search

conda-forge / matplotlib-feedstock

A conda-smithy repository for matplotlib.
BSD 3-Clause "New" or "Revised" License
22 stars 58 forks source link

Can't import matplotlib, get ImportError #353

Open dennischen opened 1 year ago

dennischen commented 1 year ago

Solution to issue cannot be found in the documentation.

Issue

I am studying python + matplotlib, Everything was ok on last Monday, but I try to re-run my case today get error.

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/dennis/.conda/envs/jplerror3/lib/python3.11/site-packages/matplotlib/__init__.py", line 129, in <module>
    from . import _api, _version, cbook, _docstring, rcsetup
  File "/home/dennis/.conda/envs/jplerror3/lib/python3.11/site-packages/matplotlib/rcsetup.py", line 27, in <module>
    from matplotlib.colors import Colormap, is_color_like
  File "/home/dennis/.conda/envs/jplerror3/lib/python3.11/site-packages/matplotlib/colors.py", line 51, in <module>
    from PIL import Image
  File "/home/dennis/.conda/envs/jplerror3/lib/python3.11/site-packages/PIL/Image.py", line 103, in <module>
    from . import _imaging as core
ImportError: libtiff.so.5: cannot open shared object file: No such file or directory

I can reporduce it by following commands in my ubuntu 20

conda create -n jplerror3 -y
conda activate jplerror3
conda install -c conda-forge python matplotlib -y
python -c "import matplotlib.pyplot as plt"

But, if I remove the -c conda-forge, it works fine

conda create -n jplerror4 -y
conda activate jplerror4
conda install python matplotlib -y
python -c "import matplotlib.pyplot as plt"

Installed packages

---From conda-forge, has error
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
brotli                    1.0.9                h166bdaf_9    conda-forge
brotli-bin                1.0.9                h166bdaf_9    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
contourpy                 1.1.0           py311h9547e67_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
dbus                      1.13.18              hb2f20db_0
expat                     2.5.0                hcb278e6_1    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonttools                 4.42.0          py311h459d7ec_0    conda-forge
freetype                  2.12.1               hca18f0e_1    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
giflib                    5.2.1                h0b41bf4_3    conda-forge
glib                      2.76.4               hfc55251_0    conda-forge
glib-tools                2.76.4               hfc55251_0    conda-forge
gst-plugins-base          1.14.1               h6a678d5_1
gstreamer                 1.14.1               h5eee18b_1
icu                       58.2              hf484d3e_1000    conda-forge
jpeg                      9e                   h0b41bf4_3    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.4           py311h4dd048b_1    conda-forge
krb5                      1.20.1               h81ceb04_0    conda-forge
lcms2                     2.15                 hfd0df8a_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libblas                   3.9.0           17_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h166bdaf_9    conda-forge
libbrotlidec              1.0.9                h166bdaf_9    conda-forge
libbrotlienc              1.0.9                h166bdaf_9    conda-forge
libcblas                  3.9.0           17_linux64_openblas    conda-forge
libclang                  10.0.1          default_hb85057a_2
libdeflate                1.17                 h5eee18b_0
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libevent                  2.1.12               hf998b51_1    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.1.0               he5830b7_0    conda-forge
libgfortran-ng            13.1.0               h69a702a_0    conda-forge
libgfortran5              13.1.0               h15d22d2_0    conda-forge
libglib                   2.76.4               hebfc3b9_0    conda-forge
libgomp                   13.1.0               he5830b7_0    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
liblapack                 3.9.0           17_linux64_openblas    conda-forge
libllvm10                 10.0.1               he513fc3_3    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.23          pthreads_h80387f5_0    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libpq                     12.15                hdbd6064_1
libsqlite                 3.42.0               h2797004_0    conda-forge
libstdcxx-ng              13.1.0               hfd8a6a1_0    conda-forge
libtiff                   4.5.0                h6adf6a1_2    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp                   1.2.4                h1daa5a0_1    conda-forge
libwebp-base              1.2.4                h5eee18b_1
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxkbcommon              1.0.1                hfa300c1_0
libxml2                   2.9.14               h74e7548_0
libxslt                   1.1.35               h4e12654_0
libzlib                   1.2.13               hd590300_5    conda-forge
matplotlib                3.7.2           py311h38be061_0    conda-forge
matplotlib-base           3.7.2           py311h54ef318_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ncurses                   6.4                  hcb278e6_0    conda-forge
nspr                      4.35                 h27087fc_0    conda-forge
nss                       3.89                 he45b914_0    conda-forge
numpy                     1.25.2          py311h64a7726_0    conda-forge
openssl                   3.1.2                hd590300_0    conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
pillow                    9.4.0           py311h6a678d5_0
pip                       23.2.1             pyhd8ed1ab_0    conda-forge
ply                       3.11                       py_1    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyqt                      5.15.7          py311h6a678d5_0
pyqt5-sip                 12.11.0         py311h6a678d5_0
python                    3.11.4          hab00c5b_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.11                    3_cp311    conda-forge
qt-main                   5.15.2               h327a75a_7
qt-webengine              5.15.9               hd2b0992_4
qtwebkit                  5.212                h4eab89a_4
readline                  8.2                  h8228510_1    conda-forge
setuptools                68.0.0             pyhd8ed1ab_0    conda-forge
sip                       6.6.2           py311h6a678d5_0
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.42.0               h2c6b66d_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tornado                   6.3.2           py311h459d7ec_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
wheel                     0.41.1             pyhd8ed1ab_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.2                hfc55251_7    conda-forge

