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#1 2020-03-28 21:48:34

evanc
Member
Registered: 2020-03-04
Posts: 23

Attempting to install osmnx fails at rtree dependency in pip3

I am relatively new to Arch linux and would like some help

I am attempting to install the python package osmnx using pip3 as instructed to in the docs, I have also tried the suggested conda but that did not work either. When I attempt with pip3 I run into an error at Rtree package that states the following.....

ERROR: Command errored out with exit status 1:
     command: /usr/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-oaom3pvj/Rtree/setup.py'"'"'; __file__='"'"'/tmp/pip-install-oaom3pvj/Rtree/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-install-oaom3pvj/Rtree/pip-egg-info
         cwd: /tmp/pip-install-oaom3pvj/Rtree/
    Complete output (15 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-oaom3pvj/Rtree/setup.py", line 3, in <module>
        import rtree
      File "/tmp/pip-install-oaom3pvj/Rtree/rtree/__init__.py", line 1, in <module>
        from .index import Rtree
      File "/tmp/pip-install-oaom3pvj/Rtree/rtree/index.py", line 6, in <module>
        from . import core
      File "/tmp/pip-install-oaom3pvj/Rtree/rtree/core.py", line 143, in <module>
        rt.Error_GetLastErrorNum.restype = ctypes.c_int
      File "/usr/lib/python3.8/ctypes/__init__.py", line 386, in __getattr__
        func = self.__getitem__(name)
      File "/usr/lib/python3.8/ctypes/__init__.py", line 391, in __getitem__
        func = self._FuncPtr((name_or_ordinal, self))
    AttributeError: /usr/bin/python: undefined symbol: Error_GetLastErrorNum
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. 

I don't know where the logs are that are mentioned because they are not in the logs application on my computer. Any help is appreciated.

https://osmnx.readthedocs.io/en/stable/

Last edited by evanc (2020-03-28 21:49:41)

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#2 2020-03-29 00:19:34

xerxes_
Member
Registered: 2018-04-29
Posts: 675

Re: Attempting to install osmnx fails at rtree dependency in pip3

Don't use conda. Don't install anything with pip as root user (or you will mess in your system and wont be able to update until you clean that mess (error: package already exist in system))! If you want to install something with pip, do it as normal user. Here is how (sentence above blue note): https://wiki.archlinux.org/index.php/Py … management

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#3 2020-03-29 09:31:00

evanc
Member
Registered: 2020-03-04
Posts: 23

Re: Attempting to install osmnx fails at rtree dependency in pip3

I didn't use sudo with pip or pip3. Is that the problem I have? The package cant be built because it is already in my system? What is the exit status 1? I have tried using pip to install rtree by itself but I am met with the same error as before.

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#4 2020-03-29 10:07:19

V1del
Forum Moderator
Registered: 2012-10-16
Posts: 21,659

Re: Attempting to install osmnx fails at rtree dependency in pip3

This seems to be some pip dependency resolution bug: https://github.com/Toblerity/rtree/issues/135 make sure libspatialindex is explicitly installed.

Or properly install python-osmnx system-wide as an AUR package exists: https://aur.archlinux.org/packages/python-osmnx  It's a bit dated, but simply bumping the pkgver and adjusting the sha256sum seems to have worked and I was able to build every package in the chain.

Last edited by V1del (2020-03-29 10:08:05)

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#5 2020-03-29 10:12:59

evanc
Member
Registered: 2020-03-04
Posts: 23

Re: Attempting to install osmnx fails at rtree dependency in pip3

So I install the AUR package libspatialindex-git and retry the pip install?

I have tried to install libspatialindex-git and I get this error:

==> WARNING: Using existing $srcdir/ tree
==> Starting pkgver()...
==> Starting build()...
/home/evan/.cache/yay/libspatialindex-git/PKGBUILD: line 27: ./autogen.sh: No such file or directory
==> ERROR: A failure occurred in build().
    Aborting...

Should I try to build the package from the Github repo?

