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#1 2022-03-11 10:50:16

funkaddict
Member
Registered: 2018-08-13
Posts: 117

[SOLVED] Spyder IDE does not run anymore after update

Hey guys,

I am using Spyder IDE for handling, plotting, etc. lab results. I recently updated my machine. Unfortunately Spyder now crashes when beeing launched:

$ spyder
Traceback (most recent call last):
  File "/usr/lib/python3.10/site-packages/pkg_resources/__init__.py", line 573, in _build_master
    ws.require(__requires__)
  File "/usr/lib/python3.10/site-packages/pkg_resources/__init__.py", line 891, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/usr/lib/python3.10/site-packages/pkg_resources/__init__.py", line 782, in resolve
    raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (mccabe 0.7.0 (/usr/lib/python3.10/site-packages), Requirement.parse('mccabe<0.7.0,>=0.6.0'), {'flake8'})

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/bin/spyder", line 33, in <module>
    sys.exit(load_entry_point('spyder==5.2.0', 'gui_scripts', 'spyder')())
  File "/usr/bin/spyder", line 25, in importlib_load_entry_point
    return next(matches).load()
  File "/usr/lib/python3.10/importlib/metadata/__init__.py", line 162, in load
    module = import_module(match.group('module'))
  File "/usr/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1050, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 688, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 883, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/usr/lib/python3.10/site-packages/spyder/app/start.py", line 47, in <module>
    from spyder.utils.external import lockfile
  File "/usr/lib/python3.10/site-packages/spyder/utils/external/lockfile.py", line 31, in <module>
    from spyder.utils.programs import is_spyder_process
  File "/usr/lib/python3.10/site-packages/spyder/utils/programs.py", line 28, in <module>
    import pkg_resources
  File "/usr/lib/python3.10/site-packages/pkg_resources/__init__.py", line 3266, in <module>
    def _initialize_master_working_set():
  File "/usr/lib/python3.10/site-packages/pkg_resources/__init__.py", line 3240, in _call_aside
    f(*args, **kwargs)
  File "/usr/lib/python3.10/site-packages/pkg_resources/__init__.py", line 3278, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/usr/lib/python3.10/site-packages/pkg_resources/__init__.py", line 575, in _build_master
    return cls._build_from_requirements(__requires__)
  File "/usr/lib/python3.10/site-packages/pkg_resources/__init__.py", line 588, in _build_from_requirements
    dists = ws.resolve(reqs, Environment())
  File "/usr/lib/python3.10/site-packages/pkg_resources/__init__.py", line 782, in resolve
    raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (mccabe 0.7.0 (/usr/lib/python3.10/site-packages), Requirement.parse('mccabe<0.7.0,>=0.6.0'), {'flake8'})

I think a similar error was discussed earlier here in the forum:

However, I am not sure how to move on here. I need Spyder for work asap, unfortunately I am not very experienced in debugging and solving such issues. The package is outdated since about 3 months. So I think, the next step would be to update the pkgbuild myself and see if latest spyder version would work again?

Edit: I uninstalled spyder with its dependencies and installed the AUR-Version, which unfortuantely fails during installation:

makepkg -sirc
==> Making package: spyder-git 5.2.1.r345.gfad14a342-1 (Fri Mar 11 12:02:28 2022)
==> Checking runtime dependencies...
==> Installing missing dependencies...
[sudo] password for user: 
error: target not found: python-pympler
==> ERROR: 'pacman' failed to install missing dependencies.
==> Missing dependencies:
  -> jupyter-nbconvert
  -> python-atomicwrites
  -> python-cloudpickle
  -> python-diff-match-patch
  -> python-intervaltree
  -> python-lsp-black
  -> python-lsp-server
  -> python-numpydoc
  -> python-jsonschema
  -> python-paramiko
  -> python-pexpect
  -> python-pickleshare
  -> python-pycodestyle
  -> python-pyflakes
  -> python-pylint
  -> python-pyls-spyder
  -> python-pympler
  -> python-pyzmq
  -> python-qdarkstyle
  -> python-qstylizer
  -> python-qtawesome
  -> python-qtconsole
  -> python-rope
  -> python-rtree
  -> python-sphinx
  -> python-spyder-kernels
  -> python-textdistance
  -> python-three-merge
  -> python-watchdog
  -> python-xdg
  -> autopep8
  -> flake8
  -> python-cookiecutter
  -> python-pydocstyle
  -> yapf
==> Checking buildtime dependencies...
==> Installing missing dependencies...
resolving dependencies...
looking for conflicting packages...