---From normal, no error
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main
_openmp_mutex             5.1                       1_gnu
blas                      1.0                         mkl
brotli                    1.0.9                h5eee18b_7
brotli-bin                1.0.9                h5eee18b_7
bzip2                     1.0.8                h7b6447c_0
ca-certificates           2023.05.30           h06a4308_0
contourpy                 1.0.5           py311hdb19cb5_0
cycler                    0.11.0             pyhd3eb1b0_0
dbus                      1.13.18              hb2f20db_0
expat                     2.4.9                h6a678d5_0
fontconfig                2.14.1               h52c9d5c_1
fonttools                 4.25.0             pyhd3eb1b0_0
freetype                  2.12.1               h4a9f257_0
giflib                    5.2.1                h5eee18b_3
glib                      2.69.1               he621ea3_2
gst-plugins-base          1.14.1               h6a678d5_1
gstreamer                 1.14.1               h5eee18b_1
icu                       58.2                 he6710b0_3
intel-openmp              2023.1.0         hdb19cb5_46305
jpeg                      9e                   h5eee18b_1
kiwisolver                1.4.4           py311h6a678d5_0
krb5                      1.20.1               h143b758_1
lcms2                     2.12                 h3be6417_0
ld_impl_linux-64          2.38                 h1181459_1
lerc                      3.0                  h295c915_0
libbrotlicommon           1.0.9                h5eee18b_7
libbrotlidec              1.0.9                h5eee18b_7
libbrotlienc              1.0.9                h5eee18b_7
libclang                  10.0.1          default_hb85057a_2
libdeflate                1.17                 h5eee18b_0
libedit                   3.1.20221030         h5eee18b_0
libevent                  2.1.12               hdbd6064_1
libffi                    3.4.4                h6a678d5_0
libgcc-ng                 11.2.0               h1234567_1
libgomp                   11.2.0               h1234567_1
libllvm10                 10.0.1               hbcb73fb_5
libpng                    1.6.39               h5eee18b_0
libpq                     12.15                hdbd6064_1
libstdcxx-ng              11.2.0               h1234567_1
libtiff                   4.5.0                h6a678d5_2
libuuid                   1.41.5               h5eee18b_0
libwebp                   1.2.4                h11a3e52_1
libwebp-base              1.2.4                h5eee18b_1
libxcb                    1.15                 h7f8727e_0
libxkbcommon              1.0.1                hfa300c1_0
libxml2                   2.9.14               h74e7548_0
libxslt                   1.1.35               h4e12654_0
lz4-c                     1.9.4                h6a678d5_0
matplotlib                3.7.1           py311h06a4308_1
matplotlib-base           3.7.1           py311ha02d727_1
mkl                       2023.1.0         h213fc3f_46343
mkl-service               2.4.0           py311h5eee18b_1
mkl_fft                   1.3.6           py311ha02d727_1
mkl_random                1.2.2           py311ha02d727_1
munkres                   1.1.4                      py_0
ncurses                   6.4                  h6a678d5_0
nspr                      4.35                 h6a678d5_0
nss                       3.89.1               h6a678d5_0
numpy                     1.25.2          py311h08b1b3b_0
numpy-base                1.25.2          py311hf175353_0
openssl                   3.0.10               h7f8727e_0
packaging                 23.0            py311h06a4308_0
pcre                      8.45                 h295c915_0
pillow                    9.4.0           py311h6a678d5_0
pip                       23.2.1          py311h06a4308_0
ply                       3.11            py311h06a4308_0
pyparsing                 3.0.9           py311h06a4308_0
pyqt                      5.15.7          py311h6a678d5_0
pyqt5-sip                 12.11.0         py311h6a678d5_0
python                    3.11.4               h955ad1f_0
python-dateutil           2.8.2              pyhd3eb1b0_0
qt-main                   5.15.2               h327a75a_7
qt-webengine              5.15.9               hd2b0992_4
qtwebkit                  5.212                h4eab89a_4
readline                  8.2                  h5eee18b_0
setuptools                68.0.0          py311h06a4308_0
sip                       6.6.2           py311h6a678d5_0
six                       1.16.0             pyhd3eb1b0_1
sqlite                    3.41.2               h5eee18b_0
tbb                       2021.8.0             hdb19cb5_0
tk                        8.6.12               h1ccaba5_0
toml                      0.10.2             pyhd3eb1b0_0
tornado                   6.3.2           py311h5eee18b_0
tzdata                    2023c                h04d1e81_0
wheel                     0.38.4          py311h06a4308_0
xz                        5.4.2                h5eee18b_0
zlib                      1.2.13               h5eee18b_0
zstd                      1.5.5                hc292b87_0