Last edited by evanc (2020-03-29 10:19:07)

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#6 2020-03-29 10:49:37

V1del
Forum Moderator
Registered: 2012-10-16
Posts: 21,659

Re: Attempting to install osmnx fails at rtree dependency in pip3

No if you want to continue with pip you have to explicitly pip libspatialindex before piping rdtree/osmnx

I suggested you use the AUR package for osmnx instead of trying to fumble with pip

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#7 2020-03-29 10:53:34

evanc
Member
Registered: 2020-03-04
Posts: 23

Re: Attempting to install osmnx fails at rtree dependency in pip3

So I've tried that as well and I get another error, specifically:

Errors occurred, no packages were upgraded.
error: target not found: python-descartes
error: target not found: cython
error: target not found: python-jmespath
error: target not found: python-docutils
error: target not found: python-botocore
error: target not found: python-s3transfer
error: target not found: python-boto3
error: target not found: python-click-plugins
error: target not found: spatialindex
error: target not found: python-rtree

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#8 2020-03-29 10:58:29

V1del
Forum Moderator
Registered: 2012-10-16
Posts: 21,659

Re: Attempting to install osmnx fails at rtree dependency in pip3

If you're using yay run an -Syu to ensure your package repos are up to date. If that doesn't help post the full command and full output.

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#9 2020-03-29 11:32:51

evanc
Member
Registered: 2020-03-04
Posts: 23

Re: Attempting to install osmnx fails at rtree dependency in pip3

I ran yay -Syu and then attempted to install python-osmnx but I still ran into the same error. the full output is very long:

$ yay -S python-osmnx
:: Checking for conflicts...
:: Checking for inner conflicts...
[Repo: 30]  python-pytz-2019.3-3  python-pandas-1.0.3-1  python-click-7.1.1-1  python-iniconfig-1.0.0-4  python-apipkg-1.5-3  python-py-1.8.1-1  python-zipp-3.1.0-1  python-importlib-metadata-1.5.0-1  python-pluggy-0.13.1-1  python-attrs-19.3.0-4  python-more-itertools-8.2.0-1  python-atomicwrites-1.3.0-3  python-wcwidth-0.1.8-1  python-pygments-2.6.1-2  python-pytest-5.4.1-1  python-coverage-4.5.4-3  python-pytest-cov-2.8.1-2  python-munch-2.5.0-1  proj-6.3.1-1  libgeotiff-1.5.1-1  libfreexl-1.0.5-1  libspatialite-4.3.0.a-5  mariadb-libs-10.4.12-1  postgresql-libs-12.2-1  gdal-3.0.4-4  python-pyproj-2.5.0-1  python-decorator-4.4.2-1  python-networkx-2.4-3  python-geographiclib-1.50-1  python-geopy-1.21.0-1
[Repo Make: 9]  cython-0.29.16-1  python-jmespath-0.9.5-1  python-docutils-0.14-4  python-botocore-1.15.26-1  python-s3transfer-0.3.3-1  python-boto3-1.12.26-1  python-click-plugins-1.1.1-4  spatialindex-1.9.3-1  python-rtree-0.9.4-1
[Aur: 4]  python-cligj-0.5.0-1  python-fiona-1.8.13-1  python-geopandas-0.7.0-1  python-osmnx-0.9-1
[Aur Make: 1]  python-descartes-1.1.0-1

==> Remove make dependencies after install? [y/N] y
  5 python-cligj                             (Build Files Exist)
  4 python-fiona                             (Build Files Exist)
  3 python-descartes                         (Build Files Exist)
  2 python-geopandas                         (Build Files Exist)
  1 python-osmnx                             (Build Files Exist)
==> Packages to cleanBuild?
==> [N]one [A]ll [Ab]ort [I]nstalled [No]tInstalled or (1 2 3, 1-3, ^4)
==> A
:: Deleting (1/5): /home/evan/.cache/yay/python-cligj
:: Deleting (2/5): /home/evan/.cache/yay/python-fiona
:: Deleting (3/5): /home/evan/.cache/yay/python-descartes
:: Deleting (4/5): /home/evan/.cache/yay/python-geopandas
:: Deleting (5/5): /home/evan/.cache/yay/python-osmnx
:: Downloaded PKGBUILD (1/5): python-osmnx
:: Downloaded PKGBUILD (2/5): python-cligj
:: Downloaded PKGBUILD (3/5): python-fiona
:: Downloaded PKGBUILD (4/5): python-geopandas
:: Downloaded PKGBUILD (5/5): python-descartes
  5 python-cligj                             (Build Files Exist)
  4 python-fiona                             (Build Files Exist)
  3 python-descartes                         (Build Files Exist)
  2 python-geopandas                         (Build Files Exist)
  1 python-osmnx                             (Build Files Exist)
==> Diffs to show?
==> [N]one [A]ll [Ab]ort [I]nstalled [No]tInstalled or (1 2 3, 1-3, ^4)
==> I
:: Parsing SRCINFO (1/5): python-cligj
:: Parsing SRCINFO (2/5): python-fiona
:: Parsing SRCINFO (3/5): python-descartes
:: Parsing SRCINFO (4/5): python-geopandas
:: Parsing SRCINFO (5/5): python-osmnx
resolving dependencies...
looking for conflicting packages...

