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Anaconda issue tracking
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libstdc++.so.6 not found by anaconda-navigator #12522

Open GiulioCentorame opened 3 years ago

GiulioCentorame commented 3 years ago

Actual Behavior

Launching anaconda-navigator on a fresh install results in the following error, despite having libstdc++ installed:

$ anaconda-navigator
libGL error: MESA-LOADER: failed to open iris: /home/giuliocentorame/anaconda3/lib/python3.8/site-packages/PyQt5/../../../libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/lib64/dri/iris_dri.so) (search paths /usr/lib64/dri)
libGL error: failed to load driver: iris
libGL error: MESA-LOADER: failed to open iris: /home/giuliocentorame/anaconda3/lib/python3.8/site-packages/PyQt5/../../../libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/lib64/dri/iris_dri.so) (search paths /usr/lib64/dri)
libGL error: failed to load driver: iris
libGL error: MESA-LOADER: failed to open swrast: /home/giuliocentorame/anaconda3/lib/python3.8/site-packages/PyQt5/../../../libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/lib64/dri/swrast_dri.so) (search paths /usr/lib64/dri)
libGL error: failed to load driver: swrast

libstdc++.so.6 is present in /usr/lib64:

$ pwd
/usr/lib64
$ ls | grep libstdc++
libstdc++.so.6
libstdc++.so.6.0.29

Expected Behavior

It should launch with no errors under Fedora 34 if libstdc++-11.1.1-3.fc34.x86_64 is installed.

Steps to Reproduce

Anaconda or Miniconda version:

2021.05

Operating System:

