numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject. #3655

simonm3 · 2019-01-17T20:53:48Z

Help! I am installing from source because I need a bug fix for houghlines that is not in the latest release.

I get the message "Expected 216 from C header, got 192 from PyObject."

Possibly it is a numpy incompatibility. However I was also getting the reverse message "Expected 192 but got 216" for bcolz until I moved it to later in the install.

How can I install bcolz, numpy, pytorch, skimage at the same time?

stefanv · 2019-01-17T21:00:34Z

The new NumPy release is tripping a lot of people up. Please downgrade your NumPy to a previous version, or use conda-forge for now. We are planning a new release for later today. See also #3649

simonm3 · 2019-01-18T13:55:04Z

New release of skimage fixed it thanks. Not sure of cause but was not using latest release of numpy.

hmaarrfk · 2019-01-18T14:01:35Z

Interesting. Maybe you can tell us more about how you installed numpy, scikit-image, and pytorch if it happens again.

Things like OS, python version, pip vs conda are important.

simonm3 · 2019-01-18T14:07:26Z

FYI ubuntu18.04, python 3.7 via miniconda latest pip install numpy conda install pytorch-cpu -c pytorch compile skimage according to instructions Pytorch is not available on pip. If I took out the pytorch install then skimage worked. The version of pytorch is same as previously worked but it installs dependencies which have changed including numpy (though not the latest version).

…

On Fri, 18 Jan 2019 at 14:01, Mark Harfouche ***@***.***> wrote: Interesting. Maybe you can tell us more about how you installed numpy, scikit-image, and pytorch if it happens again. Things like OS, python version, pip vs conda are important. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3655 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABJN6U2I9AQEBKi4VEwjFxTcV3thV7mHks5vEdPDgaJpZM4aGuDE> .

hmaarrfk · 2019-01-18T14:09:29Z

is there a particular reason why you are compiling skimage from source?
do the packages on conda not work?
are you using conda-forge???

the issue is likely (though not 100% sure) that you are likely compiling skimage with a newer version of numpy than pytorch was compiled with

hmaarrfk · 2019-01-18T14:09:51Z

oh yeah, also, don't install one package with pip, the other with conda. that is a recipe for disaster.

hmaarrfk · 2019-01-18T14:10:33Z

mostly, you really shouldn't install numpy via pip. if a package exists on conda, you should use that. if it doesn't you can probably request it to be on conda-forge
https://github.com/conda-forge/staged-recipes

simonm3 · 2019-01-18T14:22:33Z

Required the source as there was a bug in houghlines which was fixed in source but not in the release at the time - it is now!. I was trying to install everything with pip so it would all be in one install and more things are on pip than conda. The only ones not on pip were Pytorch and skimage which was from source.

…

On Fri, 18 Jan 2019 at 14:09, Mark Harfouche ***@***.***> wrote: is there a particular reason why you are compiling skimage from source? do the packages on conda not work? are you using conda-forge??? the issue is likely (though not 100% sure) that you are likely compiling skimage with a newer version of numpy than pytorch was compiled with — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3655 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABJN6YxwqK3Kn510E4UMWa3k7PEmG-Muks5vEdWdgaJpZM4aGuDE> .

hmaarrfk · 2019-01-18T14:27:47Z

oh man, it was a bug in the pyx file, so you couldn't have just fixed it yourself. Yeah.....

there was some discussion about having more frequent releases. unfortunately, it doesn't seem to have gone anywhere, likely due to lack of bandwidth.

I think it is reasonable to try and find that issue, or to open a new one asking for more releases. Explaining your story (wanting to install pytorch and scikit-image) is likely good enough.

pytorch now exists on pip no?

https://pytorch.org/

stefanv · 2019-01-18T18:29:15Z

mostly, you really shouldn't install numpy via pip. if a package exists on conda, you should use that. if it doesn't you can probably request it to be on conda-forge
https://github.com/conda-forge/staged-recipes

Many of us use pip exclusively, actually; so, use whatever the default installer of your environment is. Try to stick to "all conda" or "all pip".

hmaarrfk · 2019-01-18T18:45:39Z

Many of us use pip exclusively, actually; so, use whatever the default installer of your environment is. Try to stick to "all conda" or "all pip".

