lib/python3.6/site-packages/fiona/collection.py", line 9, in <module>
    from fiona.ogrext import Iterator, ItemsIterator, KeysIterator
ImportError: libpoppler.so.66: cannot open shared object file: No such file or directory

This was referenced Nov 23, 2017
Merged
Closed
@ocefpaf
Copy link
Member

ocefpaf commented Nov 24, 2017

Thanks for the report! This will be solved as soon as conda-forge/poppler-feedstock#8 and conda-forge/libgdal-feedstock#24 are merged. Meanwhile you can pin to the previous version of popppler 0.52.0 by specifying it explicitly on the env.

@ocefpaf
Copy link
Member

ocefpaf commented Nov 24, 2017

@jorisvandenbossche I merged conda-forge/libgdal-feedstock#24 and just tested the env above. Everything should be working. Let me know if you find any issue.

@ocefpaf ocefpaf closed this as completed Nov 24, 2017
@jorisvandenbossche
Copy link
Member Author

Thanks! CI is already running to see if it is solved: pandas-dev/pandas#18466, but on the geopandas docs it now works, so I assume everything is working again

@jorisvandenbossche
Copy link
Member Author

Our CI is green again!

@ocefpaf
Copy link
Member

ocefpaf commented Nov 24, 2017

Our CI is green again!

Awesome!

@jorisvandenbossche
Copy link
Member Author

New issue with libxerces-c, see eg https://travis-ci.org/pandas-dev/pandas/jobs/306830766

@ocefpaf
Copy link
Member

ocefpaf commented Nov 24, 2017

Should be gone soon. I thought I'd be the only one working on the Thanksgiving weekend but I guess I forgot about people in the old continent 😉

I am updating a bunch of stuff and you are hitting the Travis-CI backlog. The builds with latest xerces-c should be in the channel in ~ 30 min.

@jorisvandenbossche
Copy link
Member Author

Good to hear!

(Yes, here it was just a normal working day ;-))

@ocefpaf
Copy link
Member

ocefpaf commented Nov 24, 2017

@jorisvandenbossche it should be OK now. Let me know if you see any other errors.

PS: you'll probably get gdal 2.1.3 for now. Once conda-forge/gdal-feedstock#185 is merged you'll get gdal 2.1.4.

@shoyer shoyer mentioned this issue Nov 28, 2017
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@ocefpaf @jorisvandenbossche