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installation problem #42

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caseylam opened this issue Feb 13, 2024 · 2 comments
Closed

installation problem #42

caseylam opened this issue Feb 13, 2024 · 2 comments

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@caseylam
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Hi,

I'm trying to install specmatch-emp but am running into a problem with hdf5. I installed hdf5, and tried following the error message by setting the HDF5_DIR environment, but am still not able to install. Any chance you might be able to help? Thanks!

Below is the error message.

$ export HDF5_DIR=/opt/mambaforge/envs/astro
$ sudo python setup.py install
running install
/opt/mambaforge/envs/astro/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
/opt/mambaforge/envs/astro/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` and ``easy_install``.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://github.com/pypa/setuptools/issues/917 for details.
        ********************************************************************************

!!
  self.initialize_options()
running bdist_egg
running egg_info
writing SpecMatch_Emp.egg-info/PKG-INFO
writing dependency_links to SpecMatch_Emp.egg-info/dependency_links.txt
writing entry points to SpecMatch_Emp.egg-info/entry_points.txt
writing requirements to SpecMatch_Emp.egg-info/requires.txt
writing top-level names to SpecMatch_Emp.egg-info/top_level.txt
reading manifest file 'SpecMatch_Emp.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'SpecMatch_Emp.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-11.0-arm64/egg
running install_lib
running build_py
creating build/bdist.macosx-11.0-arm64/egg
creating build/bdist.macosx-11.0-arm64/egg/specmatchemp
copying build/lib/specmatchemp/diagplots.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp
copying build/lib/specmatchemp/library.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp
copying build/lib/specmatchemp/analysis.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp
copying build/lib/specmatchemp/detrend.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp
creating build/bdist.macosx-11.0-arm64/egg/specmatchemp/io
copying build/lib/specmatchemp/io/pdplus.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp/io
copying build/lib/specmatchemp/io/specmatchio.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp/io
copying build/lib/specmatchemp/io/h5plus.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp/io
copying build/lib/specmatchemp/io/__init__.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp/io
copying build/lib/specmatchemp/__init__.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp
copying build/lib/specmatchemp/core.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp
creating build/bdist.macosx-11.0-arm64/egg/specmatchemp/utils
copying build/lib/specmatchemp/utils/__init__.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp/utils
copying build/lib/specmatchemp/utils/utils.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp/utils
copying build/lib/specmatchemp/utils/cpsutils.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp/utils
copying build/lib/specmatchemp/plots.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp
copying build/lib/specmatchemp/spectrum.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp
copying build/lib/specmatchemp/shift.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp
copying build/lib/specmatchemp/cli.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp
copying build/lib/specmatchemp/specmatch.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp
copying build/lib/specmatchemp/kernels.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp
creating build/bdist.macosx-11.0-arm64/egg/specmatchemp/buildlib
copying build/lib/specmatchemp/buildlib/read_catalogs.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp/buildlib
copying build/lib/specmatchemp/buildlib/generate_shift_script.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp/buildlib
copying build/lib/specmatchemp/buildlib/shift_references.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp/buildlib
copying build/lib/specmatchemp/buildlib/get_isochrones.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp/buildlib
copying build/lib/specmatchemp/buildlib/__init__.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp/buildlib
copying build/lib/specmatchemp/buildlib/combine_library.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp/buildlib
copying build/lib/specmatchemp/buildlib/shift_spectrum.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp/buildlib
copying build/lib/specmatchemp/match.py -> build/bdist.macosx-11.0-arm64/egg/specmatchemp
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/diagplots.py to diagplots.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/library.py to library.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/analysis.py to analysis.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/detrend.py to detrend.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/io/pdplus.py to pdplus.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/io/specmatchio.py to specmatchio.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/io/h5plus.py to h5plus.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/io/__init__.py to __init__.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/__init__.py to __init__.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/core.py to core.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/utils/__init__.py to __init__.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/utils/utils.py to utils.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/utils/cpsutils.py to cpsutils.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/plots.py to plots.cpython-311.pyc
build/bdist.macosx-11.0-arm64/egg/specmatchemp/plots.py:102: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if param_x is 'Teff':
build/bdist.macosx-11.0-arm64/egg/specmatchemp/plots.py:108: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if param_x is 'feh':
build/bdist.macosx-11.0-arm64/egg/specmatchemp/plots.py:111: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if param_x is 'radius':
build/bdist.macosx-11.0-arm64/egg/specmatchemp/plots.py:117: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if param_y is 'radius':
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/spectrum.py to spectrum.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/shift.py to shift.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/cli.py to cli.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/specmatch.py to specmatch.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/kernels.py to kernels.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/buildlib/read_catalogs.py to read_catalogs.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/buildlib/generate_shift_script.py to generate_shift_script.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/buildlib/shift_references.py to shift_references.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/buildlib/get_isochrones.py to get_isochrones.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/buildlib/__init__.py to __init__.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/buildlib/combine_library.py to combine_library.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/buildlib/shift_spectrum.py to shift_spectrum.cpython-311.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/specmatchemp/match.py to match.cpython-311.pyc
creating build/bdist.macosx-11.0-arm64/egg/EGG-INFO
copying SpecMatch_Emp.egg-info/PKG-INFO -> build/bdist.macosx-11.0-arm64/egg/EGG-INFO
copying SpecMatch_Emp.egg-info/SOURCES.txt -> build/bdist.macosx-11.0-arm64/egg/EGG-INFO
copying SpecMatch_Emp.egg-info/dependency_links.txt -> build/bdist.macosx-11.0-arm64/egg/EGG-INFO
copying SpecMatch_Emp.egg-info/entry_points.txt -> build/bdist.macosx-11.0-arm64/egg/EGG-INFO
copying SpecMatch_Emp.egg-info/requires.txt -> build/bdist.macosx-11.0-arm64/egg/EGG-INFO
copying SpecMatch_Emp.egg-info/top_level.txt -> build/bdist.macosx-11.0-arm64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
creating 'dist/SpecMatch_Emp-0.3-py3.11.egg' and adding 'build/bdist.macosx-11.0-arm64/egg' to it
removing 'build/bdist.macosx-11.0-arm64/egg' (and everything under it)
Processing SpecMatch_Emp-0.3-py3.11.egg
Removing /opt/mambaforge/envs/astro/lib/python3.11/site-packages/SpecMatch_Emp-0.3-py3.11.egg
Copying SpecMatch_Emp-0.3-py3.11.egg to /opt/mambaforge/envs/astro/lib/python3.11/site-packages
Adding SpecMatch-Emp 0.3 to easy-install.pth file
Installing smemp script to /opt/mambaforge/envs/astro/bin

