Open
Description
Description
What steps will reproduce the problem?
- Load a large CSV dataset (~800,000 rows, ~40 features).
- Perform standard preprocessing: drop IDs, fill missing values, scale numeric features using StandardScaler.
- Split the dataset into training and validation sets using train_test_split.
- Apply PCA with different component sizes (e.g., 10, 30, 50, 100) on the training/validation sets.
- Train an SVM (SVC with RBF kernel) on the PCA-reduced training data.
- Spyder suddenly freezes or shows the internal error reporter after fit() is called.
The crash often occurs when using larger PCA dimensions like 100 and with relatively large training sets (e.g., > 100,000 samples).
System Info:
- macOS
- Spyder version: [insert your version, e.g., 5.4.3]
- Python version: 3.9
- Installed via Anaconda
No traceback is printed in the IPython console. Only the internal issue reporter pops up.
This script works fine in terminal or Jupyter Notebook, but Spyder freezes while training the model inside its IDE environment.
Traceback
Traceback (most recent call last):
File "/opt/anaconda3/lib/python3.12/site-packages/spyder/app/mainwindow.py", line 547, in switch_to_plugin
self.layouts.switch_to_plugin(plugin, force_focus=force_focus)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'switch_to_plugin'Versions
- Spyder version: 6.0.7 (conda)
- Python version: 3.12.4 64-bit
- Qt version: 5.15.2
- PyQt5 version: 5.15.10
- Operating System: macOS-14.6.1-arm64-arm-64bit
Dependencies
# Mandatory:
aiohttp >=3.9.3 : 3.9.5 (OK)
applaunchservices >=0.3.0 : 0.3.0 (OK)
asyncssh >=2.14.0,<3.0.0 : 2.17.0 (OK)
atomicwrites >=1.2.0 : 1.4.0 (OK)
bcrypt >=4.3.0 : 4.3.0 (OK)
chardet >=2.0.0 : 4.0.0 (OK)
cloudpickle >=0.5.0 : 2.2.1 (OK)
cookiecutter >=1.6.0 : 2.6.0 (OK)
diff_match_patch >=20181111 : 20200713 (OK)
github >=2.3.0 : 2.4.0 (OK)
importlib_metadata >=4.6.0 : 7.0.1 (OK)
intervaltree >=3.0.2 : 3.1.0 (OK)
IPython >=8.13.0,<9.0.0,!=8.17.1 : 8.25.0 (OK)
jedi >=0.17.2,<0.20.0 : 0.18.1 (OK)
jellyfish >=0.7 : 1.0.1 (OK)
jsonschema >=3.2.0 : 4.19.2 (OK)
keyring >=17.0.0 : 24.3.1 (OK)
nbconvert >=4.0 : 7.10.0 (OK)
numpydoc >=0.6.0 : 1.7.0 (OK)
packaging >=20.0 : 23.2 (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 : 5.9.0 (OK)
pygments >=2.0 : 2.15.1 (OK)
pylint >=3.1,<4 : 3.2.7 (OK)
pylint_venv >=3.0.2 : 3.0.3 (OK)
pyls_spyder >=0.4.0 : 0.4.0 (OK)
