DominikBuchner
commented
2 months ago Hi Patrick, I'm sure we can fix this. Which os is this?
€: Okay, seems to be MacOS. Have you installed via brew? First thing I would try is to:
- Uninstall boldigger2
- Install PyTables via pip (https://pypi.org/project/tables/)
- Reinstall boldigger2 and see if the problem persists.
Additionally, check this issue which seems to be related to this problem but according to the author is fixed: https://github.com/PyTables/PyTables/issues/998
partridc @.***> schrieb am Di., 23. Juli 2024, 00:37:
Hi. Thanks so much for this great package. Our lab has been using the first version of boldigger with great success. We recently have been trying to update to boldigger2, and I'm coming across some issues when trying to install it. I'm sure it is something I'm doing wrong, but I'm not sure how to fix it. We just upgraded to python3.10 and when trying to install boldigger2, we are hitting an error when it tries to build the wheel. It states that it couldn't find the HDF5 runtime, the LZO 2 runtime,, or the BLOSC2_DIR. I've posted some of the output below that shows the error information. Do you have any suggestions as to what I could be doing wrong? Thanks so much.
Installing build dependencies ... done Getting requirements to build wheel ... error error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> [32 lines of output] /var/folders/rb/vvhcl8md0w7gqct9h41m92kc0000gn/T/blosc_list_compressors6u01n4jz.c:1:10: fatal error: 'blosc.h' file not found
include "blosc.h"
^
~~~~ 1 error generated. ld: warning: ignoring file /usr/local/lib/libblosc2.dylib, building for macOS-arm64 but attempting to link with file built for macOS-x86_64 Undefined symbols for architecture arm64: "_blosc2_list_compressors", referenced from: _main in blosc2_list_compressorskeog9pdp.o ld: symbol(s) not found for architecture arm64 clang: error: linker command failed with exit code 1 (use -v to see invocation) cpuinfo failed, assuming no CPU features: 'flags'
- Using Python 3.10.0 (v3.10.0:b494f5935c, Oct 4 2021, 14:59:19) [Clang 12.0.5 (clang-1205.0.22.11)]
- Found cython 3.0.10
- USE_PKGCONFIG: True
- Found HDF5 headers at /usr/local/include, library at /usr/local/lib. .. WARNING:: Could not find the HDF5 runtime. The HDF5 shared library was not found in the default library paths. In case of runtime problems, please remember to install it.
- Found LZO 2 headers at /usr/local/include, library at /usr/local/lib. .. WARNING:: Could not find the LZO 2 runtime. The LZO 2 shared library was not found in the default library paths. In case of runtime problems, please remember to install it.
- Skipping detection of LZO 1 since LZO 2 has already been found.
- Could not find bzip2 headers and library; disabling support for it.
- Could not find blosc headers and library; using internal sources.
- pkg-config header dirs for blosc2: /Users/runner/work/python-blosc2/python-blosc2/_skbuild/macosx-10.9-x86_64-3.9/cmake-install/include
- pkg-config library dirs for blosc2: /Users/runner/work/python-blosc2/python-blosc2/_skbuild/macosx-10.9-x86_64-3.9/cmake-install/lib
- Run 'blosc2_find_directories_hook' .. ERROR:: Could not find a local blosc2 installation. You may need to explicitly state where your local blosc2 headers and library can be found by setting the BLOSC2_DIR environment variable or by using the --blosc2 command-line option. [end of output]
note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> See above for output.
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partridc
Hi. Thanks so much for this great package. Our lab has been using the first version of boldigger with great success. We recently have been trying to update to boldigger2, and I'm coming across some issues when trying to install it. I'm sure it is something I'm doing wrong, but I'm not sure how to fix it. We just upgraded to python3.10 and when trying to install boldigger2, we are hitting an error when it tries to build the wheel. It states that it couldn't find the HDF5 runtime, the LZO 2 runtime,, or the BLOSC2_DIR. I've posted some of the output below that shows the error information. Do you have any suggestions as to what I could be doing wrong? Thanks so much.
Installing build dependencies ... done Getting requirements to build wheel ... error error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> [32 lines of output] /var/folders/rb/vvhcl8md0w7gqct9h41m92kc0000gn/T/blosc_list_compressors6u01n4jz.c:1:10: fatal error: 'blosc.h' file not found
include "blosc.h"
note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> See above for output.