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Installation error with Julia 1.9.0 #236

Open JackDunnNZ opened 1 year ago

JackDunnNZ commented 1 year ago

I don't think this is a bug in Conda.jl, but I am seeing the following error during the miniconda installation when running under Julia 1.9.0 on M1 Mac (13.3.1):

critical libmamba Could not codesign executable: Invalid argument
ERROR: failed process: Process(`/var/folders/5y/x64z5hsx13bf0x35qdg_n2l80000gn/T/installer.sh -b -f -p /tmp/conda/.julia/conda/3/aarch64`, ProcessExited(1)) [1]
Full log ``` julia> versioninfo() Julia Version 1.9.0 Commit 8e630552924 (2023-05-07 11:25 UTC) Platform Info: OS: macOS (arm64-apple-darwin22.4.0) CPU: 8 × Apple M1 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-14.0.6 (ORCJIT, apple-m1) Threads: 1 on 4 virtual cores Environment: JULIA_DEPOT_PATH = /tmp/conda/.julia (conda) pkg> st Status `/private/tmp/conda/Project.toml` [8f4d0f93] Conda v1.8.0 julia> using Conda julia> Conda.add("numpy") [ Info: Downloading miniconda installer ... [ Info: Installing miniconda ... PREFIX=/tmp/conda/.julia/conda/3/aarch64 Unpacking payload ... Extracting bzip2-1.0.8-h3422bc3_4.tar.bz2 Extracting ca-certificates-2022.12.7-h4653dfc_0.conda Extracting libcxx-16.0.0-h75e25f2_0.conda Extracting libffi-3.4.2-h3422bc3_5.tar.bz2 Extracting libzlib-1.2.13-h03a7124_4.tar.bz2 Extracting ncurses-6.3-h07bb92c_1.tar.bz2 Extracting python_abi-3.10-3_cp310.conda Extracting tzdata-2023c-h71feb2d_0.conda Extracting xz-5.2.6-h57fd34a_0.tar.bz2 Extracting libsqlite-3.40.0-h76d750c_0.tar.bz2 Extracting openssl-3.1.0-h03a7124_0.conda Extracting readline-8.2-h92ec313_1.conda Extracting tk-8.6.12-he1e0b03_0.tar.bz2 Extracting zstd-1.5.2-hf913c23_6.conda Extracting python-3.10.10-h3ba56d0_0_cpython.conda Extracting certifi-2022.12.7-pyhd8ed1ab_0.conda Extracting charset-normalizer-3.1.0-pyhd8ed1ab_0.conda Extracting colorama-0.4.6-pyhd8ed1ab_0.tar.bz2 Extracting idna-3.4-pyhd8ed1ab_0.tar.bz2 Extracting pluggy-1.0.0-pyhd8ed1ab_5.tar.bz2 Extracting pycosat-0.6.4-py310h8e9501a_1.tar.bz2 Extracting pycparser-2.21-pyhd8ed1ab_0.tar.bz2 Extracting pysocks-1.7.1-pyha2e5f31_6.tar.bz2 Extracting ruamel.yaml.clib-0.2.7-py310h8e9501a_1.conda Extracting setuptools-65.6.3-pyhd8ed1ab_0.conda Extracting toolz-0.12.0-pyhd8ed1ab_0.tar.bz2 Extracting wheel-0.40.0-pyhd8ed1ab_0.conda Extracting cffi-1.15.1-py310h2399d43_3.conda Extracting pip-23.0.1-pyhd8ed1ab_0.conda Extracting ruamel.yaml-0.17.21-py310h8e9501a_3.conda Extracting tqdm-4.65.0-pyhd8ed1ab_1.conda Extracting brotlipy-0.7.0-py310h8e9501a_1005.tar.bz2 Extracting cryptography-40.0.1-py310hfc83b78_0.conda Extracting zstandard-0.19.0-py310had9512b_1.conda Extracting conda-package-streaming-0.7.0-pyhd8ed1ab_1.conda Extracting pyopenssl-23.1.1-pyhd8ed1ab_0.conda Extracting conda-package-handling-2.0.2-pyh38be061_0.conda Extracting urllib3-1.26.15-pyhd8ed1ab_0.conda Extracting requests-2.28.2-pyhd8ed1ab_1.conda