pylsp >=1.12.0,<1.13.0 : 1.12.0 (OK)
pylsp_black >=2.0.0,<3.0.0 : 2.0.0 (OK)
pyuca >=1.2 : 1.2 (OK)
qdarkstyle >=3.2.0,<3.3.0 : 3.2.3 (OK)
qstylizer >=0.2.2 : 0.2.2 (OK)
qtawesome >=1.4.0,<1.5.0 : 1.4.0 (OK)
qtconsole >=5.6.1,<5.7.0 : 5.6.1 (OK)
qtpy >=2.4.0 : 2.4.1 (OK)
rtree >=0.9.7 : 1.0.1 (OK)
sphinx >=0.6.6 : 7.3.7 (OK)
spyder_kernels >=3.0.5,<3.1.0 : 3.0.5 (OK)
superqt >=0.6.2,<1.0.0 : 0.6.7 (OK)
textdistance >=4.2.0 : 4.2.1 (OK)
three_merge >=0.1.1 : 0.1.1 (OK)
watchdog >=0.10.3 : 4.0.1 (OK)
yarl >=1.9.4 : 1.11.0 (OK)
zmq >=24.0.0 : 25.1.2 (OK)
# Optional:
cython >=0.21 : None (NOK)
matplotlib >=3.0.0 : 3.8.4 (OK)
numpy >=1.7 : 1.26.4 (OK)
pandas >=1.1.1 : 2.2.2 (OK)
scipy >=0.17.0 : 1.13.1 (OK)
sympy >=0.7.3 : 1.12 (OK)
Environment
Environment
# packages in environment at /opt/anaconda3:
#
# Name Version Build Channel
_anaconda_depends 2024.06 py312_openblas_2
abseil-cpp 20230802.0 h313beb8_2
aext-assistant 4.0.15 py312hca03da5_jl4_0
aext-assistant-server 4.0.15 py312hca03da5_0
aext-core 4.0.15 py312hca03da5_jl4_0
aext-core-server 4.0.15 py312hca03da5_1
aext-panels 4.0.15 py312hca03da5_0
aext-panels-server 4.0.15 py312hca03da5_0
aext-share-notebook 4.0.15 py312hca03da5_0
aext-share-notebook-server 4.0.15 py312hca03da5_0
aext-shared 4.0.15 py312hca03da5_0
aiobotocore 2.12.3 py312hca03da5_0
aiohttp 3.9.5 py312h80987f9_0
aioitertools 0.7.1 pyhd3eb1b0_0
aiosignal 1.2.0 pyhd3eb1b0_0
alabaster 0.7.16 py312hca03da5_0
altair 5.0.1 py312hca03da5_0
anaconda-anon-usage 0.4.4 py312hd6b623d_100
anaconda-catalogs 0.2.0 py312hca03da5_1
anaconda-client 1.12.3 py312hca03da5_0
anaconda-cloud-auth 0.5.1 py312hca03da5_0
anaconda-navigator 2.6.0 py312hca03da5_0
anaconda-project 0.11.1 py312hca03da5_0
anaconda-toolbox 4.0.15 py312hca03da5_0
annotated-types 0.6.0 py312hca03da5_0
anyio 4.2.0 py312hca03da5_0
aom 3.6.0 h313beb8_0
appdirs 1.4.4 pyhd3eb1b0_0
applaunchservices 0.3.0 py312hca03da5_0
appnope 0.1.3 py312hca03da5_1001
appscript 1.1.2 py312h80987f9_0
archspec 0.2.3 pyhd3eb1b0_0
argon2-cffi 21.3.0 pyhd3eb1b0_0
argon2-cffi-bindings 21.2.0 py312h80987f9_0
arrow 1.2.3 py312hca03da5_1
arrow-cpp 14.0.2 hc7aafb3_1
astroid 3.2.4 py312hca03da5_0
astropy 6.1.0 py312ha86b861_0
astropy-iers-data 0.2024.6.3.0.31.14 py312hca03da5_0
asttokens 2.0.5 pyhd3eb1b0_0
async-lru 2.0.4 py312hca03da5_0
asyncssh 2.17.0 py312hca03da5_0
atomicwrites 1.4.0 py_0
