Hi, I am trying to release a small application which bundles a conda environment and a python script. I am using Platypus to turn it into a .app, and I include all necessary resources (libraries, binaries etc) inside the Resources directory. My application works correctly before code signing, and is portable between machines (so I don't think it is the case that the conda environment is missing something). However, after signing, it crashes when it runs one of the programs within the conda environment. I am first signing all .so, .dylib and all files in conda_env/bin as follows: # Within the conda environment directory in Resources find bin -type f | xargs -n1 codesign -f -o runtime --timestamp --sign "Developer ID Application: Whatever (123456789)" find . -name "*.dylib" -o -name "*.so" -type f | xargs -n1 codesign -f -o runtime --timestamp --sign "Developer ID Application: Whatever (123456789)" I am then signing the .app itself codesign -f -o runtime --timestamp --sign "Developer ID Application: Whatever (123456789)" my_app.app Finally, I convert it into a .dmg (with appdmg) and sign that. codesign -f --sign "Developer ID Application: Whatever (123456789)" --timestamp my_app.dmg I submit to the notary service, which succeeds, and then I staple the ticket to the .dmg: xcrun notarytool submit my_app.dmg --keychain-profile my_notarytool_keychain_id --wait xcrun stapler staple my_app.dmg spcl is happy with the signed .app and .dmg and accepts them both. spctl -a -vv my_app.app # my_app.app: accepted # source=Notarized Developer ID # origin=Whatever (123456789) spctl -a -vv -t install my_app.dmg # my_app.dmg: accepted # source=Notarized Developer ID # origin=Whatever (123456789) I have a valid Developer Application ID. All good, right? Except, during execution, the signed .app crashes. When I look in the Console, the error log always looks similar - something like: Exception Type: EXC_BAD_ACCESS (SIGKILL (Code Signature Invalid)) Termination Reason: Namespace CODESIGNING, Code 2 Invalid Page Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libsystem_platform.dylib 0x186e15848 sys_icache_invalidate + 40 1 libllvmlite.dylib 0x2a022f8e8 llvm::sys::Memory::protectMappedMemory(llvm::sys::MemoryBlock const&, unsigned int) + 384 2 libllvmlite.dylib 0x29d765528 LLVMPY_TryAllocateExecutableMemory + 92 3 libffi.8.dylib 0x103abc04c ffi_call_SYSV + 76 etc I think all the .dylib, .so, and binaries are signed in my codesign scripts, except for the libsystem_platform.dylib mentioned in the first line of the log. Could this be the problem? How can I find if I am not signing something that is being used? Are there other types of files that I should be signing that I am missing? I've been trying to fix this for several days and I feel I have tried everything (constructing the conda env in different ways, signing in different ways, e.g. with/without --deep, with/without signing each type of library/binary) to no avail... Any help would be greatly appreciated! All the best, George

Hi, I have created a conda python environment which I have packaged into a .tar.gz (using conda-pack) and which runs correctly when extracted (in this example, it only contains the scipy package). However, when I sign the necessary files within the environment (i.e. the binaries, the dylibs, the .so files), attempting to load scipy.sparse now fails with the error "mapped file has no cdhash, completely unsigned" about one of the .so files. Furthermore, I believe that this file does in fact have a cdhash. The signing process represented by my example below has been working for about a year, and I am unsure why it has suddenly stopped working. I am on a 2020 MacBook Pro with an i7 processor and running Sequoia 15.1.1. Here is a minimal example showing the creating of the conda environment, codesigning, and the error message. Many thanks in advance! # Create and activate conda env > conda create -y -n mwe_env python=3.10 > conda activate mwe_env # Verify scipy not initially installed (mwe_env) > python Python 3.10.16 (main, Dec 11 2024, 10:24:41) [Clang 14.0.6 ] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import scipy Traceback (most recent call last): File "<stdin>", line 1, in <module> ModuleNotFoundError: No module named 'scipy' (mwe_env) > pip install scipy Collecting scipy Downloading scipy-1.15.2-cp310-cp310-macosx_14_0_x86_64.whl.metadata (61 kB) Collecting numpy<2.5,>=1.23.5 (from scipy) Downloading numpy-2.2.4-cp310-cp310-macosx_14_0_x86_64.whl.metadata (62 kB) Downloading scipy-1.15.2-cp310-cp310-macosx_14_0_x86_64.whl (25.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 25.1/25.1 MB 17.3 MB/s eta 0:00:00 Downloading numpy-2.2.4-cp310-cp310-macosx_14_0_x86_64.whl (7.