Closed andrea-escartin closed 10 months ago
There has been a new release, can you try if it works now?
Can you try again with version 0.1.28 ?
I am facing the same install issue with Python 3.9.13. Both with pip and the latest dev version.
I am having the same issue. I'm on an M1 mac if that helps.
@bendichter @pravsripad @andrea-escartin
Is this still an issue with 1.32?
$ pip install -U pyedflib
Collecting pyedflib
Using cached pyEDFlib-0.1.32.tar.gz (2.1 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy>=1.9.1 in /Users/bendichter/opt/miniconda3/envs/neuroconv/lib/python3.9/site-packages (from pyedflib) (1.23.5)
Building wheels for collected packages: pyedflib
Building wheel for pyedflib (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for pyedflib (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [53 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-11.1-arm64-cpython-39
creating build/lib.macosx-11.1-arm64-cpython-39/pyedflib
copying pyedflib/version.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib
copying pyedflib/highlevel.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib
copying pyedflib/__init__.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib
copying pyedflib/edfreader.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib
copying pyedflib/edfwriter.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib
creating build/lib.macosx-11.1-arm64-cpython-39/pyedflib/_extensions
copying pyedflib/_extensions/__init__.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/_extensions
creating build/lib.macosx-11.1-arm64-cpython-39/pyedflib/data
copying pyedflib/data/_readers.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/data
copying pyedflib/data/__init__.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/data
creating build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests
copying pyedflib/tests/test_edfwriter.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests
copying pyedflib/tests/test_edfreader.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests
copying pyedflib/tests/test_doc.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests
copying pyedflib/tests/test_highlevel.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests
copying pyedflib/data/test_generator.edf -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/data
creating build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests/data
copying pyedflib/tests/data/test_generator.edf -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests/data
copying pyedflib/tests/data/test_legacy.edf -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests/data
copying pyedflib/tests/data/test_subsecond.edf -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests/data
copying pyedflib/tests/data/test_generator.bdf -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests/data
copying pyedflib/tests/data/test_generator_datarec_generator_0_5.bdf -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests/data
copying pyedflib/tests/data/test_generator_datarec_generator_2.bdf -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests/data
running build_clib
building 'c_edf' library
creating build/temp.macosx-11.1-arm64-cpython-39
creating build/temp.macosx-11.1-arm64-cpython-39/pyedflib
creating build/temp.macosx-11.1-arm64-cpython-39/pyedflib/_extensions
creating build/temp.macosx-11.1-arm64-cpython-39/pyedflib/_extensions/c
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/bendichter/opt/miniconda3/envs/neuroconv/include -arch arm64 -I/Users/bendichter/opt/miniconda3/envs/neuroconv/include -fPIC -O2 -isystem /Users/bendichter/opt/miniconda3/envs/neuroconv/include -arch arm64 -DPY_EXTENSION -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -Ipyedflib/_extensions/c -I/Users/bendichter/opt/miniconda3/envs/neuroconv/include/python3.9 -c pyedflib/_extensions/c/edflib.c -o build/temp.macosx-11.1-arm64-cpython-39/pyedflib/_extensions/c/edflib.o
pyedflib/_extensions/c/edflib.c:39:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma warning( disable : 4996 ) // ignore unsafe strncpy
^
pyedflib/_extensions/c/edflib.c:40:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma warning( disable : 4244 ) // ignore precision loss
^
pyedflib/_extensions/c/edflib.c:2629:37: warning: format specifies type 'int' but the argument has type 'off_t' (aka 'long long') [-Wformat]
printf("filesize %d != %d*%d+%d ",ftello(inputfile),edfhdr->recordsize, edfhdr->datarecords, edfhdr->hdrsize);
~~ ^~~~~~~~~~~~~~~~~
%lld
pyedflib/_extensions/c/edflib.c:2629:75: warning: format specifies type 'int' but the argument has type 'long long' [-Wformat]
printf("filesize %d != %d*%d+%d ",ftello(inputfile),edfhdr->recordsize, edfhdr->datarecords, edfhdr->hdrsize);
~~ ^~~~~~~~~~~~~~~~~~~
%lld
4 warnings generated.
/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_648976sdlo/croot/python-split_1669299891106/_build_env/bin/llvm-ar rcs build/temp.macosx-11.1-arm64-cpython-39/libc_edf.a build/temp.macosx-11.1-arm64-cpython-39/pyedflib/_extensions/c/edflib.o
error: command '/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_648976sdlo/croot/python-split_1669299891106/_build_env/bin/llvm-ar' failed: No such file or directory
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pyedflib
Failed to build pyedflib
ERROR: Could not build wheels for pyedflib, which is required to install pyproject.toml-based projects
Same issue on my M1 Mac with pyEDFlib-0.1.32 and python 3.9.13. Installation works perfectly on my Intel-based Mac.
It seems to be working for me now
Mac M1, Python 3.9.16
Collecting pyedflib
Downloading pyEDFlib-0.1.32.tar.gz (2.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 867.7 kB/s eta 0:00:00
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy>=1.9.1 in ./miniconda3/envs/primary/lib/python3.9/site-packages (from pyedflib) (1.23.5)
Building wheels for collected packages: pyedflib
Building wheel for pyedflib (pyproject.toml) ... done
Created wheel for pyedflib: filename=pyEDFlib-0.1.32-cp39-cp39-macosx_11_0_arm64.whl size=2214561 sha256=c4460d3405fe5bee521fd0eb7e8e1a5ad26d72d444345c280752e847d005c5fd
Stored in directory: /Users/praveen.sripad/Library/Caches/pip/wheels/7b/b8/95/3553c5897b957e79e5f24cf3eb585ad62ee615b48cfe38bd98
Successfully built pyedflib
Installing collected packages: pyedflib
Successfully installed pyedflib-0.1.32
@bendichter try installing with --no-cache-dir
option to pip to avoid using cache.
--no-cache-dir
does not help for me unfortunately. @pravsripad Can you share your pip list
here by chance?
--no-cache-dir
does not help for me unfortunately. @pravsripad Can you share yourpip list
here by chance?
Sure,
$pip list --exclude-editable
Package Version
----------------------------- -----------
absl-py 1.4.0
accelerate 0.15.0
aiofiles 22.1.0
aiohttp 3.8.3
aiosignal 1.3.1
alabaster 0.7.13
altair 4.2.1
anyio 3.6.2
appdirs 1.4.4
appnope 0.1.3
apptools 5.2.0
argcomplete 1.10.3
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
astor 0.8.1
asttokens 2.2.1
async-timeout 4.0.2
attrs 22.2.0
autopep8 2.0.1
Babel 2.11.0
backcall 0.2.0
backports.functools-lru-cache 1.6.4
base58 2.1.1
beautifulsoup4 4.11.2
beautifultable 1.1.0
bert-score 0.3.12
bibtexparser 1.4.0
bids-validator 1.9.9
binaryornot 0.4.4
black 21.12b0
bleach 6.0.0
blinker 1.5
blis 0.7.9
bokeh 3.0.3
Bottleneck 1.3.6
Brotli 1.0.9
brotlipy 0.7.0
cached-property 1.5.2
cachetools 5.3.0
catalogue 2.0.8
certifi 2022.12.7
cffi 1.15.1
chardet 5.1.0
charset-normalizer 2.1.1
click 8.1.3
cloudpickle 2.2.1
code2flow 2.5.1
colorama 0.4.6
comm 0.1.2
commonmark 0.9.1
compressed-rtf 1.0.6
conda 23.1.0
conda-build 3.23.3
conda-package-handling 2.0.2
conda_package_streaming 0.7.0
confection 0.0.4
configobj 5.0.8
contourpy 1.0.7
coverage 7.1.0
cryptography 39.0.0
cycler 0.11.0
cymem 2.0.7
Cython 0.29.33
cytoolz 0.12.0
dacite 1.8.0
dask 2023.1.1
datasets 2.9.0
datefinder 0.7.3
debugpy 1.6.6
decorator 5.1.1
defusedxml 0.7.1
dill 0.3.6
dipy 1.6.0
distlib 0.3.6
docker 6.0.1
docopt 0.6.2
docutils 0.17.1
docx2txt 0.8
dominate 2.7.0
ebcdic 1.1.1
ecdsa 0.18.0
EDFlib-Python 1.0.6
entrypoints 0.4
envisage 6.1.0
et-xmlfile 1.1.0
exceptiongroup 1.1.0
executing 1.2.0
extract-msg 0.28.7
fastjsonschema 2.16.2
fastrlock 0.8.1
feedparser 6.0.10
filelock 3.9.0
flake8 6.0.0
flit_core 3.8.0
fonttools 4.38.0
fooof 1.0.0
frozenlist 1.3.3
fsspec 2023.1.0
future 0.18.3
genson 1.2.2
ghp-import 2.1.0
gitdb 4.0.10
GitPython 3.1.30
glob2 0.7
gmpy2 2.1.2
graphql-core 3.2.3
graphviz 0.20.1
greenlet 2.0.2
h11 0.14.0
h5io 0.1.7
h5netcdf 1.1.0
h5py 3.8.0
hickle 5.0.2
httpcore 0.16.3
httpx 0.23.3
huggingface-hub 0.12.0
hypothesis 6.67.1
idna 3.4
imagecodecs 2023.1.23
imageio 2.25.0
imagesize 1.4.1
IMAPClient 2.1.0
importlib-metadata 6.0.0
importlib-resources 5.10.2
inflate64 0.3.1
iniconfig 2.0.0
ipykernel 6.21.1
ipympl 0.9.2
ipython 8.9.0
ipython-genutils 0.2.0
ipywidgets 8.0.4
isodate 0.6.1
isort 5.8.0
itk 5.3.0
itk-core 5.3.0
itk-filtering 5.3.0
itk-io 5.3.0
itk-numerics 5.3.0
itk-registration 5.3.0
itk-segmentation 5.3.0
itsdangerous 2.1.2
jedi 0.18.2
Jinja2 3.1.2
joblib 1.2.0
joppy 0.1.0
json5 0.9.6
jsoneditor 1.5.1
jsonref 1.1.0
jsonschema 4.17.3
jupyter 1.0.0
jupyter_client 8.0.2
jupyter-console 6.4.4
jupyter_core 5.2.0
jupyter-events 0.6.3
jupyter_server 2.1.0
jupyter_server_terminals 0.4.4
jupyterlab 3.5.3
jupyterlab-pygments 0.2.2
jupyterlab_server 2.19.0
jupyterlab-widgets 3.0.5
kiwisolver 1.4.4
langcodes 3.3.0
lazy_loader 0.1rc2
libarchive-c 4.0
littleutils 0.2.2
llvmlite 0.39.1
locket 1.0.0
lxml 4.9.2
Markdown 3.3.7
markdown-it-py 2.1.0
markdown-to-json 1.0.0
marko 1.2.2
MarkupSafe 2.1.2
matplotlib 3.6.3
matplotlib-inline 0.1.6
mayavi 4.8.1
mccabe 0.7.0
mdurl 0.1.2
medimages4tests 0.3
memory-profiler 0.61.0
mergedeep 1.3.4
mistune 2.0.4
mkdocs 1.4.2
mkdocs-material 9.0.13
mkdocs-material-extensions 1.1.1
mne-nirs 0.5.0
more-itertools 9.0.0
mpmath 1.2.1
msgpack 1.0.4
multidict 6.0.4
multiprocess 0.70.14
multivolumefile 0.2.3
munkres 1.1.4
murmurhash 1.0.9
mypy-extensions 1.0.0
nanoid 2.0.0
nbclassic 0.4.8
nbclient 0.7.2
nbconvert 7.2.9
nbformat 5.7.3
nest-asyncio 1.5.6
networkx 3.0
nibabel 5.0.0
nilearn 0.10.0
nltk 3.8.1
nose 1.3.7
notebook 6.5.2
notebook_shim 0.2.2
numba 0.56.4
numexpr 2.8.4
numpy 1.23.5
numpydoc 1.5.0
odML 1.5.2
olefile 0.46
openneuro-py 2022.4.0
openpyxl 3.0.10
outdated 0.2.2
packaging 23.0
pandas 1.5.3
pandas-flavor 0.3.0
pandocfilters 1.5.0
parallelformers 1.2.7
parso 0.8.3
partd 1.3.0
pathlib 1.0.1
pathspec 0.11.0
pathy 0.10.1
patsy 0.5.3
pdfminer.six 20191110
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.4.0
pingouin 0.5.3
pip 23.0
pipenv 2022.12.19
pipx 1.1.0
pkginfo 1.9.6
pkgutil_resolve_name 1.3.10
platformdirs 2.6.2
plotly 5.13.0
pluggy 1.0.0
ply 3.11
pooch 1.6.0
preshed 3.0.8
progressbar2 4.2.0
prometheus-client 0.16.0
prompt-toolkit 3.0.36
promptsource 0.2.3
protobuf 4.21.12
psutil 5.9.4
ptitprince 0.2.6
ptyprocess 0.7.0
pure-eval 0.2.2
py 1.11.0
py7zr 0.20.2
pyarrow 10.0.1
pyasn1 0.4.8
pybcj 1.0.1
pycodestyle 2.10.0
pycosat 0.6.4
pycparser 2.21
pycryptodome 3.17
pycryptodomex 3.16.0
pydantic 1.10.4
pydeck 0.8.0
pydicom 2.3.1
pyEDFlib 0.1.32
pyface 7.4.4
pyflakes 3.0.1
Pygments 2.14.0
PyHamcrest 2.0.4
pymatreader 0.0.30
pymdown-extensions 9.9.2
pymed 0.8.9
pyOpenSSL 23.0.0
pyparsing 3.0.9
PyPDF2 3.0.1
pyperclip 1.8.2
pyppmd 1.0.0
PyQt5-sip 12.11.0
pyqtgraph 0.13.1
pyrsistent 0.19.3
PySocks 1.7.1
pysondb 1.6.7
pysurfer 0.11.0
pytest 7.2.1
pytest-cov 4.0.0
python-dateutil 2.8.2
python-jose 3.3.0
python-json-logger 2.0.4
python-louvain 0.16
python-pptx 0.6.21
python-pygaze 0.7.5
python-utils 3.4.5
pytz 2022.7.1
pytz-deprecation-shim 0.1.0.post0
pyvista 0.37.0
pyvistaqt 0.9.0
PyWavelets 1.4.1
pyxnat 1.5
PyYAML 6.0
pyyaml_env_tag 0.1
pyzmq 25.0.0
pyzotero 1.5.5
pyzstd 0.15.3
qtconsole 5.4.0
QtPy 2.3.0
rdflib 5.0.0
recommonmark 0.7.1
regex 2022.10.31
reportlab 3.6.12
repro-catalogue 1.0.0
requests 2.28.2
responses 0.18.0
rfc3339-validator 0.1.4
rfc3986 1.5.0
rfc3986-validator 0.1.1
rich 13.2.0
rouge-score 0.1.2
rsa 4.9
ruamel.yaml 0.17.21
ruamel.yaml.clib 0.2.7
ruamel-yaml-conda 0.17.21
scikit-image 0.19.3
scikit-learn 1.2.1
scipy 1.10.0
scooby 0.7.1
seaborn 0.12.2
Send2Trash 1.8.0
setuptools 67.1.0
sgmllib3k 1.0.0
sgqlc 16.1
sip 6.7.7
six 1.16.0
smart-open 6.3.0
smmap 5.0.0
SnakeMD 0.12.1
sniffio 1.3.0
snowballstemmer 2.2.0
sortedcontainers 2.4.0
soupsieve 2.3.2.post1
spacy 3.5.0
spacy-legacy 3.0.12
spacy-loggers 1.0.4
SpeechRecognition 3.8.1
Sphinx 5.3.0
sphinx-bootstrap-theme 0.8.1
sphinx-gallery 0.11.1
sphinx-rtd-theme 1.1.1
sphinxcontrib-applehelp 1.0.4
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 2.0.1
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.5
SQLAlchemy 2.0.1
srsly 2.4.5
stack-data 0.6.2
statsmodels 0.13.5
streamlit 0.82.0
svn 1.0.1
sympy 1.11.1
systems 0.1.0
tabulate 0.9.0
telepot 12.7
tenacity 8.1.0
terminado 0.17.1
termtime 0.2.2
testpath 0.6.0
texttable 1.6.7
textual 0.10.1
thefuzz 0.19.0
thinc 8.1.7
threadpoolctl 3.1.0
tifffile 2023.2.2
tinycss2 1.2.1
tinydb 4.7.1
tinydb-serialization 2.1.0
tokenizers 0.13.2
toml 0.10.2
tomli 2.0.1
toolz 0.12.0
torch 1.13.1
tornado 6.2
tqdm 4.64.1
traitlets 5.9.0
traits 6.4.1
traitsui 7.4.3
transformers 4.26.0
transitions 0.9.0
transitions-gui 0.1.0
typed-ast 1.5.4
typer 0.7.0
typing_extensions 4.4.0
tzdata 2022.7
tzlocal 4.2
unicodedata2 15.0.0
urllib3 1.26.14
userpath 1.8.0
validators 0.20.0
virtualenv 20.17.1
virtualenv-clone 0.5.7
visitor 0.1.3
vtk 9.2.5
wasabi 1.1.1
watchdog 2.2.1
wcwidth 0.2.6
webencodings 0.5.1
websocket-client 1.5.1
Werkzeug 2.2.2
wheel 0.38.4
widgetsnbextension 4.0.5
wrapt 1.14.1
wslink 1.10.0
WTForms 3.0.1
xarray 2023.1.0
xlrd 1.2.0
XlsxWriter 3.0.8
xmltodict 0.13.0
xnat 0.4.3
xnat4tests 0.3.3
xxhash 3.2.0
xyzservices 2022.9.0
yarl 1.8.2
zipp 3.12.1
zstandard 0.19.0
I tried a fresh conda env with --no-cache-dir and I'm still getting the same installation issues.
I tried a fresh conda env with --no-cache-dir and I'm still getting the same installation issues.
I have the same error. Do you figure it out now?
I'm a bit clueless to what the problem could be here (and I have no Mac to investigate)
If anyone finds a solution, let us know!
Since the error is related to an attempt to use llvm-ar that cannot be found:
error: command '/opt/concourse/worker/volumes/live/c1a1a6ef-e724-4ad9-52a7-d6d68451dacb/volume/python-split_1631807121927/_build_env/bin/llvm-ar' failed: No such file or directory
Could this possibly be related to the NumpyExtension? The error may revolve around conda/pip environments and the use of llvm-ar vs local ar and a potential work around is described here. Worked for me.
Is there any update on this? Does installation now work on Mac?
I just retried and installation was successful on my M1 MacBook Pro 🎉
nice, thanks!
I just retried and installation was successful on my M1 MacBook Pro 🎉
Works for me as well. Thanks.
Confirmed here as well. Thanks for following up!
Trying to install
pyedflib
Version 0.1.22 OS: MacOS Big Sur (v 11.5.2) Python-3.9
Installation works when using python 3.7