Segmentation Fault due To build conflicts
SoundsSerious opened this issue · 4 comments
Hi, I'm observing a segmentation fault as described in jupyter/qtconsole#585 of which I believe basemap is the root cause.
This is due to underlying conda c-library conflicts.
It seems the underlying issue with basemap support is the build process for libgeos. I wonder if life would be easier by making calls to https://pygeos.readthedocs.io/en/stable/ instead?
To replicate this issue, this is the minimal build script that results in failure.
This occurs on windows system linux - ubuntu 22.04 & 20.04
conda env remove nept -y
conda create -n nept -c conda-forge python=3.9.12 -y
conda activate nept
conda install -c conda-forge basemap qtconsole -y
jupyter qtconsole #This fails with segmentation fault.
Hi @SoundsSerious! I am not an expert on Miniforge/Anaconda, but I tried to follow your steps in a clean Miniforge installation on Windows 64-bit and your commands seem to work successfully.
First I create the new environment:
(base) C:\Users\vic>conda create -y -n nept -c conda-forge python=3.9.12
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 23.3.1
latest version: 23.11.0
Please update conda by running
$ conda update -n base -c conda-forge conda
Or to minimize the number of packages updated during conda update use
conda install conda=23.11.0
## Package Plan ##
environment location: C:\Users\vic\miniforge3\envs\nept
added / updated specs:
- python=3.9.12
The following packages will be downloaded:
package | build
---------------------------|-----------------
bzip2-1.0.8 | hcfcfb64_5 122 KB conda-forge
ca-certificates-2023.11.17 | h56e8100_0 151 KB conda-forge
libsqlite-3.44.2 | hcfcfb64_0 833 KB conda-forge
openssl-3.2.0 | hcfcfb64_1 7.9 MB conda-forge
pip-23.3.2 | pyhd8ed1ab_0 1.3 MB conda-forge
python-3.9.12 |hcf16a7b_1_cpython 17.9 MB conda-forge
setuptools-68.2.2 | pyhd8ed1ab_0 454 KB conda-forge
sqlite-3.44.2 | hcfcfb64_0 836 KB conda-forge
tk-8.6.13 | h5226925_1 3.3 MB conda-forge
tzdata-2023d | h0c530f3_0 117 KB conda-forge
vc-14.3 | hcf57466_18 17 KB conda-forge
vc14_runtime-14.38.33130 | h82b7239_18 732 KB conda-forge
vs2015_runtime-14.38.33130 | hcb4865c_18 17 KB conda-forge
wheel-0.42.0 | pyhd8ed1ab_0 56 KB conda-forge
------------------------------------------------------------
Total: 33.7 MB
The following NEW packages will be INSTALLED:
bzip2 conda-forge/win-64::bzip2-1.0.8-hcfcfb64_5
ca-certificates conda-forge/win-64::ca-certificates-2023.11.17-h56e8100_0
libffi conda-forge/win-64::libffi-3.4.2-h8ffe710_5
libsqlite conda-forge/win-64::libsqlite-3.44.2-hcfcfb64_0
libzlib conda-forge/win-64::libzlib-1.2.13-hcfcfb64_5
openssl conda-forge/win-64::openssl-3.2.0-hcfcfb64_1
pip conda-forge/noarch::pip-23.3.2-pyhd8ed1ab_0
python conda-forge/win-64::python-3.9.12-hcf16a7b_1_cpython
setuptools conda-forge/noarch::setuptools-68.2.2-pyhd8ed1ab_0
sqlite conda-forge/win-64::sqlite-3.44.2-hcfcfb64_0
tk conda-forge/win-64::tk-8.6.13-h5226925_1
tzdata conda-forge/noarch::tzdata-2023d-h0c530f3_0
ucrt conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_0
vc conda-forge/win-64::vc-14.3-hcf57466_18
vc14_runtime conda-forge/win-64::vc14_runtime-14.38.33130-h82b7239_18
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.38.33130-hcb4865c_18
wheel conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0
xz conda-forge/win-64::xz-5.2.6-h8d14728_0