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.0/7.0 MB 16.4 MB/s eta 0:00:00 Installing collected packages: numpy, scipy Successfully installed numpy-2.2.4 scipy-1.15.2 (mwe_env) > python Python 3.10.16 (main, Dec 11 2024, 10:24:41) [Clang 14.0.6 ] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import scipy.sparse >>> # success! # Package conda env (mwe_env) > conda-pack --output mwe_env.tar.gz --name mwe_env Collecting packages... Packing environment at '/path/to/my/conda/envs/mwe_env' to 'mwe_env.tar.gz' [########################################] | 100% Completed | 7.8s (mwe_env) > conda deactivate > mkdir mwe_dir && cd mwe_dir > tar -xzvf ../mwe_env.tar.gz > source bin/activate (mwe_dir) > python Python 3.10.16 (main, Dec 11 2024, 10:24:41) [Clang 14.0.6 ] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import scipy.sparse >>> # success! # Sign the binaries and .dylibs and .so files (mwe_dir) > find bin -type f | xargs -n1 xcrun codesign -f -o runtime --timestamp --sign "Developer ID Application: MY_TEAM_ID" (mwe_dir) > find . -name "*.dylib" -o -name "*.so" -type f | xargs -n1 xcrun codesign -f -o runtime --timestamp --sign "Developer ID Application: MY_TEAM_ID" # the second command prints many lines saying it is "replacing existing signature" (mwe_dir) > python Python 3.10.16 (main, Dec 11 2024, 10:24:41) [Clang 14.0.6 ] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import scipy.sparse Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/path/to/mwe_dir/conda_env/lib/python3.10/site-packages/scipy/sparse/__init__.py", line 315, in <module> from . import csgraph File "/path/to/mwe_dir/conda_env/lib/python3.10/site-packages/scipy/sparse/csgraph/__init__.py", line 187, in <module> from ._laplacian import laplacian File "/path/to/mwe_dir/conda_env/lib/python3.10/site-packages/scipy/sparse/csgraph/_laplacian.py", line 7, in <module> from scipy.sparse.linalg import LinearOperator File "/path/to/mwe_dir/conda_env/lib/python3.10/site-packages/scipy/sparse/linalg/__init__.py", line 134, in <module> from ._eigen import * File "/path/to/mwe_dir/conda_env/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/__init__.py", line 9, in <module> from .arpack import * File "/path/to/mwe_dir/conda_env/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/__init__.py", line 20, in <module> from .arpack import * File "/path/to/mwe_dir/conda_env/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/arpack.py", line 50, in <module> from . import _arpack ImportError: dlopen(/path/to/mwe_dir/conda_env/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/_arpack.cpython-310-darwin.so, 0x0002): tried: '/path/to/mwe_dir/conda_env/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/_arpack.cpython-310-darwin.so' (code signature in <5DD8FC01-7360-3DB9-8273-C8A45ABB19A9> '/path/to/mwe_dir/conda_env/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/_arpack.cpython-310-darwin.so' not valid for use in process: mapped file has no cdhash, completely unsigned? Code has to be at least ad-hoc signed.), '/System/Volumes/Preboot/Cryptexes/OS/path/to/mwe_dir/conda_env/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/_arpack.cpython-310-darwin.so' (no such file), '/path/to/mwe_dir/conda_env/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/_arpack.cpython-310-darwin.so' (code signature in <5DD8FC01-7360-3DB9-8273-C8A45ABB19A9> '/path/to/mwe_dir/conda_env/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/_arpack.cpython-310-darwin.so' not valid for use in process: mapped file has no cdhash, completely unsigned? Code has to be at least ad-hoc signed.) # But: (mwe_dir) > xcrun codesign -dvvv /path/to/mwe_dir/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/_arpack.cpython-310-darwin.so Executable=/path/to/mwe_dir/lib/python3.10/site-packages/scipy/sparse/linalg/_eigen/arpack/_arpack.cpython-310-darwin.so Identifier=_arpack.cpython-310-darwin Format=Mach-O thin (x86_64) CodeDirectory v=20400 size=4318 flags=0x10000(runtime) hashes=129+2 location=embedded Library validation warning=OS X SDK version before 10.9 does not support Library Validation Hash type=sha256 size=32 CandidateCDHash sha256=816731ecd1ad01b38555cbfef8c000628696d0ca CandidateCDHashFull sha256=816731ecd1ad01b38555cbfef8c000628696d0ca53376aebf6fae28d8c02f519 Hash choices=sha256 CMSDigest=816731ecd1ad01b38555cbfef8c000628696d0ca53376aebf6fae28d8c02f519 CMSDigestType=2 CDHash=816731ecd1ad01b38555cbfef8c000628696d0ca Signature size=9000 Authority=Developer ID Application: MY_TEAM_ID Authority=Developer ID Certification Authority Authority=Apple Root CA Timestamp=2 Apr 2025 at 16:24:52 Info.plist=not bound TeamIdentifier=MY_TEAM_ID Sealed Resources=none Internal requirements count=1 size=188