Fedora 34

conda info
``` active environment : base active env location : /home/giuliocentorame/anaconda3 shell level : 1 user config file : /home/giuliocentorame/.condarc populated config files : /home/giuliocentorame/.condarc conda version : 4.10.3 conda-build version : 3.21.4 python version : 3.8.8.final.0 virtual packages : __cuda=11.3=0 __linux=5.12.13=0 __glibc=2.33=0 __unix=0=0 __archspec=1=x86_64 base environment : /home/giuliocentorame/anaconda3 (writable) conda av data dir : /home/giuliocentorame/anaconda3/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 : /home/giuliocentorame/anaconda3/pkgs /home/giuliocentorame/.conda/pkgs envs directories : /home/giuliocentorame/anaconda3/envs /home/giuliocentorame/.conda/envs platform : linux-64 user-agent : conda/4.10.3 requests/2.25.1 CPython/3.8.8 Linux/5.12.13-300.fc34.x86_64 fedora/34 glibc/2.33 UID:GID : 1000:1000 netrc file : None offline mode : False ```
conda list --show-channel-urls
``` # packages in environment at /home/giuliocentorame/anaconda3: # # Name Version Build Channel _ipyw_jlab_nb_ext_conf 0.1.0 py38_0 defaults _libgcc_mutex 0.1 main defaults alabaster 0.7.12 pyhd3eb1b0_0 defaults anaconda 2021.05 py38_0 defaults anaconda-client 1.7.2 py38_0 defaults anaconda-navigator 2.0.3 py38_0 defaults anaconda-project 0.9.1 pyhd3eb1b0_1 defaults anyio 2.2.0 py38h06a4308_1 defaults appdirs 1.4.4 py_0 defaults argh 0.26.2 py38_0 defaults argon2-cffi 20.1.0 py38h27cfd23_1 defaults asn1crypto 1.4.0 py_0 defaults astroid 2.5 py38h06a4308_1 defaults astropy 4.2.1 py38h27cfd23_1 defaults async_generator 1.10 pyhd3eb1b0_0 defaults atomicwrites 1.4.0 py_0 defaults attrs 20.3.0 pyhd3eb1b0_0 defaults autopep8 1.5.6 pyhd3eb1b0_0 defaults babel 2.9.0 pyhd3eb1b0_0 defaults backcall 0.2.0 pyhd3eb1b0_0 defaults backports 1.0 pyhd3eb1b0_2 defaults backports.shutil_get_terminal_size 1.0.0 pyhd3eb1b0_3 defaults backports.tempfile 1.0 pyhd3eb1b0_1 defaults backports.weakref 1.0.post1 py_1 defaults beautifulsoup4 4.9.3 pyha847dfd_0 defaults bitarray 2.1.0 py38h27cfd23_1 defaults bkcharts 0.2 py38_0 defaults black 19.10b0 py_0 defaults blas 1.0 mkl defaults bleach 3.3.0 pyhd3eb1b0_0 defaults blosc 1.21.0 h8c45485_0 defaults bokeh 2.3.2 py38h06a4308_0 defaults boto 2.49.0 py38_0 defaults bottleneck 1.3.2 py38heb32a55_1 defaults brotlipy 0.7.0 py38h27cfd23_1003 defaults bzip2 1.0.8 h7b6447c_0 defaults c-ares 1.17.1 h27cfd23_0 defaults ca-certificates 2021.4.13 h06a4308_1 defaults cairo 1.16.0 hf32fb01_1 defaults certifi 2020.12.5 py38h06a4308_0 defaults cffi 1.14.5 py38h261ae71_0 defaults chardet 4.0.0 py38h06a4308_1003 defaults click 7.1.2 pyhd3eb1b0_0 defaults cloudpickle 1.6.0 py_0 defaults clyent 1.2.2 py38_1 defaults colorama 0.4.4 pyhd3eb1b0_0 defaults conda 4.10.3 py38h06a4308_0 defaults conda-build 3.21.4 py38h06a4308_0 defaults conda-content-trust 