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate nept
#
# To deactivate an active environment, use
#
# $ conda deactivate
Second, I activate the "nept" environment and install basemap and qtconsole from the conda-forge channel:
(base) C:\Users\vic>conda activate nept
(nept) C:\Users\vic>conda install -y -c conda-forge basemap qtconsole
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 23.3.1
latest version: 23.11.0
Please update conda by running
$ conda update -n base -c conda-forge conda
Or to minimize the number of packages updated during conda update use
conda install conda=23.11.0
## Package Plan ##
environment location: C:\Users\vic\miniforge3\envs\nept
added / updated specs:
- basemap
- qtconsole
The following packages will be downloaded:
package | build
---------------------------|-----------------
asttokens-2.4.1 | pyhd8ed1ab_0 28 KB conda-forge
basemap-1.3.9 | py39hbe530b1_0 257 KB conda-forge
basemap-data-1.3.2 | pyhd8ed1ab_3 24.1 MB conda-forge
brotli-1.1.0 | hcfcfb64_1 19 KB conda-forge
brotli-bin-1.1.0 | hcfcfb64_1 20 KB conda-forge
certifi-2023.11.17 | pyhd8ed1ab_0 155 KB conda-forge
comm-0.1.4 | pyhd8ed1ab_0 11 KB conda-forge
contourpy-1.2.0 | py39h1f6ef14_0 182 KB conda-forge
cycler-0.12.1 | pyhd8ed1ab_0 13 KB conda-forge
debugpy-1.8.0 | py39h99910a6_1 3.1 MB conda-forge
decorator-5.1.1 | pyhd8ed1ab_0 12 KB conda-forge
exceptiongroup-1.2.0 | pyhd8ed1ab_0 20 KB conda-forge
executing-2.0.1 | pyhd8ed1ab_0 27 KB conda-forge
fonttools-4.47.0 | py39ha55989b_0 1.8 MB conda-forge
freetype-2.12.1 | hdaf720e_2 498 KB conda-forge
geos-3.12.1 | h1537add_0 1.5 MB conda-forge
gettext-0.21.1 | h5728263_0 5.3 MB conda-forge
glib-2.78.3 | h12be248_0 495 KB conda-forge
glib-tools-2.78.3 | h12be248_0 141 KB conda-forge
gst-plugins-base-1.22.8 | h001b923_0 1.9 MB conda-forge
gstreamer-1.22.8 | hb4038d2_0 1.8 MB conda-forge
icu-72.1 | h63175ca_0 12.6 MB conda-forge
importlib-metadata-7.0.1 | pyha770c72_0 26 KB conda-forge
importlib-resources-6.1.1 | pyhd8ed1ab_0 9 KB conda-forge
importlib_metadata-7.0.1 | hd8ed1ab_0 9 KB conda-forge
importlib_resources-6.1.1 | pyhd8ed1ab_0 29 KB conda-forge
intel-openmp-2023.2.0 | h57928b3_50497 2.4 MB conda-forge
ipykernel-6.28.0 | pyha63f2e9_0 114 KB conda-forge
ipython-8.18.1 | pyh7428d3b_3 576 KB conda-forge
jedi-0.19.1 | pyhd8ed1ab_0 822 KB conda-forge
jupyter_client-8.6.0 | pyhd8ed1ab_0 103 KB conda-forge
jupyter_core-5.6.0 | py39hcbf5309_0 94 KB conda-forge
kiwisolver-1.4.5 | py39h1f6ef14_1 54 KB conda-forge
krb5-1.20.1 | heb0366b_0 701 KB conda-forge
lcms2-2.15 | h3e3b177_1 487 KB conda-forge
lerc-4.0.0 | h63175ca_0 190 KB conda-forge
libblas-3.9.0 | 20_win64_mkl 4.8 MB conda-forge
libbrotlicommon-1.1.0 | hcfcfb64_1 69 KB conda-forge
libbrotlidec-1.1.0 | hcfcfb64_1 32 KB conda-forge
libbrotlienc-1.1.0 | hcfcfb64_1 241 KB conda-forge
libcblas-3.9.0 | 20_win64_mkl 4.8 MB conda-forge
libclang-16.0.6 |default_heb8d277_2 35 KB conda-forge
libclang13-16.0.6 |default_hc80b9e7_2 22.1 MB conda-forge
libcurl-8.1.2 | h68f0423_0 306 KB conda-forge
libdeflate-1.18 | hcfcfb64_0 149 KB conda-forge
libglib-2.78.3 | h16e383f_0 2.5 MB conda-forge
libhwloc-2.9.3 |default_haede6df_1009 2.5 MB conda-forge
libiconv-1.17 | hcfcfb64_2 621 KB conda-forge
libjpeg-turbo-2.1.5.1 | hcfcfb64_1 672 KB conda-forge
liblapack-3.9.0 | 20_win64_mkl 4.8 MB conda-forge
libogg-1.3.4 | h8ffe710_1 34 KB conda-forge
libpng-1.6.39 | h19919ed_0 336 KB conda-forge