attrs 23.1.0 py312hca03da5_0
automat 20.2.0 py_0
autopep8 2.0.4 pyhd3eb1b0_0
aws-c-auth 0.6.19 h80987f9_0
aws-c-cal 0.5.20 h80987f9_0
aws-c-common 0.8.5 h80987f9_0
aws-c-compression 0.2.16 h80987f9_0
aws-c-event-stream 0.2.15 h313beb8_0
aws-c-http 0.6.25 h80987f9_0
aws-c-io 0.13.10 h80987f9_0
aws-c-mqtt 0.7.13 h80987f9_0
aws-c-s3 0.1.51 h80987f9_0
aws-c-sdkutils 0.1.6 h80987f9_0
aws-checksums 0.1.13 h80987f9_0
aws-crt-cpp 0.18.16 h313beb8_0
aws-sdk-cpp 1.10.55 h313beb8_0
babel 2.11.0 py312hca03da5_0
bcrypt 4.3.0 py312h2aea54e_0
beautifulsoup4 4.12.3 py312hca03da5_0
binaryornot 0.4.4 pyhd3eb1b0_1
black 24.4.2 py312hca03da5_0
blas 1.0 openblas
bleach 4.1.0 pyhd3eb1b0_0
blinker 1.6.2 py312hca03da5_0
blosc 1.21.3 h313beb8_0
bokeh 3.4.1 py312h989b03a_0
boltons 23.0.0 py312hca03da5_0
boost-cpp 1.82.0 h48ca7d4_2
botocore 1.34.69 py312hca03da5_0
bottleneck 1.3.7 py312ha86b861_0
brotli 1.0.9 h80987f9_8
brotli-bin 1.0.9 h80987f9_8
brotli-python 1.0.9 py312h313beb8_8
brunsli 0.1 hc377ac9_1
bzip2 1.0.8 h80987f9_6
c-ares 1.19.1 h80987f9_0
c-blosc2 2.12.0 h7df6c2f_0
ca-certificates 2025.2.25 hca03da5_0
cachetools 5.3.3 py312hca03da5_0
cctools 949.0.1 hc179dcd_25
cctools_osx-arm64 949.0.1 h332cad3_25
certifi 2025.6.15 py312hca03da5_0
cffi 1.16.0 py312h80987f9_1
cfitsio 3.470 h7f6438f_7
chardet 4.0.0 py312hca03da5_1003
charls 2.2.0 hc377ac9_0
charset-normalizer 2.0.4 pyhd3eb1b0_0
click 8.1.7 py312hca03da5_0
cloudpickle 2.2.1 py312hca03da5_0
colorama 0.4.6 py312hca03da5_0
colorcet 3.1.0 py312hca03da5_0
comm 0.2.1 py312hca03da5_0
conda 24.11.3 py312hca03da5_0
conda-build 24.5.1 py312hca03da5_0
conda-content-trust 0.2.0 py312hca03da5_1
conda-index 0.5.0 py312hca03da5_0
conda-libmamba-solver 24.1.0 pyhd3eb1b0_0
conda-pack 0.7.1 py312hca03da5_0
conda-package-handling 2.3.0 py312hca03da5_0
conda-package-streaming 0.10.0 py312hca03da5_0
conda-repo-cli 1.0.88 py312hca03da5_0
conda-token 0.5.0 pyhd3eb1b0_0
constantly 23.10.4 py312hca03da5_0
contourpy 1.2.0 py312h48ca7d4_0
cookiecutter 2.6.0 py312hca03da5_0
cryptography 42.0.5 py312hd4332d6_1
cssselect 1.2.0 py312hca03da5_0
curl 8.7.1 h02f6b3c_0
cycler 0.11.0 pyhd3eb1b0_0
cyrus-sasl 2.1.28 h9131b1a_1
cytoolz 0.12.2 py312h80987f9_0
dask 2024.5.0 py312hca03da5_0
dask-core 2024.5.0 py312hca03da5_0
dask-expr 1.1.0 py312hca03da5_0
datashader 0.16.2 py312hca03da5_0
dav1d 1.2.1 h80987f9_0
debugpy 1.6.7 py312h313beb8_0