0.1.1 pyhd3eb1b0_0 defaults conda-env 2.6.0 1 defaults conda-package-handling 1.7.3 py38h27cfd23_1 defaults conda-repo-cli 1.0.4 pyhd3eb1b0_0 defaults conda-token 0.3.0 pyhd3eb1b0_0 defaults conda-verify 3.4.2 pyhd3eb1b0_0 defaults contextlib2 0.6.0.post1 py_0 defaults cryptography 3.4.7 py38hd23ed53_0 defaults curl 7.71.1 hbc83047_1 defaults cycler 0.10.0 py38_0 defaults cython 0.29.23 py38h2531618_0 defaults cytoolz 0.11.0 py38h7b6447c_0 defaults dask 2021.4.0 pyhd3eb1b0_0 defaults dask-core 2021.4.0 pyhd3eb1b0_0 defaults dbus 1.13.18 hb2f20db_0 defaults decorator 5.0.6 pyhd3eb1b0_0 defaults defusedxml 0.7.1 pyhd3eb1b0_0 defaults diff-match-patch 20200713 py_0 defaults distributed 2021.4.1 py38h06a4308_0 defaults docutils 0.17.1 py38h06a4308_1 defaults entrypoints 0.3 py38_0 defaults et_xmlfile 1.0.1 py_1001 defaults expat 2.3.0 h2531618_2 defaults fastcache 1.1.0 py38h7b6447c_0 defaults filelock 3.0.12 pyhd3eb1b0_1 defaults flake8 3.9.0 pyhd3eb1b0_0 defaults flask 1.1.2 pyhd3eb1b0_0 defaults fontconfig 2.13.1 h6c09931_0 defaults freetype 2.10.4 h5ab3b9f_0 defaults fribidi 1.0.10 h7b6447c_0 defaults fsspec 0.9.0 pyhd3eb1b0_0 defaults future 0.18.2 py38_1 defaults get_terminal_size 1.0.0 haa9412d_0 defaults gevent 21.1.2 py38h27cfd23_1 defaults glib 2.68.1 h36276a3_0 defaults glob2 0.7 pyhd3eb1b0_0 defaults gmp 6.2.1 h2531618_2 defaults gmpy2 2.0.8 py38hd5f6e3b_3 defaults graphite2 1.3.14 h23475e2_0 defaults greenlet 1.0.0 py38h2531618_2 defaults gst-plugins-base 1.14.0 h8213a91_2 defaults gstreamer 1.14.0 h28cd5cc_2 defaults h5py 2.10.0 py38h7918eee_0 defaults harfbuzz 2.8.0 h6f93f22_0 defaults hdf5 1.10.4 hb1b8bf9_0 defaults heapdict 1.0.1 py_0 defaults html5lib 1.1 py_0 defaults icu 58.2 he6710b0_3 defaults idna 2.10 pyhd3eb1b0_0 defaults imageio 2.9.0 pyhd3eb1b0_0 defaults imagesize 1.2.0 pyhd3eb1b0_0 defaults importlib-metadata 3.10.0 py38h06a4308_0 defaults importlib_metadata 3.10.0 hd3eb1b0_0 defaults iniconfig 1.1.1 pyhd3eb1b0_0 defaults intel-openmp 2021.2.0 h06a4308_610 defaults intervaltree 3.1.0 py_0 defaults ipykernel 5.3.4 py38h5ca1d4c_0 defaults ipython 7.22.0 py38hb070fc8_0 defaults ipython_genutils 0.2.0 pyhd3eb1b0_1 defaults ipywidgets 7.6.3 pyhd3eb1b0_1 defaults isort 5.8.0 pyhd3eb1b0_0 defaults itsdangerous 1.1.0 pyhd3eb1b0_0 defaults jbig 2.1 hdba287a_0 defaults jdcal 1.4.1 py_0 defaults jedi 0.17.2 py38h06a4308_1 defaults jeepney 0.6.0 pyhd3eb1b0_0 defaults jinja2 2.11.3 pyhd3eb1b0_0 defaults joblib 1.0.1 pyhd3eb1b0_0 defaults jpeg 9b h024ee3a_2 defaults json5 0.9.5 py_0 defaults jsonschema 3.2.0 py_2 defaults jupyter 1.0.0 py38_7 defaults jupyter-packaging 0.7.12 pyhd3eb1b0_0 defaults jupyter_client 6.1.12 pyhd3eb1b0_0 defaults jupyter_console 6.4.0 pyhd3eb1b0_0 defaults jupyter_core 4.7.1 py38h06a4308_0 defaults jupyter_server 1.4.1 py38h06a4308_0 defaults