Packages (39) cython-0.29.16-1  gdal-3.0.4-4  libfreexl-1.0.5-1  libgeotiff-1.5.1-1
              libspatialite-4.3.0.a-5  mariadb-libs-10.4.12-1  postgresql-libs-12.2-1
              proj-6.3.1-1  python-apipkg-1.5-3  python-atomicwrites-1.3.0-3
              python-attrs-19.3.0-4  python-boto3-1.12.26-1  python-botocore-1.15.26-1
              python-click-7.1.1-1  python-click-plugins-1.1.1-4  python-coverage-4.5.4-3
              python-decorator-4.4.2-1  python-docutils-0.14-4
              python-geographiclib-1.50-1  python-geopy-1.21.0-1
              python-importlib-metadata-1.5.0-1  python-iniconfig-1.0.0-4
              python-jmespath-0.9.5-1  python-more-itertools-8.2.0-1
              python-munch-2.5.0-1  python-networkx-2.4-3  python-pandas-1.0.3-1
              python-pluggy-0.13.1-1  python-py-1.8.1-1  python-pygments-2.6.1-2
              python-pyproj-2.5.0-1  python-pytest-5.4.1-1  python-pytest-cov-2.8.1-2
              python-pytz-2019.3-3  python-rtree-0.9.4-1  python-s3transfer-0.3.3-1
              python-wcwidth-0.1.8-1  python-zipp-3.1.0-1  spatialindex-1.9.3-1