libsodium-1.0.18 | h8d14728_1 697 KB conda-forge
libtiff-4.5.1 | h6c8260b_1 931 KB conda-forge
libvorbis-1.3.7 | h0e60522_0 267 KB conda-forge
libwebp-base-1.3.2 | hcfcfb64_0 263 KB conda-forge
libxcb-1.15 | hcd874cb_0 947 KB conda-forge
libxml2-2.11.6 | hc3477c8_0 1.6 MB conda-forge
m2w64-gcc-libgfortran-5.3.0| 6 342 KB conda-forge
m2w64-gcc-libs-5.3.0 | 7 520 KB conda-forge
m2w64-gcc-libs-core-5.3.0 | 7 214 KB conda-forge
m2w64-gmp-6.1.0 | 2 726 KB conda-forge
m2w64-libwinpthread-git-5.0.0.4634.697f757| 2 31 KB conda-forge
matplotlib-base-3.7.3 | py39hf19769e_0 6.3 MB conda-forge
matplotlib-inline-0.1.6 | pyhd8ed1ab_0 12 KB conda-forge
mkl-2023.2.0 | h6a75c08_50497 138.0 MB conda-forge
msys2-conda-epoch-20160418 | 1 3 KB conda-forge
munkres-1.1.4 | pyh9f0ad1d_0 12 KB conda-forge
nest-asyncio-1.5.8 | pyhd8ed1ab_0 11 KB conda-forge
numpy-1.26.2 | py39hddb5d58_0 5.7 MB conda-forge
openjpeg-2.5.0 | ha2aaf27_2 232 KB conda-forge
packaging-23.2 | pyhd8ed1ab_0 48 KB conda-forge
parso-0.8.3 | pyhd8ed1ab_0 69 KB conda-forge
pcre2-10.42 | h17e33f8_0 860 KB conda-forge
pickleshare-0.7.5 | py_1003 9 KB conda-forge
pillow-10.0.0 | py39ha9166d5_0 43.9 MB conda-forge
platformdirs-4.1.0 | pyhd8ed1ab_0 20 KB conda-forge
ply-3.11 | py_1 44 KB conda-forge
proj-9.2.1 | h660b3b0_0 2.5 MB conda-forge
prompt-toolkit-3.0.42 | pyha770c72_0 264 KB conda-forge
psutil-5.9.7 | py39ha55989b_0 370 KB conda-forge
pthread-stubs-0.4 | hcd874cb_1001 6 KB conda-forge
pthreads-win32-2.9.1 | hfa6e2cd_3 141 KB conda-forge
pure_eval-0.2.2 | pyhd8ed1ab_0 14 KB conda-forge
pygments-2.17.2 | pyhd8ed1ab_0 840 KB conda-forge
pyparsing-3.1.1 | pyhd8ed1ab_0 87 KB conda-forge
pyproj-3.6.1 | py39hd6181e6_0 694 KB conda-forge
pyqt-5.15.9 | py39hb77abff_5 3.7 MB conda-forge
pyqt5-sip-12.12.2 | py39h99910a6_5 78 KB conda-forge
pyshp-2.3.1 | pyhd8ed1ab_0 941 KB conda-forge
python-dateutil-2.8.2 | pyhd8ed1ab_0 240 KB conda-forge
python_abi-3.9 | 4_cp39 7 KB conda-forge
pywin32-306 | py39h99910a6_2 5.5 MB conda-forge
pyzmq-25.1.2 | py39h7eaf5a6_0 398 KB conda-forge
qt-main-5.15.8 | h2c8576c_12 56.9 MB conda-forge
qtconsole-5.5.1 | pyhd8ed1ab_0 7 KB conda-forge
qtconsole-base-5.5.1 | pyha770c72_0 98 KB conda-forge
qtpy-2.4.1 | pyhd8ed1ab_0 60 KB conda-forge
sip-6.7.12 | py39h99910a6_0 491 KB conda-forge
six-1.16.0 | pyh6c4a22f_0 14 KB conda-forge
stack_data-0.6.2 | pyhd8ed1ab_0 26 KB conda-forge
tbb-2021.11.0 | h91493d7_0 157 KB conda-forge
toml-0.10.2 | pyhd8ed1ab_0 18 KB conda-forge
tomli-2.0.1 | pyhd8ed1ab_0 16 KB conda-forge
tornado-6.3.3 | py39ha55989b_1 620 KB conda-forge
traitlets-5.14.0 | pyhd8ed1ab_0 107 KB conda-forge
typing_extensions-4.9.0 | pyha770c72_0 35 KB conda-forge
unicodedata2-15.1.0 | py39ha55989b_0 365 KB conda-forge
wcwidth-0.2.12 | pyhd8ed1ab_0 32 KB conda-forge
xorg-libxau-1.0.11 | hcd874cb_0 50 KB conda-forge
xorg-libxdmcp-1.1.3 | hcd874cb_0 66 KB conda-forge
zeromq-4.3.5 | h63175ca_0 4.0 MB conda-forge
zipp-3.17.0 | pyhd8ed1ab_0 19 KB conda-forge
------------------------------------------------------------
Total: 383.7 MB
The following NEW packages will be INSTALLED:
asttokens conda-forge/noarch::asttokens-2.4.1-pyhd8ed1ab_0
basemap conda-forge/win-64::basemap-1.3.9-py39hbe530b1_0
basemap-data conda-forge/noarch::basemap-data-1.3.2-pyhd8ed1ab_3
brotli conda-forge/win-64::brotli-1.1.0-hcfcfb64_1
brotli-bin conda-forge/win-64::brotli-bin-1.1.0-hcfcfb64_1