jupyterlab 3.0.14 pyhd3eb1b0_1 defaults jupyterlab_pygments 0.1.2 py_0 defaults jupyterlab_server 2.4.0 pyhd3eb1b0_0 defaults jupyterlab_widgets 1.0.0 pyhd3eb1b0_1 defaults keyring 22.3.0 py38h06a4308_0 defaults kiwisolver 1.3.1 py38h2531618_0 defaults krb5 1.18.2 h173b8e3_0 defaults lazy-object-proxy 1.6.0 py38h27cfd23_0 defaults lcms2 2.12 h3be6417_0 defaults ld_impl_linux-64 2.33.1 h53a641e_7 defaults libarchive 3.4.2 h62408e4_0 defaults libcurl 7.71.1 h20c2e04_1 defaults libedit 3.1.20210216 h27cfd23_1 defaults libev 4.33 h7b6447c_0 defaults libffi 3.3 he6710b0_2 defaults libgcc-ng 9.1.0 hdf63c60_0 defaults libgfortran-ng 7.3.0 hdf63c60_0 defaults liblief 0.10.1 he6710b0_0 defaults libllvm10 10.0.1 hbcb73fb_5 defaults libpng 1.6.37 hbc83047_0 defaults libsodium 1.0.18 h7b6447c_0 defaults libspatialindex 1.9.3 h2531618_0 defaults libssh2 1.9.0 h1ba5d50_1 defaults libstdcxx-ng 9.1.0 hdf63c60_0 defaults libtiff 4.2.0 h85742a9_0 defaults libtool 2.4.6 h7b6447c_1005 defaults libuuid 1.0.3 h1bed415_2 defaults libuv 1.40.0 h7b6447c_0 defaults libwebp-base 1.2.0 h27cfd23_0 defaults libxcb 1.14 h7b6447c_0 defaults libxml2 2.9.10 hb55368b_3 defaults libxslt 1.1.34 hc22bd24_0 defaults llvmlite 0.36.0 py38h612dafd_4 defaults locket 0.2.1 py38h06a4308_1 defaults lxml 4.6.3 py38h9120a33_0 defaults lz4-c 1.9.3 h2531618_0 defaults lzo 2.10 h7b6447c_2 defaults markupsafe 1.1.1 py38h7b6447c_0 defaults matplotlib 3.3.4 py38h06a4308_0 defaults matplotlib-base 3.3.4 py38h62a2d02_0 defaults mccabe 0.6.1 py38_1 defaults mistune 0.8.4 py38h7b6447c_1000 defaults mkl 2021.2.0 h06a4308_296 defaults mkl-service 2.3.0 py38h27cfd23_1 defaults mkl_fft 1.3.0 py38h42c9631_2 defaults mkl_random 1.2.1 py38ha9443f7_2 defaults mock 4.0.3 pyhd3eb1b0_0 defaults more-itertools 8.7.0 pyhd3eb1b0_0 defaults mpc 1.1.0 h10f8cd9_1 defaults mpfr 4.0.2 hb69a4c5_1 defaults mpmath 1.2.1 py38h06a4308_0 defaults msgpack-python 1.0.2 py38hff7bd54_1 defaults multipledispatch 0.6.0 py38_0 defaults mypy_extensions 0.4.3 py38_0 defaults navigator-updater 0.2.1 py38_0 defaults nbclassic 0.2.6 pyhd3eb1b0_0 defaults nbclient 0.5.3 pyhd3eb1b0_0 defaults nbconvert 6.0.7 py38_0 defaults nbformat 5.1.3 pyhd3eb1b0_0 defaults ncurses 6.2 he6710b0_1 defaults nest-asyncio 1.5.1 pyhd3eb1b0_0 defaults networkx 2.5 py_0 defaults nltk 3.6.1 pyhd3eb1b0_0 defaults nose 1.3.7 pyhd3eb1b0_1006 defaults notebook 6.3.0 py38h06a4308_0 defaults numba 0.53.1 py38ha9443f7_0 defaults numexpr 2.7.3 py38h22e1b3c_1 defaults numpy 1.20.1 py38h93e21f0_0 defaults numpy-base 1.20.1 py38h7d8b39e_0 defaults numpydoc 1.1.0 pyhd3eb1b0_1 defaults olefile 0.46 py_0 defaults openpyxl 3.0.7 pyhd3eb1b0_0 defaults openssl 1.1.1k h27cfd23_0 defaults packaging 20.9 pyhd3eb1b0_0 defaults pandas 1.2.4 py38h2531618_0 defaults pandoc 2.12 h06a4308_0 defaults pandocfilters 1.4.3 