Total Installed Size:  228.48 MiB

:: Proceed with installation? [Y/n] y
(39/39) checking keys in keyring                       [############################] 100%
(39/39) checking package integrity                     [############################] 100%
(39/39) loading package files                          [############################] 100%
(39/39) checking for file conflicts                    [############################] 100%
error: failed to commit transaction (conflicting files)
python-pytz: /usr/lib/python3.8/site-packages/pytz/__init__.py exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/__pycache__/__init__.cpython-38.pyc exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/__pycache__/exceptions.cpython-38.pyc exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/__pycache__/lazy.cpython-38.pyc exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/__pycache__/reference.cpython-38.pyc exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/__pycache__/tzfile.cpython-38.pyc exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/__pycache__/tzinfo.cpython-38.pyc exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/exceptions.py exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/lazy.py exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/reference.py exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/tzfile.py exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/tzinfo.py exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Africa/Abidjan exists in filesystem
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python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Africa/Cairo exists in filesystem
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python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Africa/Juba exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Africa/Kampala exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Africa/Khartoum exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Africa/Kigali exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Africa/Kinshasa exists in filesystem
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python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Africa/Windhoek exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/America/Adak exists in filesystem
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python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Tbilisi exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Tehran exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Tel_Aviv exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Thimbu exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Thimphu exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Tokyo exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Tomsk exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Ujung_Pandang exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Ulaanbaatar exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Ulan_Bator exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Urumqi exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Ust-Nera exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Vientiane exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Vladivostok exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Yakutsk exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Yangon exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Yekaterinburg exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Asia/Yerevan exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Atlantic/Azores exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Atlantic/Bermuda exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Atlantic/Canary exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Atlantic/Cape_Verde exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Atlantic/Faeroe exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Atlantic/Faroe exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Atlantic/Jan_Mayen exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Atlantic/Madeira exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Atlantic/Reykjavik exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Atlantic/South_Georgia exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Atlantic/St_Helena exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Atlantic/Stanley exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/ACT exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Adelaide exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Brisbane exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Broken_Hill exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Canberra exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Currie exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Darwin exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Eucla exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Hobart exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/LHI exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Lindeman exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Lord_Howe exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Melbourne exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/NSW exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/North exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Perth exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Queensland exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/South exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Sydney exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Tasmania exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Victoria exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/West exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Australia/Yancowinna exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Brazil/Acre exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Brazil/DeNoronha exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Brazil/East exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Brazil/West exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/CET exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/CST6CDT exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Canada/Atlantic exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Canada/Central exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Canada/Eastern exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Canada/Mountain exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Canada/Newfoundland exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Canada/Pacific exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Canada/Saskatchewan exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Canada/Yukon exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Chile/Continental exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Chile/EasterIsland exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Cuba exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/EET exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/EST exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/EST5EDT exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Egypt exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Eire exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT+0 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT+1 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT+10 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT+11 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT+12 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT+2 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT+3 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT+4 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT+5 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT+6 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT+7 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT+8 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT+9 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT-0 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT-1 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT-10 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT-11 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT-12 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT-13 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT-14 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT-2 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT-3 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT-4 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT-5 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT-6 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT-7 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT-8 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT-9 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/GMT0 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/Greenwich exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/UCT exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/UTC exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/Universal exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Etc/Zulu exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Amsterdam exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Andorra exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Astrakhan exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Athens exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Belfast exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Belgrade exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Berlin exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Bratislava exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Brussels exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Bucharest exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Budapest exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Busingen exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Chisinau exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Copenhagen exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Dublin exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Gibraltar exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Guernsey exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Helsinki exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Isle_of_Man exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Istanbul exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Jersey exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Kaliningrad exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Kiev exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Kirov exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Lisbon exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Ljubljana exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/London exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Luxembourg exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Madrid exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Malta exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Mariehamn exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Minsk exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Monaco exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Moscow exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Nicosia exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Oslo exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Paris exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Podgorica exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Prague exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Riga exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Rome exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Samara exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/San_Marino exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Sarajevo exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Saratov exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Simferopol exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Skopje exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Sofia exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Stockholm exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Tallinn exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Tirane exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Tiraspol exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Ulyanovsk exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Uzhgorod exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Vaduz exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Vatican exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Vienna exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Vilnius exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Volgograd exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Warsaw exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Zagreb exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Zaporozhye exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Europe/Zurich exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Factory exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/GB exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/GB-Eire exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/GMT exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/GMT+0 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/GMT-0 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/GMT0 exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Greenwich exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/HST exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Hongkong exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Iceland exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Indian/Antananarivo exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Indian/Chagos exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Indian/Christmas exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Indian/Cocos exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Indian/Comoro exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Indian/Kerguelen exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Indian/Mahe exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Indian/Maldives exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Indian/Mauritius exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Indian/Mayotte exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Indian/Reunion exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Iran exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Israel exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Jamaica exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Japan exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Kwajalein exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Libya exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/MET exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/MST exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/MST7MDT exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Mexico/BajaNorte exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Mexico/BajaSur exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Mexico/General exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/NZ exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/NZ-CHAT exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Navajo exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/PRC exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/PST8PDT exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Pacific/Apia exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Pacific/Auckland exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Pacific/Bougainville exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Pacific/Chatham exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Pacific/Chuuk exists in filesystem
python-pytz: /usr/lib/python3.8/site-packages/pytz/zoneinfo/Pacific/Easter exists in filesystem
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python-networkx: /usr/lib/python3.8/site-packages/networkx/testing/__init__.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/testing/__pycache__/__init__.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/testing/__pycache__/test.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/testing/__pycache__/utils.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/testing/test.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/testing/tests/__init__.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/testing/tests/__pycache__/__init__.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/testing/tests/__pycache__/test_utils.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/testing/tests/test_utils.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/testing/utils.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/tests/__init__.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/tests/__pycache__/__init__.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/tests/__pycache__/test_all_random_functions.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/tests/__pycache__/test_convert.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/tests/__pycache__/test_convert_numpy.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/tests/__pycache__/test_convert_pandas.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/tests/__pycache__/test_convert_scipy.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/tests/__pycache__/test_exceptions.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/tests/__pycache__/test_relabel.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/tests/test_all_random_functions.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/tests/test_convert.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/tests/test_convert_numpy.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/tests/test_convert_pandas.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/tests/test_convert_scipy.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/tests/test_exceptions.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/tests/test_relabel.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/__init__.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/__pycache__/__init__.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/__pycache__/contextmanagers.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/__pycache__/decorators.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/__pycache__/heaps.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/__pycache__/mapped_queue.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/__pycache__/misc.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/__pycache__/random_sequence.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/__pycache__/rcm.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/__pycache__/union_find.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/contextmanagers.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/decorators.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/heaps.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/mapped_queue.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/misc.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/random_sequence.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/rcm.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/__init__.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/__pycache__/__init__.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/__pycache__/test_contextmanager.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/__pycache__/test_decorators.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/__pycache__/test_heaps.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/__pycache__/test_mapped_queue.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/__pycache__/test_misc.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/__pycache__/test_random_sequence.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/__pycache__/test_rcm.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/__pycache__/test_unionfind.cpython-38.pyc exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/test_contextmanager.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/test_decorators.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/test_heaps.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/test_mapped_queue.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/test_misc.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/test_random_sequence.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/test_rcm.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/tests/test_unionfind.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/utils/union_find.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/version.py exists in filesystem
Errors occurred, no packages were upgraded.
error: target not found: python-descartes
error: target not found: cython
error: target not found: python-jmespath
error: target not found: python-docutils
error: target not found: python-botocore
error: target not found: python-s3transfer
error: target not found: python-boto3
error: target not found: python-click-plugins
error: target not found: spatialindex
error: target not found: python-rtree