certifi conda-forge/noarch::certifi-2023.11.17-pyhd8ed1ab_0
colorama conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0
comm conda-forge/noarch::comm-0.1.4-pyhd8ed1ab_0
contourpy conda-forge/win-64::contourpy-1.2.0-py39h1f6ef14_0
cycler conda-forge/noarch::cycler-0.12.1-pyhd8ed1ab_0
debugpy conda-forge/win-64::debugpy-1.8.0-py39h99910a6_1
decorator conda-forge/noarch::decorator-5.1.1-pyhd8ed1ab_0
exceptiongroup conda-forge/noarch::exceptiongroup-1.2.0-pyhd8ed1ab_0
executing conda-forge/noarch::executing-2.0.1-pyhd8ed1ab_0
fonttools conda-forge/win-64::fonttools-4.47.0-py39ha55989b_0
freetype conda-forge/win-64::freetype-2.12.1-hdaf720e_2
geos conda-forge/win-64::geos-3.12.1-h1537add_0
gettext conda-forge/win-64::gettext-0.21.1-h5728263_0
glib conda-forge/win-64::glib-2.78.3-h12be248_0
glib-tools conda-forge/win-64::glib-tools-2.78.3-h12be248_0
gst-plugins-base conda-forge/win-64::gst-plugins-base-1.22.8-h001b923_0
gstreamer conda-forge/win-64::gstreamer-1.22.8-hb4038d2_0
icu conda-forge/win-64::icu-72.1-h63175ca_0
importlib-metadata conda-forge/noarch::importlib-metadata-7.0.1-pyha770c72_0
importlib-resourc~ conda-forge/noarch::importlib-resources-6.1.1-pyhd8ed1ab_0
importlib_metadata conda-forge/noarch::importlib_metadata-7.0.1-hd8ed1ab_0
importlib_resourc~ conda-forge/noarch::importlib_resources-6.1.1-pyhd8ed1ab_0
intel-openmp conda-forge/win-64::intel-openmp-2023.2.0-h57928b3_50497
ipykernel conda-forge/noarch::ipykernel-6.28.0-pyha63f2e9_0
ipython conda-forge/noarch::ipython-8.18.1-pyh7428d3b_3
jedi conda-forge/noarch::jedi-0.19.1-pyhd8ed1ab_0
jupyter_client conda-forge/noarch::jupyter_client-8.6.0-pyhd8ed1ab_0
jupyter_core conda-forge/win-64::jupyter_core-5.6.0-py39hcbf5309_0
kiwisolver conda-forge/win-64::kiwisolver-1.4.5-py39h1f6ef14_1
krb5 conda-forge/win-64::krb5-1.20.1-heb0366b_0
lcms2 conda-forge/win-64::lcms2-2.15-h3e3b177_1
lerc conda-forge/win-64::lerc-4.0.0-h63175ca_0
libblas conda-forge/win-64::libblas-3.9.0-20_win64_mkl
libbrotlicommon conda-forge/win-64::libbrotlicommon-1.1.0-hcfcfb64_1
libbrotlidec conda-forge/win-64::libbrotlidec-1.1.0-hcfcfb64_1
libbrotlienc conda-forge/win-64::libbrotlienc-1.1.0-hcfcfb64_1
libcblas conda-forge/win-64::libcblas-3.9.0-20_win64_mkl
libclang conda-forge/win-64::libclang-16.0.6-default_heb8d277_2
libclang13 conda-forge/win-64::libclang13-16.0.6-default_hc80b9e7_2
libcurl conda-forge/win-64::libcurl-8.1.2-h68f0423_0
libdeflate conda-forge/win-64::libdeflate-1.18-hcfcfb64_0
libglib conda-forge/win-64::libglib-2.78.3-h16e383f_0
libhwloc conda-forge/win-64::libhwloc-2.9.3-default_haede6df_1009
libiconv conda-forge/win-64::libiconv-1.17-hcfcfb64_2
libjpeg-turbo conda-forge/win-64::libjpeg-turbo-2.1.5.1-hcfcfb64_1
liblapack conda-forge/win-64::liblapack-3.9.0-20_win64_mkl
libogg conda-forge/win-64::libogg-1.3.4-h8ffe710_1
libpng conda-forge/win-64::libpng-1.6.39-h19919ed_0
libsodium conda-forge/win-64::libsodium-1.0.18-h8d14728_1
libssh2 conda-forge/win-64::libssh2-1.11.0-h7dfc565_0
libtiff conda-forge/win-64::libtiff-4.5.1-h6c8260b_1
libvorbis conda-forge/win-64::libvorbis-1.3.7-h0e60522_0
libwebp-base conda-forge/win-64::libwebp-base-1.3.2-hcfcfb64_0
libxcb conda-forge/win-64::libxcb-1.15-hcd874cb_0
libxml2 conda-forge/win-64::libxml2-2.11.6-hc3477c8_0
m2w64-gcc-libgfor~ conda-forge/win-64::m2w64-gcc-libgfortran-5.3.0-6
m2w64-gcc-libs conda-forge/win-64::m2w64-gcc-libs-5.3.0-7
