bio_embeddings
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20 hours ago •
sacdallago
sacdallago
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
I'm using Jupiter notebook to run from bio_embeddings.embed import SeqVecEmbedder reported an errorValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject. I tried the following methods, but they didn't work。
pip uninstall numpy
pip install numpy==1.21.2
Thanks for reporting the issue. Coudl you give me some more detail about how you install the pipeline (from pypi or from github?)
I ran into the same issue.
Installed into a fresh environment
conda create -n seqvec python=3.9
pip install -U "bio_embeddings[seqvec]"
# packages in environment at /Users/jonathan/miniconda3/envs/seqvec:
#
# Name Version Build Channel
alabaster 0.7.12 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
atomicwrites 1.4.0 pypi_0 pypi
attrs 21.4.0 pypi_0 pypi
babel 2.10.1 pypi_0 pypi
bio-embeddings 0.2.2 pypi_0 pypi
bio-embeddings-allennlp 0.9.2 pypi_0 pypi
biopython 1.79 pypi_0 pypi
blis 0.7.7 pypi_0 pypi
boto3 1.23.0 pypi_0 pypi
botocore 1.26.0 pypi_0 pypi
ca-certificates 2022.4.26 hecd8cb5_0
catalogue 1.0.0 pypi_0 pypi
certifi 2021.10.8 py39hecd8cb5_2
charset-normalizer 2.0.12 pypi_0 pypi
click 8.1.3 pypi_0 pypi
conllu 4.4 pypi_0 pypi
cycler 0.11.0 pypi_0 pypi
cymem 2.0.6 pypi_0 pypi
docutils 0.17.1 pypi_0 pypi
editdistance 0.6.0 pypi_0 pypi
flaky 3.7.0 pypi_0 pypi
flask 2.1.2 pypi_0 pypi
flask-cors 3.0.10 pypi_0 pypi
fonttools 4.33.3 pypi_0 pypi
ftfy 6.1.1 pypi_0 pypi
gensim 3.8.3 pypi_0 pypi
gevent 21.12.0 pypi_0 pypi
greenlet 1.1.2 pypi_0 pypi
h5py 3.6.0 pypi_0 pypi
humanize 3.14.0 pypi_0 pypi
idna 3.3 pypi_0 pypi
imagesize 1.3.0 pypi_0 pypi
importlib-metadata 4.11.3 pypi_0 pypi
iniconfig 1.1.1 pypi_0 pypi
itsdangerous 2.1.2 pypi_0 pypi
jinja2 3.1.2 pypi_0 pypi
jmespath 1.0.0 pypi_0 pypi
joblib 1.1.0 pypi_0 pypi
jsonnet 0.18.0 pypi_0 pypi
jsonpickle 2.2.0 pypi_0 pypi
kiwisolver 1.4.2 pypi_0 pypi
libcxx 12.0.0 h2f01273_0
libffi 3.3 hb1e8313_2
llvmlite 0.38.0 pypi_0 pypi
lock 2018.3.25.2110 pypi_0 pypi
markupsafe 2.1.1 pypi_0 pypi
matplotlib 3.5.2 pypi_0 pypi
murmurhash 1.0.7 pypi_0 pypi
ncurses 6.3 hca72f7f_2
nltk 3.7 pypi_0 pypi
numba 0.55.1 pypi_0 pypi
numpy 1.21.6 pypi_0 pypi
numpydoc 1.3.1 pypi_0 pypi
openssl 1.1.1o hca72f7f_0
overrides 4.1.2 pypi_0 pypi
packaging 21.3 pypi_0 pypi
pandas 1.4.2 pypi_0 pypi
parsimonious 0.9.0 pypi_0 pypi
pillow 9.1.0 pypi_0 pypi
pip 21.2.4 py39hecd8cb5_0
plac 1.1.3 pypi_0 pypi
plotly 5.8.0 pypi_0 pypi
pluggy 1.0.0 pypi_0 pypi
preshed 3.0.6 pypi_0 pypi
protobuf 3.20.1 pypi_0 pypi
py 1.11.0 pypi_0 pypi
pygments 2.12.0 pypi_0 pypi
pynndescent 0.5.7 pypi_0 pypi
pyparsing 3.0.9 pypi_0 pypi
pytest 7.1.2 pypi_0 pypi
python 3.9.12 hdfd78df_0
python-dateutil 2.8.2 pypi_0 pypi
python-slugify 5.0.2 pypi_0 pypi
pytorch-pretrained-bert 0.6.2 pypi_0 pypi
pytorch-transformers 1.1.0 pypi_0 pypi
pytz 2022.1 pypi_0 pypi
readline 8.1.2 hca72f7f_1
regex 2022.4.24 pypi_0 pypi
requests 2.27.1 pypi_0 pypi
responses 0.20.0 pypi_0 pypi
ruamel-yaml 0.17.21 pypi_0 pypi
ruamel-yaml-clib 0.2.6 pypi_0 pypi
s3transfer 0.5.2 pypi_0 pypi
scikit-learn 0.24.2 pypi_0 pypi
scipy 1.8.0 pypi_0 pypi
sentencepiece 0.1.96 pypi_0 pypi
setuptools 61.2.0 py39hecd8cb5_0
six 1.16.0 pypi_0 pypi
smart-open 6.0.0 pypi_0 pypi
snowballstemmer 2.2.0 pypi_0 pypi
spacy 2.3.7 pypi_0 pypi