py38h06a4308_1 defaults pango 1.45.3 hd140c19_0 defaults parso 0.7.0 py_0 defaults partd 1.2.0 pyhd3eb1b0_0 defaults patchelf 0.12 h2531618_1 defaults path 15.1.2 py38h06a4308_0 defaults path.py 12.5.0 0 defaults pathlib2 2.3.5 py38h06a4308_2 defaults pathspec 0.7.0 py_0 defaults patsy 0.5.1 py38_0 defaults pcre 8.44 he6710b0_0 defaults pep8 1.7.1 py38_0 defaults pexpect 4.8.0 pyhd3eb1b0_3 defaults pickleshare 0.7.5 pyhd3eb1b0_1003 defaults pillow 8.2.0 py38he98fc37_0 defaults pip 21.0.1 py38h06a4308_0 defaults pixman 0.40.0 h7b6447c_0 defaults pkginfo 1.7.0 py38h06a4308_0 defaults pluggy 0.13.1 py38h06a4308_0 defaults ply 3.11 py38_0 defaults prometheus_client 0.10.1 pyhd3eb1b0_0 defaults prompt-toolkit 3.0.17 pyh06a4308_0 defaults prompt_toolkit 3.0.17 hd3eb1b0_0 defaults psutil 5.8.0 py38h27cfd23_1 defaults ptyprocess 0.7.0 pyhd3eb1b0_2 defaults py 1.10.0 pyhd3eb1b0_0 defaults py-lief 0.10.1 py38h403a769_0 defaults pycodestyle 2.6.0 pyhd3eb1b0_0 defaults pycosat 0.6.3 py38h7b6447c_1 defaults pycparser 2.20 py_2 defaults pycurl 7.43.0.6 py38h1ba5d50_0 defaults pydocstyle 6.0.0 pyhd3eb1b0_0 defaults pyerfa 1.7.3 py38h27cfd23_0 defaults pyflakes 2.2.0 pyhd3eb1b0_0 defaults pygments 2.8.1 pyhd3eb1b0_0 defaults pylint 2.7.4 py38h06a4308_1 defaults pyls-black 0.4.6 hd3eb1b0_0 defaults pyls-spyder 0.3.2 pyhd3eb1b0_0 defaults pyodbc 4.0.30 py38he6710b0_0 defaults pyopenssl 20.0.1 pyhd3eb1b0_1 defaults pyparsing 2.4.7 pyhd3eb1b0_0 defaults pyqt 5.9.2 py38h05f1152_4 defaults pyrsistent 0.17.3 py38h7b6447c_0 defaults pysocks 1.7.1 py38h06a4308_0 defaults pytables 3.6.1 py38h9fd0a39_0 defaults pytest 6.2.3 py38h06a4308_2 defaults python 3.8.8 hdb3f193_5 defaults python-dateutil 2.8.1 pyhd3eb1b0_0 defaults python-jsonrpc-server 0.4.0 py_0 defaults python-language-server 0.36.2 pyhd3eb1b0_0 defaults python-libarchive-c 2.9 pyhd3eb1b0_1 defaults pytz 2021.1 pyhd3eb1b0_0 defaults pywavelets 1.1.1 py38h7b6447c_2 defaults pyxdg 0.27 pyhd3eb1b0_0 defaults pyyaml 5.4.1 py38h27cfd23_1 defaults pyzmq 20.0.0 py38h2531618_1 defaults qdarkstyle 2.8.1 py_0 defaults qt 5.9.7 h5867ecd_1 defaults qtawesome 1.0.2 pyhd3eb1b0_0 defaults qtconsole 5.0.3 pyhd3eb1b0_0 defaults qtpy 1.9.0 py_0 defaults readline 8.1 h27cfd23_0 defaults regex 2021.4.4 py38h27cfd23_0 defaults requests 2.25.1 pyhd3eb1b0_0 defaults ripgrep 12.1.1 0 defaults rope 0.18.0 py_0 defaults rtree 0.9.7 py38h06a4308_1 defaults ruamel_yaml 0.15.100 py38h27cfd23_0 defaults scikit-image 0.18.1 py38ha9443f7_0 defaults scikit-learn 0.24.1 py38ha9443f7_0 defaults scipy 1.6.2 py38had2a1c9_1 defaults seaborn 0.11.1 pyhd3eb1b0_0 defaults secretstorage 3.3.1 py38h06a4308_0 defaults send2trash 1.5.0 pyhd3eb1b0_1 defaults setuptools 52.0.0 py38h06a4308_0 defaults simplegeneric 0.8.1 py38_2 defaults singledispatch 3.6.1 pyhd3eb1b0_1001 defaults sip 4.19.13 py38he6710b0_0 