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#10 2020-03-29 11:49:45

V1del
Forum Moderator
Registered: 2012-10-16
Posts: 21,659

Re: Attempting to install osmnx fails at rtree dependency in pip3

That's pretty clear evidence that you did run pip with sudo. That's a problem. Uninstall all of those with sudo pip and reinstall the packaged versions.

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#11 2020-03-29 11:57:22

evanc
Member
Registered: 2020-03-04
Posts: 23

Re: Attempting to install osmnx fails at rtree dependency in pip3

sudo pip3 uninstall cython gdal libfreexl libgeotiff libspatialite mariadb-libs postgresql-libs proj python-apipkg python-atomicwrites python-attrs python-boto3
WARNING: Skipping cython as it is not installed.
WARNING: Skipping gdal as it is not installed.
WARNING: Skipping libfreexl as it is not installed.
WARNING: Skipping libgeotiff as it is not installed.
WARNING: Skipping libspatialite as it is not installed.
WARNING: Skipping mariadb-libs as it is not installed.
WARNING: Skipping postgresql-libs as it is not installed.
WARNING: Skipping proj as it is not installed.
WARNING: Skipping python-apipkg as it is not installed.
WARNING: Skipping python-atomicwrites as it is not installed.
WARNING: Skipping python-attrs as it is not installed.
WARNING: Skipping python-boto3 as it is not installed.

I looked at what packages pip says I have installed and this is what I get:

