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Bug 791316 - dev-python/spyder-5.0.3 does not start due to missing sci-libs/rtree-0.9.7
Summary: dev-python/spyder-5.0.3 does not start due to missing sci-libs/rtree-0.9.7
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Python Gentoo Team
URL: https://github.com/spyder-ide/spyder/...
Whiteboard:
Keywords:
Depends on: 791766
Blocks:
  Show dependency tree
 
Reported: 2021-05-21 11:53 UTC by Erik Quaeghebeur
Modified: 2021-06-05 10:47 UTC (History)
2 users (show)

See Also:
Package list:
Runtime testing required: ---


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Description Erik Quaeghebeur 2021-05-21 11:53:21 UTC
When I try to start spyder 5.0.3, the following exception is raised:

Traceback (most recent call last):
  File "/usr/lib/python-exec/python3.8/spyder", line 33, in <module>
    sys.exit(load_entry_point('spyder==5.0.3', 'gui_scripts', 'spyder')())
  File "/usr/lib/python-exec/python3.8/spyder", line 25, in importlib_load_entry_point
    return next(matches).load()
  File "/usr/lib/python3.8/importlib/metadata.py", line 77, in load
    module = import_module(match.group('module'))
  File "/usr/lib/python3.8/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
  File "<frozen importlib._bootstrap>", line 991, in _find_and_load
  File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 783, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/usr/lib/python3.8/site-packages/spyder/app/start.py", line 34, in <module>
    from spyder.utils.external import lockfile
  File "/usr/lib/python3.8/site-packages/spyder/utils/external/lockfile.py", line 31, in <module>
    from spyder.utils.programs import is_spyder_process
  File "/usr/lib/python3.8/site-packages/spyder/utils/programs.py", line 28, in <module>
    import pkg_resources
  File "/usr/lib/python3.8/site-packages/pkg_resources/__init__.py", line 3243, in <module>
    def _initialize_master_working_set():
  File "/usr/lib/python3.8/site-packages/pkg_resources/__init__.py", line 3226, in _call_aside
    f(*args, **kwargs)
  File "/usr/lib/python3.8/site-packages/pkg_resources/__init__.py", line 3255, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/usr/lib/python3.8/site-packages/pkg_resources/__init__.py", line 568, in _build_master
    ws.require(__requires__)
  File "/usr/lib/python3.8/site-packages/pkg_resources/__init__.py", line 886, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/usr/lib/python3.8/site-packages/pkg_resources/__init__.py", line 772, in resolve
    raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'rtree>=0.9.7' distribution was not found and is required by spyder

[1]+  Exit 1                  spyder

Reproducible: Always
Comment 1 Ionen Wolkens gentoo-dev 2021-05-21 22:01:09 UTC
## Version 5.0.3 (2021-05-17)

### Important fixes
* Fix Help pane in the macOS installer.
* Add rtree as a dependency for our pip packages.
Comment 2 Andrew Nowa Ammerlaan gentoo-dev 2021-05-22 07:55:17 UTC
Oops, terribly sorry about this. I'm sure I tested it earlier but apparently I messed up somewhere. Will look into bumping sci-libs/rtree and adding the missing dependency ASAP.
Comment 3 Larry the Git Cow gentoo-dev 2021-05-22 09:11:14 UTC
The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8aa1a0f0b77059aeedc0cbfc11df2fc483190dfd

commit 8aa1a0f0b77059aeedc0cbfc11df2fc483190dfd
Author:     Andrew Ammerlaan <andrewammerlaan@gentoo.org>
AuthorDate: 2021-05-22 09:10:42 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan@gentoo.org>
CommitDate: 2021-05-22 09:11:11 +0000

    dev-python/spyder: add missing dep on rtree
    
    temporary workaround allows use of older rtree versions
    until 3dprint project gives the OK to bump rtree to the
    correct version.
    
    Bug: https://bugs.gentoo.org/791316
    Package-Manager: Portage-3.0.18, Repoman-3.0.3
    Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

 dev-python/spyder/{spyder-5.0.3.ebuild => spyder-5.0.3-r1.ebuild} | 5 +++++
 1 file changed, 5 insertions(+)
Comment 4 Andrew Nowa Ammerlaan gentoo-dev 2021-05-22 09:14:57 UTC
The rtree version in ::gentoo is older then the one upstream specifies should be used, but as a temporary workaround I have removed this constraint which allows spyder to launch and run, so far I have not encountered issues with this older version of rtree. However, you will get a warning about this when you start spyder (which I will fix when I get the OK to bump sci-libs/rtree (or when someone else does that)).
Comment 5 Larry the Git Cow gentoo-dev 2021-06-05 10:47:01 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0542ee78ee1d8e12d77d7b20fb935cb921c333f7

commit 0542ee78ee1d8e12d77d7b20fb935cb921c333f7
Author:     Andrew Ammerlaan <andrewammerlaan@gentoo.org>
AuthorDate: 2021-06-05 09:36:29 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan@gentoo.org>
CommitDate: 2021-06-05 10:46:57 +0000

    dev-python/spyder: fix dep on rtree
    
    Closes: https://bugs.gentoo.org/791316
    Package-Manager: Portage-3.0.19, Repoman-3.0.3
    Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

 .../spyder/{spyder-5.0.3-r1.ebuild => spyder-5.0.3-r2.ebuild}       | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)