Packages (17) python-babel-2.9.1-3  python-docutils-1:0.16-2  python-idna-3.3-4
              python-imagesize-1.3.0-3  python-jinja-3.0.3-3
              python-markupsafe-2.0.1-3  python-requests-2.27.1-1
              python-snowballstemmer-2.2.0-3
              python-sphinx-alabaster-theme-0.7.12-9
              python-sphinxcontrib-applehelp-1.0.2-8
              python-sphinxcontrib-devhelp-1.0.2-8
              python-sphinxcontrib-htmlhelp-2.0.0-3
              python-sphinxcontrib-jsmath-1.0.1-11
              python-sphinxcontrib-qthelp-1.0.3-8
              python-sphinxcontrib-serializinghtml-1.1.5-3
              python-urllib3-1.26.8-1  python-sphinx-4.4.0-1

Total Installed Size:  52.45 MiB

:: Proceed with installation? [Y/n] y
(17/17) checking keys in keyring                   [######################] 100%
(17/17) checking package integrity                 [######################] 100%
(17/17) loading package files                      [######################] 100%
(17/17) checking for file conflicts                [######################] 100%
(17/17) checking available disk space              [######################] 100%
:: Processing package changes...
( 1/17) installing python-babel                    [######################] 100%
( 2/17) installing python-docutils                 [######################] 100%
( 3/17) installing python-imagesize                [######################] 100%
( 4/17) installing python-markupsafe               [######################] 100%
( 5/17) installing python-jinja                    [######################] 100%
Optional dependencies for python-jinja
    python-babel: for i18n support [installed]
( 6/17) installing python-urllib3                  [######################] 100%
Optional dependencies for python-urllib3
    python-pysocks: SOCKS support
    python-brotli: Brotli support
    python-pyopenssl: security support
    python-idna: security support [pending]
( 7/17) installing python-idna                     [######################] 100%
( 8/17) installing python-requests                 [######################] 100%
Optional dependencies for python-requests
    python-pysocks: SOCKS proxy support
( 9/17) installing python-snowballstemmer          [######################] 100%
Optional dependencies for python-snowballstemmer
    python-pystemmer: for improved performance
(10/17) installing python-sphinx-alabaster-theme   [######################] 100%
(11/17) installing python-sphinxcontrib-applehelp  [######################] 100%
(12/17) installing python-sphinxcontrib-devhelp    [######################] 100%
(13/17) installing python-sphinxcontrib-htmlhelp   [######################] 100%
(14/17) installing python-sphinxcontrib-jsmath     [######################] 100%
(15/17) installing python-sphinxcontrib-qthelp     [######################] 100%
(16/17) installing python-sphinxcontrib-serial...  [######################] 100%
(17/17) installing python-sphinx                   [######################] 100%
Optional dependencies for python-sphinx
    imagemagick: for ext.imgconverter [installed]
    texlive-latexextra: for generation of PDF documentation [installed]
:: Running post-transaction hooks...
(1/1) Arming ConditionNeedsUpdate...
==> ERROR: Could not resolve all dependencies.
==> Removing installed dependencies...
checking dependencies...
:: python-dnspython optionally requires python-idna: support for updated IDNA 2008
:: python-pandas optionally requires python-jinja: needed for conditional HTML formatting
:: python-pyparsing optionally requires python-jinja: for generating Railroad Diagrams



Packages (17) python-babel-2.9.1-3  python-docutils-1:0.16-2  python-idna-3.3-4
              python-imagesize-1.3.0-3  python-jinja-3.0.3-3
              python-markupsafe-2.0.1-3  python-requests-2.27.1-1
              python-snowballstemmer-2.2.0-3  python-sphinx-4.4.0-1
              python-sphinx-alabaster-theme-0.7.12-9
              python-sphinxcontrib-applehelp-1.0.2-8
              python-sphinxcontrib-devhelp-1.0.2-8
              python-sphinxcontrib-htmlhelp-2.0.0-3
              python-sphinxcontrib-jsmath-1.0.1-11
              python-sphinxcontrib-qthelp-1.0.3-8
              python-sphinxcontrib-serializinghtml-1.1.5-3
              python-urllib3-1.26.8-1