$ pip3 list
Package          Version     
---------------- ------------
appdirs          1.4.3       
asn1crypto       1.3.0       
attrs            19.3.0      
Brlapi           0.7.0       
btrfsutil        1.1.1       
CacheControl     0.12.6      
certifi          2019.11.28  
cffi             1.14.0      
chardet          3.0.4       
click            7.1.1       
click-plugins    1.1.1       
cligj            0.5.0       
colorama         0.4.3       
contextlib2      0.6.0.post1 
cryptography     2.8         
cycler           0.10.0      
decorator        4.4.2       
descartes        1.1.0       
distlib          0.3.0       
distro           1.4.0       
docopt           0.6.2       
Fiona            1.8.13.post1
geopandas        0.7.0       
html5lib         1.0.1       
idna             2.9         
kiwisolver       1.1.0       
lensfun          0.3.95      
louis            3.13.0      
matplotlib       3.2.1       
msgpack          0.6.2       
munch            2.5.0       
mutagen          1.44.0      
networkx         2.4         
numpy            1.18.2      
openshot-qt      2.5.1       
ordered-set      3.1.1       
overpy           0.4         
packaging        20.3        
pandas           1.0.3       
pep517           0.8.1       
picard           2.3.2.dev1  
pip              20.0.2      
Pivy             0.6.5       
ply              3.11        
progress         1.5         
protonvpn-cli    2.2.2       
pwquality        1.4.2       
pycosat          0.6.3       
pycparser        2.20        
PyGObject        3.36.0      
pyparsing        2.4.6       
pyproj           2.6.0       
PyQt5            5.14.1      
PyQt5-sip        12.7.1      
pyserial         3.4         
python-dateutil  2.8.1       
pythondialog     3.5.1       
pytoml           0.1.21      
pytz             2019.3      
pyxdg            0.26        
pyzmq            19.0.0      
requests         2.23.0      
retrying         1.3.3       
ruamel.yaml      0.16.10     
ruamel.yaml.clib 0.2.0       
scipy            1.4.1       
setproctitle     1.1.10      
setuptools       46.1.3      
Shapely          1.7.0       
sip              4.19.21     
six              1.14.0      
sounddevice      0.3.15      
team             1.0         
toml             0.10.0      
urllib3          1.25.8      
Wave             0.0.2       
webencodings     0.5.1 

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#12 2020-03-29 12:05:16

V1del
Forum Moderator
Registered: 2012-10-16
Posts: 21,659

Re: Attempting to install osmnx fails at rtree dependency in pip3

You should ideally not have any packages installed system wide with pip. Remove those. installing the relevant repo packages shouldn't fail anymore

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#13 2020-03-29 12:10:20

evanc
Member
Registered: 2020-03-04
Posts: 23

Re: Attempting to install osmnx fails at rtree dependency in pip3

So I should be attempting to uninstall all the packages that are not listed in the pip list output?

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#14 2020-03-29 12:31:51

V1del
Forum Moderator
Registered: 2012-10-16
Posts: 21,659

Re: Attempting to install osmnx fails at rtree dependency in pip3

No you should attempt to uninstall  packages listed in the pip output (that have conflicting file errors in pacman/yay) with pip (so they aren't installed via pip anymore) and then retry installing the actual pacman packages. You need to get rid of the "exist in file systems" errors when installing pacman packages. https://wiki.archlinux.org/index.php/Pa … )%22_error

You could abuse the overwrite flag, but it'd be better you leave the system in a consistent state by properly uninstalling pip installed packages and replacing them with repo versions.

Last edited by V1del (2020-03-29 12:32:25)

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#15 2020-03-29 12:40:57

loqs
Member
Registered: 2014-03-06
Posts: 17,322

Re: Attempting to install osmnx fails at rtree dependency in pip3

python-pytz: /usr/lib/python3.8/site-packages/pytz/__init__.py exists in filesystem
python-pandas: /usr/lib/python3.8/site-packages/pandas/__init__.py exists in filesystem
python-click: /usr/lib/python3.8/site-packages/click/__init__.py exists in filesystem
python-attrs: /usr/lib/python3.8/site-packages/attr/__init__.py exists in filesystem
python-munch: /usr/lib/python3.8/site-packages/munch/__init__.py exists in filesystem
python-click-plugins: /usr/lib/python3.8/site-packages/click_plugins/__init__.py exists in filesystem
python-pyproj: /usr/lib/python3.8/site-packages/pyproj/__init__.py exists in filesystem
python-decorator: /usr/lib/python3.8/site-packages/decorator.py exists in filesystem
python-networkx: /usr/lib/python3.8/site-packages/networkx/__init__.py exists in filesystem

Indicates the packages you want to uninstall with pip3 are pytz pandas click attrs munch click_plugins pyproj decorator networkx

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#16 2020-03-29 13:04:13

evanc
Member
Registered: 2020-03-04
Posts: 23

Re: Attempting to install osmnx fails at rtree dependency in pip3

I manually removed the packages listed in the output. I was misnaming the packages by adding the "python-" in front. You were correct, of course. I had fucked up my install by using sudo pip. I didn't try using sudo pip to install osmnx but i did obviously to packages before I learned not to do that. I downloaded and successfully installed osmnx using the aur repo after sudo pip uninstalling all the packages listed as existing on the file system.

Thank you for all the help @V1del

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