python-ibmdb: ibm-db broken for many users
We have a tool called detect-secrets that depends on ibm-db. Many of our users can’t properly install/import it right now, and are experiencing the error below (including myself). We’ve had to pull the ibm-db dependency from our installation and make it an optional feature, but we’d prefer to see this fixed permanently at the source. It’s not the first time we’ve seen a similar bug. Thank you!
OS (and OS of all users seeing the bug, so far): Mac OS
Traceback (most recent call last):
File "/Users/justineyster/.pyenv/versions/3.8.6/bin/detect-secrets", line 33, in <module>
sys.exit(load_entry_point('detect-secrets==0.13.1+ibm.29.dss', 'console_scripts', 'detect-secrets')())
File "/Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/detect_secrets/main.py", line 40, in main
plugins = initialize.from_parser_builder(
File "/Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/detect_secrets/plugins/common/initialize.py", line 38, in from_parser_builder
from_plugin_classname(
File "/Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/detect_secrets/plugins/common/initialize.py", line 181, in from_plugin_classname
klass = import_plugins(plugin_filenames)[plugin_classname]
File "/Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/detect_secrets/plugins/common/util.py", line 46, in import_plugins
module = import_module('detect_secrets.plugins.{}'.format(module_name))
File "/Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 783, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/detect_secrets/plugins/db2.py", line 17, in <module>
raise ie
File "/Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/detect_secrets/plugins/db2.py", line 7, in <module>
import ibm_db
ImportError: dlopen(/Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/ibm_db.cpython-38-darwin.so, 2): Symbol not found: ___cxa_throw_bad_array_new_length
Referenced from: /Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/clidriver/lib/libdb2.dylib
Expected in: /usr/lib/libstdc++.6.dylib
in /Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/clidriver/lib/libdb2.dylib
Justins-MBP:whitewater-detect-secrets justineyster$ detect-secrets scan --update .secrets.baseline --db2-scan
Traceback (most recent call last):
File "/Users/justineyster/.pyenv/versions/3.8.6/bin/detect-secrets", line 33, in <module>
sys.exit(load_entry_point('detect-secrets==0.13.1+ibm.29.dss', 'console_scripts', 'detect-secrets')())
File "/Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/detect_secrets/main.py", line 40, in main
plugins = initialize.from_parser_builder(
File "/Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/detect_secrets/plugins/common/initialize.py", line 38, in from_parser_builder
from_plugin_classname(
File "/Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/detect_secrets/plugins/common/initialize.py", line 181, in from_plugin_classname
klass = import_plugins(plugin_filenames)[plugin_classname]
File "/Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/detect_secrets/plugins/common/util.py", line 46, in import_plugins
module = import_module('detect_secrets.plugins.{}'.format(module_name))
File "/Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 783, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/detect_secrets/plugins/db2.py", line 17, in <module>
raise ie
File "/Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/detect_secrets/plugins/db2.py", line 7, in <module>
import ibm_db
ImportError: dlopen(/Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/ibm_db.cpython-38-darwin.so, 2): Symbol not found: ___cxa_throw_bad_array_new_length
Referenced from: /Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/clidriver/lib/libdb2.dylib
Expected in: /usr/lib/libstdc++.6.dylib
in /Users/justineyster/.pyenv/versions/3.8.6/lib/python3.8/site-packages/clidriver/lib/libdb2.dylib
About this issue
- Original URL
- State: closed
- Created 3 years ago
- Reactions: 1
- Comments: 24 (9 by maintainers)
We had a recent upgrade of the clidriver and look the old issue is haunting us again. I will check on the at the earliest and come back with an update.
Thanks.
Looks like we have check the library being shipped and check on the packaging again.
I will work on this and have an update at the earliest.
Thanks.
Hi,
This issue is caused due to the version mismatch of the libstdc++.6.dylib library.
The clidriver downloaded along with the ibm_db driver has a dependency on this particular library. So we are shipping this library along the clidriver for mac in order to resolve the dependency. However for few users this library dependency in met from a different path /usr/lib.
Now this causes the dependency to break and hence the error.
So my suggestion is to try out the following options.
Please let me know if this could be worked out.
Thanks.
Hi,
After considering every options possible we have updated the clidriver from our end to include the new library where the loading path of libstdc++.so.6 has been updated.
@rredburn @drewmullen @justineyster @craigcurtin @jaykodeveloper can you please uninstall the ibm_db driver and install again to allow the new clidriver to be downloaded and test your applications.
This time you should not get the error as the library is now loaded with new dependency path and has been corrected.
Please let me know your observations on the same.
Thanks.
I had a similar issue when I was trying to install the
ibm_db. I had to spend many days digging into it but no luck and finally reached to here. I hope this issue get solved as soon as possible!Hi @amukherjee28, I have same issue when trying to install the ibm_db package. I’m on Python 3.8 Please advise how to work around this lib issue to install the ibm_db package for the short term, assuming there is a longer term fix. I’ve had some colleagues auggest “$ brew install db2” first … is this correct? How does one install python3-devl on mac-os ? Thanks, Craig
I helped a user fix this by exporting DYLD_LIBRARY_PATH as suggested, thanks.
in .zshrc/.bashrc/etc. (modify for your path):
export DYLD_LIBRARY_PATH=/usr/local/lib/python3.9/site-packages/clidriver/lib:$DYLD_LIBRARY_PATHI tried using it with multiple versions of Python using pyenv and saw similar results.