m2w64-gcc-libs-co~ conda-forge/win-64::m2w64-gcc-libs-core-5.3.0-7
m2w64-gmp conda-forge/win-64::m2w64-gmp-6.1.0-2
m2w64-libwinpthre~ conda-forge/win-64::m2w64-libwinpthread-git-5.0.0.4634.697f757-2
matplotlib-base conda-forge/win-64::matplotlib-base-3.7.3-py39hf19769e_0
matplotlib-inline conda-forge/noarch::matplotlib-inline-0.1.6-pyhd8ed1ab_0
mkl conda-forge/win-64::mkl-2023.2.0-h6a75c08_50497
msys2-conda-epoch conda-forge/win-64::msys2-conda-epoch-20160418-1
munkres conda-forge/noarch::munkres-1.1.4-pyh9f0ad1d_0
nest-asyncio conda-forge/noarch::nest-asyncio-1.5.8-pyhd8ed1ab_0
numpy conda-forge/win-64::numpy-1.26.2-py39hddb5d58_0
openjpeg conda-forge/win-64::openjpeg-2.5.0-ha2aaf27_2
packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0
parso conda-forge/noarch::parso-0.8.3-pyhd8ed1ab_0
pcre2 conda-forge/win-64::pcre2-10.42-h17e33f8_0
pickleshare conda-forge/noarch::pickleshare-0.7.5-py_1003
pillow conda-forge/win-64::pillow-10.0.0-py39ha9166d5_0
platformdirs conda-forge/noarch::platformdirs-4.1.0-pyhd8ed1ab_0
ply conda-forge/noarch::ply-3.11-py_1
proj conda-forge/win-64::proj-9.2.1-h660b3b0_0
prompt-toolkit conda-forge/noarch::prompt-toolkit-3.0.42-pyha770c72_0
psutil conda-forge/win-64::psutil-5.9.7-py39ha55989b_0
pthread-stubs conda-forge/win-64::pthread-stubs-0.4-hcd874cb_1001
pthreads-win32 conda-forge/win-64::pthreads-win32-2.9.1-hfa6e2cd_3
pure_eval conda-forge/noarch::pure_eval-0.2.2-pyhd8ed1ab_0
pygments conda-forge/noarch::pygments-2.17.2-pyhd8ed1ab_0
pyparsing conda-forge/noarch::pyparsing-3.1.1-pyhd8ed1ab_0
pyproj conda-forge/win-64::pyproj-3.6.1-py39hd6181e6_0
pyqt conda-forge/win-64::pyqt-5.15.9-py39hb77abff_5
pyqt5-sip conda-forge/win-64::pyqt5-sip-12.12.2-py39h99910a6_5
pyshp conda-forge/noarch::pyshp-2.3.1-pyhd8ed1ab_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/win-64::python_abi-3.9-4_cp39
pywin32 conda-forge/win-64::pywin32-306-py39h99910a6_2
pyzmq conda-forge/win-64::pyzmq-25.1.2-py39h7eaf5a6_0
qt-main conda-forge/win-64::qt-main-5.15.8-h2c8576c_12
qtconsole conda-forge/noarch::qtconsole-5.5.1-pyhd8ed1ab_0
qtconsole-base conda-forge/noarch::qtconsole-base-5.5.1-pyha770c72_0
qtpy conda-forge/noarch::qtpy-2.4.1-pyhd8ed1ab_0
sip conda-forge/win-64::sip-6.7.12-py39h99910a6_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
stack_data conda-forge/noarch::stack_data-0.6.2-pyhd8ed1ab_0
tbb conda-forge/win-64::tbb-2021.11.0-h91493d7_0
toml conda-forge/noarch::toml-0.10.2-pyhd8ed1ab_0
tomli conda-forge/noarch::tomli-2.0.1-pyhd8ed1ab_0
tornado conda-forge/win-64::tornado-6.3.3-py39ha55989b_1
traitlets conda-forge/noarch::traitlets-5.14.0-pyhd8ed1ab_0
typing_extensions conda-forge/noarch::typing_extensions-4.9.0-pyha770c72_0
unicodedata2 conda-forge/win-64::unicodedata2-15.1.0-py39ha55989b_0
wcwidth conda-forge/noarch::wcwidth-0.2.12-pyhd8ed1ab_0
xorg-libxau conda-forge/win-64::xorg-libxau-1.0.11-hcd874cb_0
xorg-libxdmcp conda-forge/win-64::xorg-libxdmcp-1.1.3-hcd874cb_0
zeromq conda-forge/win-64::zeromq-4.3.5-h63175ca_0
zipp conda-forge/noarch::zipp-3.17.0-pyhd8ed1ab_0
zstd conda-forge/win-64::zstd-1.5.5-h12be248_0
Downloading and Extracting Packages
m2w64-libwinpthread- | 31 KB | ############################################################################ | 100%
traitlets-5.14.0 | 107 KB | ############################################################################ | 100%
