spyder: Missing dependencies: rtree

Every time I start spyder oit tells me that there are mising dependencies. rtree 0.9.7 is missing.

conda install rtree says that it is installed

workarounds on this poage are either ineffectual or too complicated

PASTE TRACEBACK HERE


## Versions

Spyder 5.2.1
Python 3.8.8 64-bit | 
Qt 5.12.9 | 
PyQt5 5.12.3 |
 Windows 10 

### Dependencies
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Mandatory:

atomicwrites >=1.2.0 : 1.4.0 (OK) chardet >=2.0.0 : 4.0.0 (OK) cloudpickle >=0.5.0 : 2.0.0 (OK) cookiecutter >=1.6.0 : 1.6.0 (OK) diff_match_patch >=20181111 : 20200713 (OK) intervaltree >=3.0.2 : 3.0.2 (OK) IPython >=7.6.0 : 7.30.1 (OK) jedi >=0.17.2;<0.19.0 : 0.18.1 (OK) jellyfish >=0.7 : 0.8.9 (OK) jsonschema >=3.2.0 : 4.3.0 (OK) keyring >=17.0.0 : 23.4.0 (OK) nbconvert >=4.0 : 6.3.0 (OK) numpydoc >=0.6.0 : 1.1.0 (OK) paramiko >=2.4.0 : 2.8.1 (OK) parso >=0.7.0;<0.9.0 : 0.8.3 (OK) pexpect >=4.4.0 : 4.8.0 (OK) pickleshare >=0.4 : 0.7.5 (OK) psutil >=5.3 : 5.8.0 (OK) pygments >=2.0 : 2.10.0 (OK) pylint >=2.5.0 : 2.12.2 (OK) pyls_spyder >=0.4.0 : 0.4.0 (OK) pylsp >=1.3.2;<1.4.0 : 1.3.3 (OK) pylsp_black >=1.0.0 : 1.0.1 (OK) qdarkstyle =3.0.2 : 3.0.2 (OK) qstylizer >=0.1.10 : 0.2.1 (OK) qtawesome >=1.0.2 : 1.1.1 (OK) qtconsole >=5.2.1;<5.3.0 : 5.2.2 (OK) qtpy >=1.5.0 : 1.11.3 (OK) rtree >=0.9.7 : None (NOK) setuptools >=49.6.0 : 59.6.0 (OK) sphinx >=0.6.6 : 4.3.1 (OK) spyder_kernels >=2.2.0;<2.3.0 : 2.2.0 (OK) textdistance >=4.2.0 : 4.2.2 (OK) three_merge >=0.1.1 : 0.1.1 (OK) watchdog >=0.10.3 : 2.1.6 (OK) zmq >=17 : 22.3.0 (OK)

Optional:

cython >=0.21 : None (NOK) matplotlib >=2.0.0 : 3.4.3 (OK) numpy >=1.7 : 1.21.3 (OK) pandas >=1.1.1 : 1.3.4 (OK) scipy >=0.17.0 : None (NOK) sympy >=0.7.3 : None (NOK)

About this issue

Original URL
State: closed
Created 3 years ago
Comments: 15 (8 by maintainers)

Most upvoted comments

Further testing, creating conda env with conda create --name spyder-env -c conda-forge python=3.9 conda activate spyder-env conda install -c conda-forge spyder works fine, while conda create --name spyder-env python=3.9 conda activate spyder-env conda install -c conda-forge spyder does not work, I can’t tell which package from conda main channel causes the problems, maybe someone can test or just install python with conda-forge for now

Hi @Hawxxer thank you for your input here! I think the problem is that installing from different conda channels (defaults vs conda-forge for example) can lead to binary incompatibilities which then can lead then to problems like the one here. I would say that the best approach is to use always the conda-forge channel for everything (so you can get the up-to-date versions of the packages).

Also, just in case, @mczakk are you mixing in your setup packages channels (e.g defaults vs conda-forge)?

dalthviz on Dec 22, 2021

I’m sorry but I really don’t understand all this env stuff, I just use python to do my dats analysis and produce pretty graphs for my PhD.

@mczakk, I also encountered a lot of problems with dependencies in Python when I was doing my PhD. Through constant troubleshooting, I finally gave up and switched to R and RStudio. In data analysis and visualization these languages are very similar, but however R is smoother and less problematic. Sorry for the offtopic, but maybe someone is also feeling overwhelmed and this tip might be helpful.

t-wojciech on Dec 19, 2021