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WonderLandxD / opensdpc

Python library for processing whole slide images (WSIs) in sdpc format
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OSError: version `GLIBC_2.33' not found #12

Closed qin1114 closed 8 months ago

qin1114 commented 8 months ago

I tried to install on my linux system and found error: OSError: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by /home/qinmenghan/miniconda3/envs/clam/lib/python3.7/site-packages/sdpc/LINUX/libDecodeSdpc.so)

Total error information: Traceback (most recent call last): File "/home/qinmenghan/Pathology/code/test_openslide.py", line 1, in import sdpc File "/home/qinmenghan/miniconda3/envs/clam/lib/python3.7/site-packages/sdpc/init.py", line 1, in from sdpc.Sdpc import Sdpc File "/home/qinmenghan/miniconda3/envs/clam/lib/python3.7/site-packages/sdpc/Sdpc.py", line 24, in so = ctypes.CDLL(soPath) File "/home/qinmenghan/miniconda3/envs/clam/lib/python3.7/ctypes/init.py", line 364, in init self._handle = _dlopen(self._name, mode) OSError: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by /home/qinmenghan/miniconda3/envs/clam/lib/python3.7/site-packages/sdpc/LINUX/libDecodeSdpc.so)

It is impossible to update GLIBC which will cause a lot of trouble, I wonder what can I do?

WonderLandxD commented 8 months ago

Maybe you can install the sdpc with a higher python version of conda, e.g. python 3.11.4

qin1114 commented 8 months ago

Thank you for your reply! I've tried to create a new conda environment with python 3.11.2, but the error still exists

Traceback (most recent call last): File "", line 1, in File "/home/qinmenghan/miniconda3/envs/sdpc/lib/python3.11/site-packages/sdpc/init.py", line 1, in from sdpc.Sdpc import Sdpc File "/home/qinmenghan/miniconda3/envs/sdpc/lib/python3.11/site-packages/sdpc/Sdpc.py", line 37, in so = ctypes.CDLL(soPath) ^^^^^^^^^^^^^^^^^^^ File "/home/qinmenghan/miniconda3/envs/sdpc/lib/python3.11/ctypes/init.py", line 376, in init self._handle = _dlopen(self._name, mode) ^^^^^^^^^^^^^^^^^^^^^^^^^ OSError: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by /home/qinmenghan/miniconda3/envs/sdpc/lib/python3.11/site-packages/sdpc/LINUX/libDecodeSdpc.so)

maybe there are something wrong with GLIBC version compatibility, my GLIBC version list with command "strings /lib/x8664-linux-gnu/libc.so.6 |grep GLIBC": GLIBC_2.2.5 GLIBC_2.2.6 GLIBC_2.3 GLIBC_2.3.2 GLIBC_2.3.3 GLIBC_2.3.4 GLIBC_2.4 GLIBC_2.5 GLIBC_2.6 GLIBC_2.7 GLIBC_2.8 GLIBC_2.9 GLIBC_2.10 GLIBC_2.11 GLIBC_2.12 GLIBC_2.13 GLIBC_2.14 GLIBC_2.15 GLIBC_2.16 GLIBC_2.17 GLIBC_2.18 GLIBC_2.22 GLIBC_2.23 GLIBC_2.24 GLIBC_2.25 GLIBC_2.26 GLIBC_2.27 GLIBC_2.28 GLIBC_2.29 GLIBC_2.30 GLIBC_PRIVATE

WonderLandxD commented 8 months ago

You can try to use the old version of the compiled file, here is the download link: https://cloud.tsinghua.edu.cn/f/ff9288a0533d489584da/?dl=1 This requires you to replace all the files in the LINUX folder of sdpc library, which may help you.

qin1114 commented 8 months ago

Thank you very much for your reply! This has truly solved my problem perfectly!