Consistency is more what I was looking for. Thanks for making that clear @stefanv

simonm3 · 2019-01-18T21:03:50Z

I just tried doing it all in conda. First difference is that it takes longer or seems to because nothing happens for ages. Second thing is it downgrades python from 3.7 to 2.7 and as I am doing this in one line for a docker build it is unclear which of the 30+ packages is doing that. And the latest skimage release isn't available on conda-forge yet!

…

On Fri, 18 Jan 2019 at 18:45, Mark Harfouche ***@***.***> wrote: Many of us use pip exclusively, actually; so, use whatever the default installer of your environment is. Try to stick to "all conda" or "all pip". Consistency is more what I was looking for. Thanks for making that clear @stefanv <https://github.com/stefanv> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3655 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABJN6blp9Qs9oPlhU148kZiJz3GClDlyks5vEhZXgaJpZM4aGuDE> .

hmaarrfk · 2019-01-18T21:44:09Z

it might be because you have something like a dependency that only exists on python2.7. for example, enum34 is one of these.

conda knows that it is being slow these days. they are trying to fix it.....

odb2 · 2019-04-18T07:07:29Z

As of now, I tried rolling back numpy to 1.14.5 and all other versions but none worked but upgrading to 1.16.1 finally fixed it!.

pip install numpy==1.16.1

patsotoe · 2019-05-13T14:56:26Z

this works.

yustiks · 2019-05-24T10:34:48Z

As of now, I tried rolling back numpy to 1.14.5 and all other versions but none worked but upgrading to 1.16.1 finally fixed it!.

pip install numpy==1.16.1

thank You! it helped

NumPy changed the ``numpy.ufunc`` size which could lead to inconsistencies with other (compiled) packages. The issue is supposed to be fixed vor version >1.16.1 scikit-image/scikit-image#3655 (comment)

mdtahsinasif · 2019-12-06T11:15:54Z

HI Everyone .. i m getting below error need your help
from .murmurhash import murmurhash3_32

File "init.pxd", line 918, in init sklearn.utils.murmurhash

ValueError: numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject

i m using version:
Package Version

absl-py 0.8.1
alabaster 0.7.12
asn1crypto 0.24.0
astor 0.8.0
astroid 1.6.5
Babel 2.7.0
backcall 0.1.0
bleach 1.5.0
certifi 2018.8.24
cffi 1.11.5
chardet 3.0.4
cloudpickle 1.2.2
colorama 0.4.1
cryptography 2.3.1
cycler 0.10.0
decorator 4.4.1
defusedxml 0.6.0
docutils 0.14
entrypoints 0.2.3
gast 0.3.2
grpcio 1.25.0
h5py 2.8.0
html5lib 0.9999999
idna 2.7
imagesize 1.1.0
ipykernel 4.10.0
ipython 6.5.0
ipython-genutils 0.2.0
isort 4.3.4
jedi 0.12.1
Jinja2 2.10.3
joblib 0.14.0
jsonschema 2.6.0
jupyter-client 5.3.3
jupyter-core 4.5.0
Keras 2.2.2
Keras-Applications 1.0.8
Keras-Preprocessing 1.1.0
keyring 13.2.1
kiwisolver 1.0.1
lazy-object-proxy 1.3.1
List 1.3.0
Markdown 3.1.1
MarkupSafe 1.0
matplotlib 3.0.0
mccabe 0.6.1
mistune 0.8.3
nbconvert 5.5.0
nbformat 4.4.0
numpy 1.17.4
numpydoc 0.9.1
packaging 19.2
pandas 0.23.4
pandocfilters 1.4.2
parso 0.5.1
pickleshare 0.7.4
pip 10.0.1
prompt-toolkit 1.0.15
protobuf 3.11.1
psutil 5.4.7
pycodestyle 2.4.0
pycparser 2.19
pyflakes 2.0.0
Pygments 2.5.2
pylint 1.9.2
pyOpenSSL 18.0.0
pyparsing 2.4.5
PySocks 1.6.8
python-dateutil 2.8.1
pytz 2019.3
pywin32 223
PyYAML 3.13
pyzmq 17.1.2
QtAwesome 0.6.0
qtconsole 4.6.0
QtPy 1.9.0
requests 2.19.1
rope 0.14.0
scikit-learn 0.18
scipy 1.1.0
setuptools 39.1.0
simplegeneric 0.8.1
six 1.13.0
sklearn 0.0
snowballstemmer 2.0.0
Sphinx 2.2.2
sphinxcontrib-applehelp 1.0.1
sphinxcontrib-devhelp 1.0.1
sphinxcontrib-htmlhelp 1.0.2
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.2
sphinxcontrib-serializinghtml 1.1.3
spyder 3.3.1
spyder-kernels 0.2.6
tensorboard 1.11.0
tensorflow 1.11.0
termcolor 1.1.0
testpath 0.4.4
tornado 5.1.1
traitlets 4.3.2
urllib3 1.23
wcwidth 0.1.7
webencodings 0.5.1
Werkzeug 0.16.0
wheel 0.33.6
win-inet-pton 1.0.1
win-unicode-console 0.5
wincertstore 0.2
wrapt 1.10.11