decorator 5.1.1 pyhd3eb1b0_0
defusedxml 0.7.1 pyhd3eb1b0_0
deprecated 1.2.13 py312hca03da5_0
diff-match-patch 20200713 pyhd3eb1b0_0
dill 0.3.8 py312hca03da5_0
distributed 2024.5.0 py312hca03da5_0
distro 1.9.0 py312hca03da5_0
docstring-to-markdown 0.11 py312hca03da5_0
docutils 0.18.1 py312hca03da5_3
entrypoints 0.4 py312hca03da5_0
et_xmlfile 1.1.0 py312hca03da5_1
executing 0.8.3 pyhd3eb1b0_0
expat 2.6.2 h313beb8_0
filelock 3.13.1 py312hca03da5_0
flake8 7.1.1 py312hca03da5_0
flask 3.0.3 py312hca03da5_0
fmt 9.1.0 h48ca7d4_1
fonttools 4.51.0 py312h80987f9_0
freetype 2.12.1 h1192e45_0
frozendict 2.4.2 py312hca03da5_0
frozenlist 1.4.0 py312h80987f9_0
fsspec 2024.3.1 py312hca03da5_0
gensim 4.3.2 py312hd77ebd4_0
gettext 0.21.0 h13f89a0_1
gflags 2.2.2 h313beb8_1
giflib 5.2.1 h80987f9_3
gitdb 4.0.7 pyhd3eb1b0_0
gitpython 3.1.37 py312hca03da5_0
glib 2.78.4 h313beb8_0
glib-tools 2.78.4 h313beb8_0
glog 0.5.0 h313beb8_1
graphviz 0.20.3 pypi_0 pypi
greenlet 3.0.1 py312h313beb8_0
grpc-cpp 1.48.2 hc60591f_4
gst-plugins-base 1.14.1 h313beb8_1
gstreamer 1.14.1 h80987f9_1
gtest 1.14.0 h48ca7d4_1
h11 0.14.0 py312hca03da5_0
h5py 3.11.0 py312haac6407_0
hdf5 1.12.1 h05c076b_3
heapdict 1.0.1 pyhd3eb1b0_0
holoviews 1.19.0 py312hca03da5_0
httpcore 1.0.2 py312hca03da5_0
httpx 0.27.0 py312hca03da5_0
hvplot 0.10.0 py312hca03da5_0
hyperlink 21.0.0 pyhd3eb1b0_0
icu 73.1 h313beb8_0
idna 3.7 py312hca03da5_0
imagecodecs 2023.1.23 py312h75b721f_1
imageio 2.33.1 py312hca03da5_0
imagesize 1.4.1 py312hca03da5_0
imbalanced-learn 0.12.3 py312hca03da5_1
importlib-metadata 7.0.1 py312hca03da5_0
incremental 22.10.0 pyhd3eb1b0_0
inflection 0.5.1 py312hca03da5_1
iniconfig 1.1.1 pyhd3eb1b0_0
intake 0.7.0 py312hca03da5_0
intervaltree 3.1.0 pyhd3eb1b0_0
ipykernel 6.29.5 py312hca03da5_0
ipython 8.25.0 py312hca03da5_0
ipython_genutils 0.2.0 pyhd3eb1b0_1
ipywidgets 7.8.1 py312hca03da5_0
isort 5.13.2 py312hca03da5_0
itemadapter 0.3.0 pyhd3eb1b0_0
itemloaders 1.1.0 py312hca03da5_0
itsdangerous 2.2.0 py312hca03da5_0
jaraco.classes 3.2.1 pyhd3eb1b0_0
jedi 0.18.1 py312hca03da5_1
jellyfish 1.0.1 py312h15d1925_0
jinja2 3.1.4 py312hca03da5_0
jmespath 1.0.1 py312hca03da5_0
joblib 1.4.2 py312hca03da5_0
jpeg 9e h80987f9_1
jq 1.6 h1a28f6b_1
json5 0.9.6 pyhd3eb1b0_0
jsonpatch 1.33 py312hca03da5_1
jsonpointer 2.1 pyhd3eb1b0_0
jsonschema 4.19.2 py312hca03da5_0
jsonschema-specifications 2023.7.1 py312hca03da5_0