Installed /opt/mambaforge/envs/astro/lib/python3.11/site-packages/SpecMatch_Emp-0.3-py3.11.egg
Processing dependencies for SpecMatch-Emp==0.3
Searching for h5py
Reading https://pypi.org/simple/h5py/
Downloading https://files.pythonhosted.org/packages/8d/70/2b0b99507287f66e71a6b2e66c5ad2ec2461ef2c534668eef96c3b48eb6d/h5py-3.10.0-cp311-cp311-macosx_11_0_arm64.whl#sha256=667fe23ab33d5a8a6b77970b229e14ae3bb84e4ea3382cc08567a02e1499eedd
Best match: h5py 3.10.0
Processing h5py-3.10.0-cp311-cp311-macosx_11_0_arm64.whl
removing '/opt/mambaforge/envs/astro/lib/python3.11/site-packages/h5py-3.10.0-py3.11-macosx-11.0-arm64.egg' (and everything under it)
Installing h5py-3.10.0-cp311-cp311-macosx_11_0_arm64.whl to /opt/mambaforge/envs/astro/lib/python3.11/site-packages
Adding h5py 3.10.0 to easy-install.pth file

Installed /opt/mambaforge/envs/astro/lib/python3.11/site-packages/h5py-3.10.0-py3.11-macosx-11.0-arm64.egg
Searching for tables>=3.0
Reading https://pypi.org/simple/tables/
Downloading https://files.pythonhosted.org/packages/31/83/8a13be8338219c3fe0aa7357d1ec4edb27bc346e0f224df7212892b243b5/tables-3.9.2.tar.gz#sha256=d470263c2e50c4b7c8635a0d99ac1ff2f9e704c24d71e5fa33c4529e7d0ad9c3
Best match: tables 3.9.2
Processing tables-3.9.2.tar.gz
Writing /tmp/easy_install-axvdw5eg/tables-3.9.2/setup.cfg
Running tables-3.9.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-axvdw5eg/tables-3.9.2/egg-dist-tmp-ip85mysn
cpuinfo failed, assuming no CPU features: 'flags'
* Using Python 3.11.5 | packaged by conda-forge | (main, Aug 27 2023, 03:33:12) [Clang 15.0.7 ]
* Found cython 3.0.7
* USE_PKGCONFIG: True
creating tmp
creating tmp/easy_install-axvdw5eg
creating tmp/easy_install-axvdw5eg/tables-3.9.2
creating tmp/easy_install-axvdw5eg/tables-3.9.2/temp
clang -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/mambaforge/envs/astro/include -arch arm64 -fPIC -O2 -isystem /opt/mambaforge/envs/astro/include -arch arm64 -I/opt/mambaforge/envs/astro/include/python3.11 -c /tmp/easy_install-axvdw5eg/tables-3.9.2/temp/H5closep6rx4ua4.c -o tmp/easy_install-axvdw5eg/tables-3.9.2/temp/H5closep6rx4ua4.o
clang tmp/easy_install-axvdw5eg/tables-3.9.2/temp/H5closep6rx4ua4.o -lhdf5 -o a.out
ld: library not found for -lhdf5
clang: error: linker command failed with exit code 1 (use -v to see invocation)
.. 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_DIR`` environment
   variable or by using the ``--hdf5`` command-line option.
error: Setup script exited with 1
@samuelyeewl
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samuelyeewl commented Feb 13, 2024 via email

@caseylam
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Hi Sam,

Thanks for the quick reply, that worked and I was able to install!

Casey

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@samuelyeewl @caseylam