Mandatory:

rtree >=0.8.3 : None (NOK)

Please install them to avoid this message.

Expected Behavior

No error

The latest Anaconda update breaks Spyder.

Steps to Reproduce

1) Download and install Anaconda3-2020.11-Linux-x86_64.sh; 2) After installation, launching spyder and notice there is no above mentioned error. 3) Update Anaconda by command "conda update --all" 4) After update, launching spyder and above mentioned error appears.

Anaconda or Miniconda version:

2020.11 ##### Operating System: ##### `conda info`

 active environment : None
   user config file : /NFS/ud1/home1/pzha/.condarc

populated config files : conda version : 4.9.2 conda-build version : 3.21.4 python version : 3.8.8.final.0 virtual packages : cuda=10.2=0 glibc=2.17=0 unix=0=0 archspec=1=x86_64 base environment : /NFS/ud1/home1/pzha/anaconda3 (writable) channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /NFS/ud1/home1/pzha/anaconda3/pkgs /NFS/ud1/home1/pzha/.conda/pkgs envs directories : /NFS/ud1/home1/pzha/anaconda3/envs /NFS/ud1/home1/pzha/.conda/envs platform : linux-64 user-agent : conda/4.9.2 requests/2.25.1 CPython/3.8.8 Linux/3.10.0-693.17.1.el7.x86_64 centos/7.4.1708 glibc/2.17 UID:GID : 26491:26491 netrc file : None offline mode : False

``` PASTE OUTPUT HERE: ```

`conda list --show-channel-urls`

``` PASTE OUTPUT HERE: ```

Samk19 commented 3 years ago

same here and missing package are already installed rtree v0.9.4 and spyder v4.2.1

OS: pop os Screenshot from 2021-02-28 19-00-11

manfred2020 commented 3 years ago

you may have a look at this: https://github.com/spyder-ide/spyder/issues/14466

Samk19 commented 3 years ago

Fix found for Linux

Got few solutions FOR LINUX (tested and worked): sudo apt install libspatialindex-dev FOR MAC: brew install spatialindex

still not sure if its a permanent fix or not

after using above command (i.e linux one).....spyder rtree error message gone

Mandatory: atomicwrites >=1.2.0 : 1.4.0 (OK) chardet >=2.0.0 : 4.0.0 (OK) cloudpickle >=0.5.0 : 1.6.0 (OK) diff_match_patch >=20181111 : 20200713 (OK) intervaltree >=3.0.2 : 3.1.0 (OK) IPython >=7.6.0 : 7.21.0 (OK) jedi =0.17.2 : 0.17.2 (OK) jsonschema >=3.2.0 : 3.2.0 (OK) keyring >=17.0.0 : 22.3.0 (OK) nbconvert >=4.0 : 6.0.7 (OK) numpydoc >=0.6.0 : 1.1.0 (OK) parso =0.7.0 : 0.7.0 (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 : 2.8.0 (OK) pylint >=1.0 : 2.7.2 (OK) pyls >=0.36.2;<1.0.0 : 0.36.2 (OK) pyls_black >=0.4.6 : 0.4.6 (OK) pyls_spyder >=0.3.0 : 0.3.2 (OK) qdarkstyle >=2.8 : 2.8.1 (OK) qtawesome >=0.5.7 : 1.0.1 (OK) qtconsole >=5.0.1 : 5.0.2 (OK) qtpy >=1.5.0 : 1.9.0 (OK) rtree >=0.8.3 : 0.9.4 (OK) setuptools >=39.0.0 : 52.0.0.post20210125 (OK) sphinx >=0.6.6 : 3.5.1 (OK) spyder_kernels >=1.10.1;<1.11.0 : 1.10.2 (OK) textdistance >=4.2.0 : 4.2.1 (OK) three_merge >=0.1.1 : 0.1.1 (OK) watchdog >=0.10.3 : 1.0.2 (OK) xdg >=0.26 : 0.27 (OK) zmq >=17 : 20.0.0 (OK)

Optional: cython >=0.21 : 0.29.22 (OK) matplotlib >=2.0.0 : 3.3.4 (OK) numpy >=1.7 : 1.19.2 (OK) pandas >=1.1.1 : 1.2.3 (OK) scipy >=0.17.0 : 1.6.1 (OK) sympy >=0.7.3 : 1.7.1 (OK)

sweettyler commented 3 years ago

The problem is python 3.8.8. If I downgrade it to 3.8.5, then everything is fine. With python version 3.8.8, even rtree can't be imported. There following is what I got when I tried to "import rtee" in ipython console:

Python 3.8.8 (default, Feb 24 2021, 21:46:12) Type 'copyright', 'credits' or 'license' for more information IPython 7.21.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import rtree

AttributeError Traceback (most recent call last)

in ----> 1 import rtree ~/anaconda3/lib/python3.8/site-packages/rtree/__init__.py in ----> 1 from .index import Rtree 2 3 from .core import rt 4 5 __version__ = '0.9.4' ~/anaconda3/lib/python3.8/site-packages/rtree/index.py in 4 import pprint 5 ----> 6 from . import core 7 8 import pickle ~/anaconda3/lib/python3.8/site-packages/rtree/core.py in 141 raise RTreeError('Unsupported OS "%s"' % os.name) 142 --> 143 rt.Error_GetLastErrorNum.restype = ctypes.c_int 144 145 rt.Error_GetLastErrorMsg.argtypes = [] ~/anaconda3/lib/python3.8/ctypes/__init__.py in __getattr__(self, name) 392 if name.startswith('__') and name.endswith('__'): 393 raise AttributeError(name) --> 394 func = self.__getitem__(name) 395 setattr(self, name, func) 396 return func ~/anaconda3/lib/python3.8/ctypes/__init__.py in __getitem__(self, name_or_ordinal) 397 398 def __getitem__(self, name_or_ordinal): --> 399 func = self._FuncPtr((name_or_ordinal, self)) 400 if not isinstance(name_or_ordinal, int): 401 func.__name__ = name_or_ordinal AttributeError: ~/anaconda3/bin/python: undefined symbol: Error_GetLastErrorNum

ContinuumIO / anaconda-issues

The latest Anaconda update breaks Spyder #12301