jupyter 1.0.0 py312hca03da5_9
jupyter-lsp 2.2.0 py312hca03da5_0
jupyter_client 8.6.0 py312hca03da5_0
jupyter_console 6.6.3 py312hca03da5_1
jupyter_core 5.7.2 py312hca03da5_0
jupyter_events 0.10.0 py312hca03da5_0
jupyter_server 2.14.1 py312hca03da5_0
jupyter_server_terminals 0.4.4 py312hca03da5_1
jupyterlab 4.0.11 py312hca03da5_0
jupyterlab-variableinspector 3.1.0 py312hca03da5_0
jupyterlab_pygments 0.1.2 py_0
jupyterlab_server 2.25.1 py312hca03da5_0
jupyterlab_widgets 1.0.0 pyhd3eb1b0_1
jxrlib 1.1 h1a28f6b_2
keyring 24.3.1 py312hca03da5_0
kiwisolver 1.4.4 py312h313beb8_0
kneed 0.8.5 pypi_0 pypi
krb5 1.20.1 hf3e1bf2_1
lazy-object-proxy 1.10.0 py312h80987f9_0
lazy_loader 0.4 py312hca03da5_0
lcms2 2.12 hba8e193_0
ld64 530 hb29bf3f_25
ld64_osx-arm64 530 h001ce53_25
ldid 2.1.5 h20b2a84_3
lerc 3.0 hc377ac9_0
libaec 1.0.4 hc377ac9_1
libarchive 3.6.2 h62fee54_3
libavif 0.11.1 h80987f9_0
libboost 1.82.0 h0bc93f9_2
libbrotlicommon 1.0.9 h80987f9_8
libbrotlidec 1.0.9 h80987f9_8
libbrotlienc 1.0.9 h80987f9_8
libclang 14.0.6 default_h1b80db6_1
libclang13 14.0.6 default_h24352ff_1
libcurl 8.7.1 h3e2b118_0
libcxx 14.0.6 h848a8c0_0
libdeflate 1.17 h80987f9_1
libedit 3.1.20230828 h80987f9_0
libev 4.33 h1a28f6b_1
libevent 2.1.12 h02f6b3c_1
libffi 3.4.4 hca03da5_1
libgfortran 5.0.0 11_3_0_hca03da5_28
libgfortran5 11.3.0 h009349e_28
libglib 2.78.4 h0a96307_0
libiconv 1.16 h80987f9_3
liblief 0.12.3 h313beb8_0
libllvm14 14.0.6 h7ec7a93_3
libmamba 1.5.8 haeffa04_2
libmambapy 1.5.8 py312h1c5506f_2
libnghttp2 1.57.0 h62f6fdd_0
libopenblas 0.3.21 h269037a_0
libpng 1.6.39 h80987f9_0
libpq 12.17 h02f6b3c_0
libprotobuf 3.20.3 h514c7bf_0
libsodium 1.0.18 h1a28f6b_0
libsolv 0.7.24 h514c7bf_1
libspatialindex 1.9.3 hc377ac9_0
libssh2 1.11.0 h3e2b118_0
libthrift 0.15.0 h73c2103_2
libtiff 4.5.1 h313beb8_0
libwebp-base 1.3.2 h80987f9_0
libxml2 2.10.4 h0b34f26_2
libxslt 1.1.37 h80987f9_1
libzopfli 1.0.3 hc377ac9_0
linkify-it-py 2.0.0 py312hca03da5_0
llvm-openmp 14.0.6 hc6e5704_0
llvmlite 0.42.0 py312h313beb8_0
locket 1.0.0 py312hca03da5_0
lxml 5.2.1 py312h50ffb84_0
lz4 4.3.2 py312h80987f9_0
lz4-c 1.9.4 h313beb8_1
lzo 2.10 h1a28f6b_2
markdown 3.4.1 py312hca03da5_0
markdown-it-py 2.2.0 py312hca03da5_1
markupsafe 2.1.3 py312h80987f9_0
matplotlib 3.8.4 py312hca03da5_0
matplotlib-base 3.8.4 py312hd77ebd4_0
matplotlib-inline 0.1.6 py312hca03da5_0