sphinx 4.5.0 pypi_0 pypi
sphinxcontrib-applehelp 1.0.2 pypi_0 pypi
sphinxcontrib-devhelp 1.0.2 pypi_0 pypi
sphinxcontrib-htmlhelp 2.0.0 pypi_0 pypi
sphinxcontrib-jsmath 1.0.1 pypi_0 pypi
sphinxcontrib-qthelp 1.0.3 pypi_0 pypi
sphinxcontrib-serializinghtml 1.1.5 pypi_0 pypi
sqlite 3.38.3 h707629a_0
sqlparse 0.4.2 pypi_0 pypi
srsly 1.0.5 pypi_0 pypi
tenacity 8.0.1 pypi_0 pypi
tensorboardx 2.5 pypi_0 pypi
text-unidecode 1.3 pypi_0 pypi
thinc 7.4.5 pypi_0 pypi
threadpoolctl 3.1.0 pypi_0 pypi
tk 8.6.11 h3fd3227_1
tomli 2.0.1 pypi_0 pypi
torch 1.10.0 pypi_0 pypi
tqdm 4.64.0 pypi_0 pypi
typing-extensions 4.2.0 pypi_0 pypi
typing-utils 0.1.0 pypi_0 pypi
tzdata 2022a hda174b7_0
umap-learn 0.5.3 pypi_0 pypi
unidecode 1.3.4 pypi_0 pypi
urllib3 1.26.9 pypi_0 pypi
wasabi 0.9.1 pypi_0 pypi
wcwidth 0.2.5 pypi_0 pypi
werkzeug 2.1.2 pypi_0 pypi
wheel 0.37.1 pyhd3eb1b0_0
word2number 1.1 pypi_0 pypi
xz 5.2.5 hca72f7f_1
zipp 3.8.0 pypi_0 pypi
zlib 1.2.12 h4dc903c_2
zope-event 4.5.0 pypi_0 pypi
zope-interface 5.4.0 pypi_0 pypi
Execute
>>> from bio_embeddings.embed import SeqVecEmbedder
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/jonathan/miniconda3/envs/seqvec/lib/python3.9/site-packages/bio_embeddings/__init__.py", line 12, in <module>
import bio_embeddings.embed
File "/Users/jonathan/miniconda3/envs/seqvec/lib/python3.9/site-packages/bio_embeddings/embed/__init__.py", line 68, in <module>
from bio_embeddings.embed.fasttext_embedder import FastTextEmbedder
File "/Users/jonathan/miniconda3/envs/seqvec/lib/python3.9/site-packages/bio_embeddings/embed/fasttext_embedder.py", line 4, in <module>
from gensim.models.keyedvectors import KeyedVectors
File "/Users/jonathan/miniconda3/envs/seqvec/lib/python3.9/site-packages/gensim/__init__.py", line 5, in <module>
from gensim import parsing, corpora, matutils, interfaces, models, similarities, summarization, utils # noqa:F401
File "/Users/jonathan/miniconda3/envs/seqvec/lib/python3.9/site-packages/gensim/corpora/__init__.py", line 6, in <module>
from .indexedcorpus import IndexedCorpus # noqa:F401 must appear before the other classes
File "/Users/jonathan/miniconda3/envs/seqvec/lib/python3.9/site-packages/gensim/corpora/indexedcorpus.py", line 15, in <module>
from gensim import interfaces, utils
File "/Users/jonathan/miniconda3/envs/seqvec/lib/python3.9/site-packages/gensim/interfaces.py", line 21, in <module>
from gensim import utils, matutils
File "/Users/jonathan/miniconda3/envs/seqvec/lib/python3.9/site-packages/gensim/matutils.py", line 1104, in <module>
from gensim._matutils import logsumexp, mean_absolute_difference, dirichlet_expectation
File ".eggs/Cython-0.29.14-py2.7-linux-x86_64.egg/Cython/Includes/numpy/__init__.pxd", line 242, in init gensim._matutils
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
Looks like this is an issue with pinning numpy and gensim issues. gensim also claim that [email protected] is no longer supported and users should upgrade to 4.0.0+
If I force gensim==4.2.0 and numpy==1.22.0 I no longer get the error, but a few warnings about bio_embeddings compatibility, of course.
Trying numpy<1.22 errors out and fails to build the wheel thats PEP 517 compliant.
Thanks @jondeans . I noticed that CI also started failing us recently do to the outdated depenency stack. I guess I'll make a student' life miserable for the next week by tasking him with cleaning up :)