Total Removed Size:  52.45 MiB

:: Do you want to remove these packages? [Y/n] y
:: Processing package changes...
( 1/17) removing python-sphinx                     [######################] 100%
( 2/17) removing python-sphinxcontrib-serializ...  [######################] 100%
( 3/17) removing python-sphinxcontrib-qthelp       [######################] 100%
( 4/17) removing python-sphinxcontrib-jsmath       [######################] 100%
( 5/17) removing python-sphinxcontrib-htmlhelp     [######################] 100%
( 6/17) removing python-sphinxcontrib-devhelp      [######################] 100%
( 7/17) removing python-sphinxcontrib-applehelp    [######################] 100%
( 8/17) removing python-sphinx-alabaster-theme     [######################] 100%
( 9/17) removing python-snowballstemmer            [######################] 100%
(10/17) removing python-requests                   [######################] 100%
(11/17) removing python-urllib3                    [######################] 100%
(12/17) removing python-jinja                      [######################] 100%
(13/17) removing python-markupsafe                 [######################] 100%
(14/17) removing python-imagesize                  [######################] 100%
(15/17) removing python-idna                       [######################] 100%
(16/17) removing python-docutils                   [######################] 100%
(17/17) removing python-babel                      [######################] 100%
:: Running post-transaction hooks...
(1/1) Arming ConditionNeedsUpdate...

Last edited by funkaddict (2022-03-11 15:06:54)

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#2 2022-03-11 11:08:49

Lone_Wolf
Administrator
From: Netherlands, Europe
Registered: 2005-10-04
Posts: 14,893

Re: [SOLVED] Spyder IDE does not run anymore after update

(mccabe 0.7.0 (/usr/lib/python3.10/site-packages), Requirement.parse('mccabe<0.7.0,>=0.6.0'), {'flake8'})

Looks like this version of spyder / flake 8 needs mccabe to be less than version 0.7.0 , and python-mccabe was upgraded to 0.7.0 not long ago

You're not the only one with this issue : https://bugs.archlinux.org/task/73953

There's a workaround mentioned in it, downgrading mccabe .

Disliking systemd intensely, but not satisfied with alternatives so focusing on taming systemd.

clean chroot building not flexible enough ?
Try clean chroot manager by graysky

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#3 2022-03-11 11:19:13

Slithery
Administrator
From: Norfolk, UK
Registered: 2013-12-01
Posts: 5,776

Re: [SOLVED] Spyder IDE does not run anymore after update

funkaddict wrote:

Thank you, I will try that and report back.

You clicked on 'report post' instead of 'reply'.

No, it didn't "fix" anything. It just shifted the brokeness one space to the right. - jasonwryan
Closing -- for deletion; Banning -- for muppetry. - jasonwryan

aur - dotfiles

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#4 2022-03-11 11:25:02

funkaddict
Member
Registered: 2018-08-13
Posts: 117

Re: [SOLVED] Spyder IDE does not run anymore after update

Slithery wrote:
funkaddict wrote:

Thank you, I will try that and report back.

You clicked on 'report post' instead of 'reply'.

Oh, sorry my bad!

Lone_Wolf wrote:
(mccabe 0.7.0 (/usr/lib/python3.10/site-packages), Requirement.parse('mccabe<0.7.0,>=0.6.0'), {'flake8'})

Looks like this version of spyder / flake 8 needs mccabe to be less than version 0.7.0 , and python-mccabe was upgraded to 0.7.0 not long ago

You're not the only one with this issue : https://bugs.archlinux.org/task/73953

There's a workaround mentioned in it, downgrading mccabe .

Thanks, I will downgrade that package and report back.

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#5 2022-03-11 13:43:12

funkaddict
Member
Registered: 2018-08-13
Posts: 117

Re: [SOLVED] Spyder IDE does not run anymore after update

Okay that worked. Thanks again. However, one question remains. How do I freeze the package and does this makes sense? Or where can I find more information about it?

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#6 2022-03-11 14:36:08

icar
Member
Registered: 2020-07-31
Posts: 560

Re: [SOLVED] Spyder IDE does not run anymore after update

Take a look at pipx. It's very useful to have python apps without dependency issues, specially on Arch, which is a fast moving target for upstream to catch up on dependency versions. I just tried installing spyder (pipx install spyder) and it worked nicely. Other software, such as pgAdmin4, which is broken in Arch, works using this method. Other conflicting Python packages that have dependency issues are, for example, catt, which works using pipx.

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#7 2022-03-11 15:06:39

funkaddict
Member
Registered: 2018-08-13
Posts: 117

Re: [SOLVED] Spyder IDE does not run anymore after update

icar wrote:

Take a look at pipx. It's very useful to have python apps without dependency issues, specially on Arch, which is a fast moving target for upstream to catch up on dependency versions. I just tried installing spyder (pipx install spyder) and it worked nicely. Other software, such as pgAdmin4, which is broken in Arch, works using this method. Other conflicting Python packages that have dependency issues are, for example, catt, which works using pipx.

Thank you, I take a look at pipx.

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