while using

from sklearn.model_selection import train_test_split

juniorojha · 2019-12-17T05:57:54Z

HI Everyone .. i m getting below error need your help
from .murmurhash import murmurhash3_32

File "init.pxd", line 918, in init sklearn.utils.murmurhash

ValueError: numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject

i m using version:
Package Version

absl-py 0.8.1
alabaster 0.7.12
asn1crypto 0.24.0
astor 0.8.0
astroid 1.6.5
Babel 2.7.0
backcall 0.1.0
bleach 1.5.0
certifi 2018.8.24
cffi 1.11.5
chardet 3.0.4
cloudpickle 1.2.2
colorama 0.4.1
cryptography 2.3.1
cycler 0.10.0
decorator 4.4.1
defusedxml 0.6.0
docutils 0.14
entrypoints 0.2.3
gast 0.3.2
grpcio 1.25.0
h5py 2.8.0
html5lib 0.9999999
idna 2.7
imagesize 1.1.0
ipykernel 4.10.0
ipython 6.5.0
ipython-genutils 0.2.0
isort 4.3.4
jedi 0.12.1
Jinja2 2.10.3
joblib 0.14.0
jsonschema 2.6.0
jupyter-client 5.3.3
jupyter-core 4.5.0
Keras 2.2.2
Keras-Applications 1.0.8
Keras-Preprocessing 1.1.0
keyring 13.2.1
kiwisolver 1.0.1
lazy-object-proxy 1.3.1
List 1.3.0
Markdown 3.1.1
MarkupSafe 1.0
matplotlib 3.0.0
mccabe 0.6.1
mistune 0.8.3
nbconvert 5.5.0
nbformat 4.4.0
numpy 1.17.4
numpydoc 0.9.1
packaging 19.2
pandas 0.23.4
pandocfilters 1.4.2
parso 0.5.1
pickleshare 0.7.4
pip 10.0.1
prompt-toolkit 1.0.15
protobuf 3.11.1
psutil 5.4.7
pycodestyle 2.4.0
pycparser 2.19
pyflakes 2.0.0
Pygments 2.5.2
pylint 1.9.2
pyOpenSSL 18.0.0
pyparsing 2.4.5
PySocks 1.6.8
python-dateutil 2.8.1
pytz 2019.3
pywin32 223
PyYAML 3.13
pyzmq 17.1.2
QtAwesome 0.6.0
qtconsole 4.6.0
QtPy 1.9.0
requests 2.19.1
rope 0.14.0
scikit-learn 0.18
scipy 1.1.0
setuptools 39.1.0
simplegeneric 0.8.1
six 1.13.0
sklearn 0.0
snowballstemmer 2.0.0
Sphinx 2.2.2
sphinxcontrib-applehelp 1.0.1
sphinxcontrib-devhelp 1.0.1
sphinxcontrib-htmlhelp 1.0.2
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.2
sphinxcontrib-serializinghtml 1.1.3
spyder 3.3.1
spyder-kernels 0.2.6
tensorboard 1.11.0
tensorflow 1.11.0
termcolor 1.1.0
testpath 0.4.4
tornado 5.1.1
traitlets 4.3.2
urllib3 1.23
wcwidth 0.1.7
webencodings 0.5.1
Werkzeug 0.16.0
wheel 0.33.6
win-inet-pton 1.0.1
win-unicode-console 0.5
wincertstore 0.2
wrapt 1.10.11