defaults six 1.15.0 py38h06a4308_0 defaults sniffio 1.2.0 py38h06a4308_1 defaults snowballstemmer 2.1.0 pyhd3eb1b0_0 defaults sortedcollections 2.1.0 pyhd3eb1b0_0 defaults sortedcontainers 2.3.0 pyhd3eb1b0_0 defaults soupsieve 2.2.1 pyhd3eb1b0_0 defaults sphinx 4.0.1 pyhd3eb1b0_0 defaults sphinxcontrib 1.0 py38_1 defaults sphinxcontrib-applehelp 1.0.2 pyhd3eb1b0_0 defaults sphinxcontrib-devhelp 1.0.2 pyhd3eb1b0_0 defaults sphinxcontrib-htmlhelp 1.0.3 pyhd3eb1b0_0 defaults sphinxcontrib-jsmath 1.0.1 pyhd3eb1b0_0 defaults sphinxcontrib-qthelp 1.0.3 pyhd3eb1b0_0 defaults sphinxcontrib-serializinghtml 1.1.4 pyhd3eb1b0_0 defaults sphinxcontrib-websupport 1.2.4 py_0 defaults spyder 4.2.5 py38h06a4308_0 defaults spyder-kernels 1.10.2 py38h06a4308_0 defaults sqlalchemy 1.4.15 py38h27cfd23_0 defaults sqlite 3.35.4 hdfb4753_0 defaults statsmodels 0.12.2 py38h27cfd23_0 defaults sympy 1.8 py38h06a4308_0 defaults tbb 2020.3 hfd86e86_0 defaults tblib 1.7.0 py_0 defaults terminado 0.9.4 py38h06a4308_0 defaults testpath 0.4.4 pyhd3eb1b0_0 defaults textdistance 4.2.1 pyhd3eb1b0_0 defaults threadpoolctl 2.1.0 pyh5ca1d4c_0 defaults three-merge 0.1.1 pyhd3eb1b0_0 defaults tifffile 2020.10.1 py38hdd07704_2 defaults tk 8.6.10 hbc83047_0 defaults toml 0.10.2 pyhd3eb1b0_0 defaults toolz 0.11.1 pyhd3eb1b0_0 defaults tornado 6.1 py38h27cfd23_0 defaults tqdm 4.59.0 pyhd3eb1b0_1 defaults traitlets 5.0.5 pyhd3eb1b0_0 defaults typed-ast 1.4.2 py38h27cfd23_1 defaults typing_extensions 3.7.4.3 pyha847dfd_0 defaults ujson 4.0.2 py38h2531618_0 defaults unicodecsv 0.14.1 py38_0 defaults unixodbc 2.3.9 h7b6447c_0 defaults urllib3 1.26.4 pyhd3eb1b0_0 defaults watchdog 1.0.2 py38h06a4308_1 defaults wcwidth 0.2.5 py_0 defaults webencodings 0.5.1 py38_1 defaults werkzeug 1.0.1 pyhd3eb1b0_0 defaults wheel 0.36.2 pyhd3eb1b0_0 defaults widgetsnbextension 3.5.1 py38_0 defaults wrapt 1.12.1 py38h7b6447c_1 defaults wurlitzer 2.1.0 py38h06a4308_0 defaults xlrd 2.0.1 pyhd3eb1b0_0 defaults xlsxwriter 1.3.8 pyhd3eb1b0_0 defaults xlwt 1.3.0 py38_0 defaults xmltodict 0.12.0 py_0 defaults xz 5.2.5 h7b6447c_0 defaults yaml 0.2.5 h7b6447c_0 defaults yapf 0.31.0 pyhd3eb1b0_0 defaults zeromq 4.3.4 h2531618_0 defaults zict 2.0.0 pyhd3eb1b0_0 defaults zipp 3.4.1 pyhd3eb1b0_0 defaults zlib 1.2.11 h7b6447c_3 defaults zope 1.0 py38_1 defaults zope.event 4.5.0 py38_0 defaults zope.interface 5.3.0 py38h27cfd23_0 defaults zstd 1.4.5 h9ceee32_0 defaults ```
GiulioCentorame commented 3 years ago

I discovered there is a similar issue with Spyder too: https://ask.fedoraproject.org/t/unable-to-load-swrast-and-iris/15531

cspipaon commented 2 years ago

Any updates on how to fix this? I also get the LibGL errors when using matplotlib in environments I created recently. Environments I created a long time ago (around 2+ years) do not give me these errors.