mccabe 0.7.0 pyhd3eb1b0_0
mdit-py-plugins 0.3.0 py312hca03da5_0
mdurl 0.1.0 py312hca03da5_0
menuinst 2.2.0 py312hca03da5_0
mistune 2.0.4 py312hca03da5_0
mlxtend 0.23.1 py312hca03da5_0
more-itertools 10.1.0 py312hca03da5_0
mpmath 1.3.0 py312hca03da5_0
msgpack-python 1.0.3 py312h48ca7d4_0
multidict 6.0.4 py312h80987f9_0
multipledispatch 0.6.0 py312hca03da5_0
mypy 1.10.0 py312h80987f9_0
mypy_extensions 1.0.0 py312hca03da5_0
mysql 5.7.24 ha71a6ea_2
navigator-updater 0.5.1 py312hca03da5_0
nbclient 0.8.0 py312hca03da5_0
nbconvert 7.10.0 py312hca03da5_0
nbformat 5.9.2 py312hca03da5_0
ncurses 6.4 h313beb8_0
nest-asyncio 1.6.0 py312hca03da5_0
networkx 3.2.1 py312hca03da5_0
nltk 3.8.1 py312hca03da5_0
notebook 7.0.8 py312hca03da5_0
notebook-shim 0.2.3 py312hca03da5_0
numba 0.59.1 py312hd77ebd4_0
numexpr 2.8.7 py312h0f3ea24_0
numpy 1.26.4 py312h7f4fdc5_0
numpy-base 1.26.4 py312he047099_0
numpydoc 1.7.0 py312hca03da5_0
oniguruma 6.9.7.1 h1a28f6b_0
openjpeg 2.3.0 h7a6adac_2
openpyxl 3.1.2 py312h80987f9_0
openssl 3.0.16 h02f6b3c_0
orc 1.7.4 hdca1487_1
overrides 7.4.0 py312hca03da5_0
packaging 23.2 py312hca03da5_0
pandas 2.2.2 py312hd77ebd4_0
pandocfilters 1.5.0 pyhd3eb1b0_0
panel 1.4.4 py312hca03da5_0
param 2.1.0 py312hca03da5_0
parsel 1.8.1 py312hca03da5_0
parso 0.8.3 pyhd3eb1b0_0
partd 1.4.1 py312hca03da5_0
patch 2.7.6 h1a28f6b_1001
pathspec 0.10.3 py312hca03da5_0
patsy 0.5.6 py312hca03da5_0
pcre2 10.42 hb066dcc_1
pexpect 4.8.0 pyhd3eb1b0_3
pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 10.3.0 py312h80987f9_0
pip 24.2 pypi_0 pypi
pkce 1.0.3 py312hca03da5_0
pkginfo 1.10.0 py312hca03da5_0
platformdirs 3.10.0 py312hca03da5_0
plotly 5.22.0 py312h989b03a_0
pluggy 1.0.0 py312hca03da5_1
ply 3.11 py312hca03da5_1
prometheus_client 0.14.1 py312hca03da5_0
prompt-toolkit 3.0.43 py312hca03da5_0
prompt_toolkit 3.0.43 hd3eb1b0_0
protego 0.1.16 py_0
protobuf 3.20.3 py312h313beb8_0
psutil 5.9.0 py312h80987f9_0
ptyprocess 0.7.0 pyhd3eb1b0_2
pure_eval 0.2.2 pyhd3eb1b0_0
py-cpuinfo 9.0.0 py312hca03da5_0
py-lief 0.12.3 py312h313beb8_0
pyarrow 14.0.2 py312h8604a13_0
pyasn1 0.4.8 pyhd3eb1b0_0
pyasn1-modules 0.2.8 py_0
pybind11-abi 5 hd3eb1b0_0
pycodestyle 2.12.1 py312hca03da5_0
pycosat 0.6.6 py312h80987f9_1
pycparser 2.21 pyhd3eb1b0_0
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pycurl 7.45.2 py312h02f6b3c_1
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