libwebp-base-1.3.2 | 263 KB | ############################################################################ | 100%
importlib-metadata-7 | 26 KB | ############################################################################ | 100%
libsodium-1.0.18 | 697 KB | ############################################################################ | 100%
python-dateutil-2.8. | 240 KB | ############################################################################ | 100%
libdeflate-1.18 | 149 KB | ############################################################################ | 100%
xorg-libxdmcp-1.1.3 | 66 KB | ############################################################################ | 100%
pyparsing-3.1.1 | 87 KB | ############################################################################ | 100%
jedi-0.19.1 | 822 KB | ############################################################################ | 100%
platformdirs-4.1.0 | 20 KB | ############################################################################ | 100%
lerc-4.0.0 | 190 KB | ############################################################################ | 100%
unicodedata2-15.1.0 | 365 KB | ############################################################################ | 100%
glib-tools-2.78.3 | 141 KB | ############################################################################ | 100%
pickleshare-0.7.5 | 9 KB | ############################################################################ | 100%
krb5-1.20.1 | 701 KB | ############################################################################ | 100%
pywin32-306 | 5.5 MB | ############################################################################ | 100%
openjpeg-2.5.0 | 232 KB | ############################################################################ | 100%
brotli-bin-1.1.0 | 20 KB | ############################################################################ | 100%
pyqt-5.15.9 | 3.7 MB | ############################################################################ | 100%
executing-2.0.1 | 27 KB | ############################################################################ | 100%
libglib-2.78.3 | 2.5 MB | ############################################################################ | 100%
typing_extensions-4. | 35 KB | ############################################################################ | 100%
jupyter_client-8.6.0 | 103 KB | ############################################################################ | 100%
liblapack-3.9.0 | 4.8 MB | ############################################################################ | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Finally, I start the jupyter qtconsole, and it does not crash, see the screenshot below:
(nept) C:\Users\vic>jupyter qtconsole
QObject::startTimer: Timers can only be used with threads started with QThread
I may try later with Miniforge on Linux 64-bit too. In the meantime, may I ask you to provide a full traceback of all your steps? Maybe we can see there the discrepancy between your environment and mine. This kind of segfaults I got them in the past when mixing conda-forge and anaconda channels (I think it is because numpy is packaged differently).
If the issue at hand is C library conflicts, that requires two packages both requiring the same C library, but vendoring/shipping different versions of it. I can see raising the issue here to get help re-compiling basemap with whatever version of geos the other library uses, but that doesn't seem to be what you're after.