while using

from sklearn.model_selection import train_test_split

Any success in making this work?

jni · 2019-12-17T08:23:31Z

@mdtahsinasif @juniorojha This is the scikit-image issue tracker, not scikit-learn. Having said that, I expect that you need to either upgrade your scikit-image/learn or downgrade your NumPy.

manish-tiwari · 2020-02-26T06:58:25Z

oh yeah, also, don't install one package with pip, the other with conda. that is a recipe for disaster.

If that is the case then what should we do when one any package is not available in conda but exists in pip?

vamsiinmicron · 2020-03-04T07:21:46Z

As of now, I tried rolling back numpy to 1.14.5 and all other versions but none worked but upgrading to 1.16.1 finally fixed it!.
pip install numpy==1.16.1

This worked

jni · 2020-03-04T11:59:05Z

@manish-tiwari

If that is the case then what should we do when one any package is not available in conda but exists in pip?

As a last resort, you install it with pip. @hmaarrfk did not mean that as a hard rule but as a guideline. Ultimately, mixing pip and conda can lead to incompatible compiled binary code (code like NumPy that is not written in Python but rather C with Python "bindings", meaning ways to access the C code), at which point you usually have to start with a fresh environment.

hmaarrfk · 2020-03-05T05:57:13Z

Thanks for better explaining my thoughts jni.

We really want to do our best to help people still experiencing a similar issue.

Opening a new on GitHub is the best way to do that. Feel free to open them!

* provide unified benchmark pool built from specialized ones * improve wording * update benchmarks example * require numpy>=1.16 following scikit-image/scikit-image#3655 (comment) * account for legacy noaperture movshon assembly

#28)

* resize stimuli based on model's declared visual degrees * do not convert stimulus_set if target==source * set visual_degrees to assembly for unit test * add visual_degrees again * set screen degrees for Rajalingham and tolias.Cadena (#197) * Corrected stimulus size of 8deg for behavioral benchmark. Removes cropping images to 85% for tensorflow models in preprocessing. Adds stimilus size of 2deg for Cadena benchmark. Allows behavior benchmark to work on models with multiple layers. * Added V1 neural predictivity benchmark for the Movshon public dataset and for the Tolias dataset * use logging for Score warnings; add comments; quick-return nan for ost no timebins * fix tests for V1/2 aperture; download precomputed test files from S3 brain-score/brainio_collection#27 * fix lstrip_local: use name instead of fixed index * fix PrecomputedProbabilities for Rajalingham2018 tests: add visual degrees * fix test file download, add echo statement * require numpy>=1.16 following scikit-image/scikit-image#3655 (comment) * fix previous commit: need at least 1.16 * fix Kar2019ost test and add precomputed test; remove mask-benchmark test * use 3.6 again in an attempt to fix mysterious curl pull issue (in travis' `pip install .`) Collecting brainio_collection@ git+https://github.com/brain-score/brainio_collection Cloning https://github.com/brain-score/brainio_collection to /tmp/pip-install-7suake0n/brainio-collection Running command git clone -q https://github.com/brain-score/brainio_collection /tmp/pip-install-7suake0n/brainio-collection error: RPC failed; curl 56 GnuTLS recv error (-54): Error in the pull function. fatal: the remote end hung up unexpectedly fatal: early EOF fatal: index-pack failed * Add visual degrees to benchmarks; add V1 single benchmark (#199) * Adds stimulus size of 6deg for behavioral benchmark. Adds stimilus size of 2deg for Cadena benchmark. Allows behavior benchmark to work on models with multiple layers. * Corrected stimulus size of 8deg for behavioral benchmark. Removes cropping images to 85% for tensorflow models in preprocessing. Adds stimilus size of 2deg for Cadena benchmark. Allows behavior benchmark to work on models with multiple layers. * Added V1 neural predictivity benchmark for the Movshon public dataset and for the Tolias dataset * Corrected several bugs to run visual degrees Moved visual degrees implementation from stimulus set to benchmarks Added single neuron mapping * Added V1 neural predictivity benchmark for the Movshon public dataset and for the Tolias dataset * Corrected screen degrees transformation * fix PR comments: CamelCase naming, public benchmarks, correlations r Co-authored-by: Martin Schrimpf <m4rtinsch@gmail.com> * test for the correct ratio of gray in stimuli of benchmarks in response to different-sized candidates * update comment * remove out-dated global setting of stimulus set degrees * add visual degrees to public benchmarks * place stimuli on screen according to visual degrees for example benchmark Co-authored-by: tiagogmarques <tmarques@mit.edu>