Environment info

active environment : jplerror3
    active env location : /home/dennis/.conda/envs/jplerror3
            shell level : 2
       user config file : /home/dennis/.condarc
 populated config files :
          conda version : 23.5.2
    conda-build version : not installed
         python version : 3.11.4.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.31=0
                          __linux=5.4.0=0
                          __unix=0=0
       base environment : /opt/conda  (read only)
      conda av data dir : /opt/conda/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/conda/pkgs
                          /home/dennis/.conda/pkgs
       envs directories : /home/dennis/.conda/envs
                          /opt/conda/envs
               platform : linux-64
             user-agent : conda/23.5.2 requests/2.29.0 CPython/3.11.4 Linux/5.4.0-153-generic ubuntu/20.04.5 glibc/2.31
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False
dopplershift commented 1 year ago

That actually looks like a problem with PIL in your environment. What happens if you run python -c 'from PIL import Image'?

dennischen commented 1 year ago

Same error in jplerror3

(jplerror3) dennis@slurm:~$ python -c "from PIL import Image"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/dennis/.conda/envs/jplerror3/lib/python3.11/site-packages/PIL/Image.py", line 103, in <module>
    from . import _imaging as core
ImportError: libtiff.so.5: cannot open shared object file: No such file or directory

But, I made a new clean env and install pillow only, it don't throw the error by import pil.

conda create -n pilerr2
conda activate pilerr2
#force version 9.4.0 as same as instal matplotlib
conda install -c conda-forge python pillow=9.4.0 -y 
python -c "from PIL import Image"
#no error here

the conda list information

_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
freetype                  2.12.1               hca18f0e_1    conda-forge
lcms2                     2.15                 haa2dc70_1    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libdeflate                1.18                 h0b41bf4_0    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.1.0               he5830b7_0    conda-forge
libgomp                   13.1.0               he5830b7_0    conda-forge
libjpeg-turbo             2.1.5.1              h0b41bf4_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libsqlite                 3.42.0               h2797004_0    conda-forge
libstdcxx-ng              13.1.0               hfd8a6a1_0    conda-forge
libtiff                   4.5.1                h8b53f26_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp-base              1.3.1                hd590300_0    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
ncurses                   6.4                  hcb278e6_0    conda-forge
openjpeg                  2.5.0                hfec8fc6_2    conda-forge
openssl                   3.1.2                hd590300_0    conda-forge
pillow                    9.4.0           py311h573f0d3_2    conda-forge
pip                       23.2.1             pyhd8ed1ab_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
python                    3.11.4          hab00c5b_0_cpython    conda-forge
python_abi                3.11                    3_cp311    conda-forge
readline                  8.2                  h8228510_1    conda-forge
setuptools                68.0.0             pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
wheel                     0.41.1             pyhd8ed1ab_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zstd                      1.5.2                hfc55251_7    conda-forge

=== the package channel is different

# in jplerror3, pillow is not be installed directly and get libtiff.so.5 not found error
pillow                    9.4.0           py311h6a678d5_0

# in pilerr2, pillow is installed directly, no error
pillow                    9.4.0           py311h573f0d3_2    conda-forge
dennischen commented 1 year ago

A more clear test case can reproduce this.

conda create -n case1 -y
conda activate case1
conda install -c conda-forge python matplotlib -y
python -c "import matplotlib.pyplot as plt"

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/dennis/.conda/envs/case1/lib/python3.11/site-packages/matplotlib/__init__.py", line 129, in <module>
    from . import _api, _version, cbook, _docstring, rcsetup
  File "/home/dennis/.conda/envs/case1/lib/python3.11/site-packages/matplotlib/rcsetup.py", line 27, in <module>
    from matplotlib.colors import Colormap, is_color_like
  File "/home/dennis/.conda/envs/case1/lib/python3.11/site-packages/matplotlib/colors.py", line 51, in <module>
    from PIL import Image
  File "/home/dennis/.conda/envs/case1/lib/python3.11/site-packages/PIL/Image.py", line 103, in <module>
    from . import _imaging as core
ImportError: libtiff.so.5: cannot open shared object file: No such file or directory
conda create -n case2 -y
conda activate case2
conda install -c conda-forge python matplotlib pillow=9.4.0 -y
python -c "import matplotlib.pyplot as plt"

It looks like install matplotlib from conda-forge cann't get same pillow from conda-forget since this week. (no error in last week)

I am new to python and conda, no sure the root cause

dopplershift commented 1 year ago

The conda-forge environment that errors is mixing packages from different channels, which is not a supported configuration. Does it work if you create the environment using only conda-forge:

conda create -c conda-forge -n case3 python matplotlib
dennischen commented 1 year ago

just tried your suggestion

conda create -c conda-forge -n case3 python matplotlib

but the pillow is still not from conda-forge

pillow                    9.4.0           py311h6a678d5_0

and run import matpoltlib get same error.

I doubt it is a cach issue, but get same error in new VM. any other idea? cloud you run this test correctly in your env?

dopplershift commented 1 year ago

I can't reproduce this on my macOS system, so it's something specific to linux it seems. Some potential things to try: