I am building a Docker image based on alpine linux. During build I get the error when installing tables that I have no local hdf5 installation.
To solve this I tried to install hdf5 as recommended in various posts:
- `pip install tables` fail with ERROR:: Could not find a local HDF5 installation
- Cannot install h5py
- https://github.com/freqtrade/freqtrade/issues/4162
- https://github.com/PyTables/PyTables/issues/219
Yet, even if I install hdf5 package in my Docker container the same error occurs (I also tried hdf5-dev package but this includes SciPy and I don't want SciPy since it takes ages to build).
Note that I don't even know why tables is installed, or let's say which dependency installs tables. So as a solution I'd be happy to remove the dependency that installs tables, if I don't need it. Yet most of my requirements in my requirements.txt I do need. Most of all I need pandas, matplotlib and numpy.
My dockerfile looks like this:
FROM python:3.9-alpine3.14
RUN apk add --no-cache --update-cache hdf5
RUN apk update \
# psycopg2 dependencies
&& apk add --virtual build-deps gcc python3-dev musl-dev \
&& apk add postgresql-dev \
# Pillow dependencies
&& apk add jpeg-dev zlib-dev freetype-dev lcms2-dev openjpeg-dev tiff-dev tk-dev tcl-dev \
# CFFI dependencies
&& apk add libffi-dev py-cffi \
# Translations dependencies
&& apk add gettext \
# https://docs.djangoproject.com/en/dev/ref/django-admin/#dbshell
&& apk add postgresql-client \
## Needed for sphinx https://github.com/pydanny/cookiecutter-django/issues/1747
&& apk add make \
## Needed for postgis
&& apk add --no-cache --virtual .build-deps \
autoconf \
automake \
g++ \
gdal-dev \
geos-dev \
json-c-dev \
libtool \
libxml2-dev \
proj-dev \
protobuf-c-dev \
graphviz \
ttf-freefont
RUN apk update && apk add --no-cache build-base
COPY ./requirements /requirements
RUN python -m pip install -r /requirements/local.txt
Also note that my dockerfile was working perfectly fine until maybe 4 weeks ago. Then it started throwing this error. I would be happy to completely change the Docker image as long as I can install pandas, matplotlib and numpy in it.
What I also tried:
- Pulling image
python:3.8 - Changing alpine version
- Not using --virtual and removing .build-deps
The full error:
Downloading tables-3.6.1.tar.gz (4.6 MB) ERROR: Command errored out with exit status 1: command: /usr/local/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-g7jsy3s2/tables_ade9c044a3584a07b883ac519dd110db/setup.py'"'"'; file='"'"'/tmp/pip-install-g7jsy3s2/tables_ade9c044a3584a07b883ac519dd110db/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-geym875g cwd: /tmp/pip-install-g7jsy3s2/tables_ade9c044a3584a07b883ac519dd110db/ Complete output (12 lines): * Using Python 3.9.7 (default, Aug 31 2021, 19:01:35) * USE_PKGCONFIG: True /tmp/H5closelwxa646a.c: In function 'main': /tmp/H5closelwxa646a.c:2:5: warning: implicit declaration of function 'H5close' [-Wimplicit-function-declaration] 2 | H5close(); | ^~~~~~~ /usr/lib/gcc/x86_64-alpine-linux-musl/10.3.1/../../../../x86_64-alpine-linux-musl/bin/ld: cannot find -lhdf5 collect2: error: ld returned 1 exit status .. ERROR:: Could not find a local HDF5 installation. You may need to explicitly state where your local HDF5 headers and library can be found by setting the
HDF5_DIRenvironment variable or by using the--hdf5command-line option. ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/2b/32/847ee3f521aae6a0be380d923a736162d698586f444df1ac24b98c65025c/tables-3.6.1.tar.gz#sha256=49a972b8a7c27a8a173aeb05f67acb45fe608b64cd8e9fa667c0962a60b71b49 (from https://pypi.org/simple/tables/) (requires-python:>=3.5). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