didpurwanto · 2020-05-19T12:09:01Z

As of now, I tried rolling back numpy to 1.14.5 and all other versions but none worked but upgrading to 1.16.1 finally fixed it!.

pip install numpy==1.16.1

its work

iprafols · 2021-08-26T11:15:37Z

Hi all,

I just encountered the opposite problem:
<frozen importlib._bootstrap>:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject

For the record, I am running on a MacOS Catalina (v10.15.7) and using python 3.8.3 with numpy 1.21.2 and sklearn 0.23.1

stefanv closed this as completed Jan 17, 2019

psteinb mentioned this issue Apr 18, 2019

running the tests bethgelab/foolbox#296

Closed

scikit-image locked as too heated and limited conversation to collaborators May 24, 2019

scikit-image unlocked this conversation May 24, 2019

apaleyes mentioned this issue Jul 11, 2019

Not able to import GPyOpt SheffieldML/GPyOpt#251

Closed

hmaarrfk mentioned this issue Oct 27, 2019

Windows Build of 0.16.2 on python 3.6 seems to be incompatible with numpy 1.15.4 #4270

Closed

robnagler mentioned this issue Nov 25, 2019

warpvnd pytest issue radiasoft/sirepo#2082

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hellock mentioned this issue Dec 21, 2019

mmcv numpy error open-mmlab/mmcv#158

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iamDecode mentioned this issue Feb 24, 2020

Error while importing the model iamDecode/sklearn-pmml-model#18

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mschrimpf added a commit to brain-score/vision that referenced this issue Mar 22, 2020

require numpy>=1.16 following scikit-image/scikit-image#3655 (comment)

b09ea63

mschrimpf added a commit to mschrimpf/brain-score that referenced this issue Mar 24, 2020

require numpy>=1.16 following scikit-image/scikit-image#3655 (comment)

a314ebc

mschrimpf added a commit to brain-score/brainio_collection that referenced this issue Mar 24, 2020

require numpy>=1.16 following scikit-image/scikit-image#3655 (comment)

067001b

mschrimpf added a commit to brain-score/brainio_collection that referenced this issue Mar 24, 2020

require numpy>=1.16 following scikit-image/scikit-image#3655 (comment) (

f64cc95

#28)

MuellerSeb mentioned this issue May 1, 2020

"numpy.ufunc size changed" Error on Python 3.5 GeoStat-Framework/GSTools#84

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anilbey mentioned this issue Jun 5, 2020

Travis configuration BlueBrain/Search#51

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ymwdalex mentioned this issue Sep 26, 2020

Installation shows success but can not import module (improper installation) ing-bank/sparse_dot_topn#40

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joshuacwnewton mentioned this issue Jun 17, 2024

Incompatibility with Numpy 2 (numpy.dtype size changed) #7445

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numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject. #3655

numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject. #3655

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numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject. #3655

numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject. #3655

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