Since the problem as stated is that conda is installing an invalid environment, might I ask why you did not move the issue to the conda repo? There is a decent chance conda is doing the best it can with the information it has, in which case, have you tried raising this issue with the conda-forge maintainers and asking them to use the same version of geos for building basemap and the other package?
Here's where conda-forge declares basemap needs geos to build, though it looks like it specifies that the geos version installed at runtime must match that used at build time, so conflicts would be on the other package pulling in geos (presumably without that specification). It sounds like you think qtconsole is the other package that depends on geos, but it looks like the only C library qtconsole directly depends on is python. Of the other packages installed in the log on the previous post, the only ones that look likely to link against geos are dependencies of basemap (build dependencies, even).
If you're just looking for workarounds, have you checked the versions of the installed packages on the working version, then attempted to install exactly those versions (except for the different python, since you want that to be 3.9)? There is an excellent chance this won't work, but using <${version} instead of ==${version} might. What about the other way around? Does installing the package versions used by the broken installation with the newer python fix things?
I'm not seeing any obvious reason you can consistently crash qtconsole while everyone helping you can run qtconsole just fine, so could you try installing just basemap (no qtconsole) and seeing if that produces decent plots in the normal python console, then just qtconsole (without basemap) to try your test, then qtconsole and matplotlib (still no basemap), and seeing which versions cause problems?
What does pip list --user show? Is there anything there that would have a different version of geos than that used for the py39 build of basemap?
I'm suspecting you haven't set LD_PRELOAD, but echo "${LD_PRELOAD}" could check that. Does it mention a libgeos.so*? What of your LD_LIBRARY_PATH, is there a directory with a libgeos.so* before the conda environment's lib directory (echo "${LD_LIBRARY_PATH} | tr ':' '\n')?
Perhaps I am missing something. Could you explain why you think "the underlying issue with basemap support is the build process for libgeos"? I do remember libgeos conflicts causing problems, when two packages that link against geos bundled it as part of their wheels, but you're using conda, not pip, and the tools to avoid that problem have gotten better in the last decade.
Do other jupyter front-ends (jupyter console and jupyter notebook) cause the same problem? What about using the QtAgg or QtCairo backends for matplotlib when creating a figure using basemap?
Out of curiousity, what version of conda are you using? conda env remove nept -y doesn't work for me (with conda 23.11) unless I add -n before nept. What happens if you try running conda clean -a between deleting the old environment and creating the new one?
Hi I was able to solve this issue by reinstalling conda and cleaning its installation first. Sorry for not replying sooner.
I recall made a number of mistakes mixing repos from pip and the conda forge install which I think made it harder to debug.