Extracting conda-23.1.0-py310hbe9552e_0.conda Installing base environment... __ __ ______ ___ ____ _____ ___ / /_ ____ _ / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/ / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ / / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/ /_/ warning libmamba Could not find macOS version by calling 'sw_vers -productVersion' Please file a bug report. Error: Invalid argument warning libmamba osx version not found (virtual package skipped) Transaction Prefix: /private/tmp/conda/.julia/conda/3/aarch64 Updating specs: - conda-forge/osx-arm64::bzip2==1.0.8=h3422bc3_4[md5=fc76ace7b94fb1f694988ab1b14dd248] - conda-forge/osx-arm64::ca-certificates==2022.12.7=h4653dfc_0[md5=7dc111916edc905957b7417a247583b6] - conda-forge/osx-arm64::libcxx==16.0.0=h75e25f2_0[md5=d6abc5c6b3d752b6c32bd8585171da5d] - conda-forge/osx-arm64::libffi==3.4.2=h3422bc3_5[md5=086914b672be056eb70fd4285b6783b6] - conda-forge/osx-arm64::libzlib==1.2.13=h03a7124_4[md5=780852dc54c4c07e64b276a97f89c162] - conda-forge/osx-arm64::ncurses==6.3=h07bb92c_1[md5=db86e5a978380a13f5559f97afdfe99d] - conda-forge/osx-arm64::python_abi==3.10=3_cp310[md5=3f2b2974db21a33a2f45b0c9abbb7516] - conda-forge/noarch::tzdata==2023c=h71feb2d_0[md5=939e3e74d8be4dac89ce83b20de2492a] - conda-forge/osx-arm64::xz==5.2.6=h57fd34a_0[md5=39c6b54e94014701dd157f4f576ed211] - conda-forge/osx-arm64::libsqlite==3.40.0=h76d750c_0[md5=d090fcec993f4ef0a90e6df7f231a273] - conda-forge/osx-arm64::openssl==3.1.0=h03a7124_0[md5=a67e5c82b81441e972733d95e2d8832b] - conda-forge/osx-arm64::readline==8.2=h92ec313_1[md5=8cbb776a2f641b943d413b3e19df71f4] - conda-forge/osx-arm64::tk==8.6.12=he1e0b03_0[md5=2cb3d18eac154109107f093860bd545f] - conda-forge/osx-arm64::zstd==1.5.2=hf913c23_6[md5=8f346953ef63bf5fb482488a659adcf3] - conda-forge/osx-arm64::python==3.10.10=h3ba56d0_0_cpython[md5=5d0b6cef6d5b04df14a02d25c5295bcf] - conda-forge/noarch::certifi==2022.12.7=pyhd8ed1ab_0[md5=fb9addc3db06e56abe03e0e9f21a63e6] - conda-forge/noarch::charset-normalizer==3.1.0=pyhd8ed1ab_0[md5=7fcff9f6f123696e940bda77bd4d6551] - conda-forge/noarch::colorama==0.4.6=pyhd8ed1ab_0[md5=3faab06a954c2a04039983f2c4a50d99] - conda-forge/noarch::idna==3.4=pyhd8ed1ab_0[md5=34272b248891bddccc64479f9a7fffed] - conda-forge/noarch::pluggy==1.0.0=pyhd8ed1ab_5[md5=7d301a0d25f424d96175f810935f0da9] - conda-forge/osx-arm64::pycosat==0.6.4=py310h8e9501a_1[md5=a4fc977e05bd8a0be63bd96f8625df8f] - conda-forge/noarch::pycparser==2.21=pyhd8ed1ab_0[md5=076becd9e05608f8dc72757d5f3a91ff] - conda-forge/noarch::pysocks==1.7.1=pyha2e5f31_6[md5=2a7de29fb590ca14b5243c4c812c8025] - conda-forge/osx-arm64::ruamel.yaml.clib==0.2.7=py310h8e9501a_1[md5=586a1f48c1daf7874844ab090af6f191] - conda-forge/noarch::setuptools==65.6.3=pyhd8ed1ab_0[md5=9600fc9524d3f821e6a6d58c52f5bf5a] - conda-forge/noarch::toolz==0.12.0=pyhd8ed1ab_0[md5=92facfec94bc02d6ccf42e7173831a36] - conda-forge/noarch::wheel==0.40.0=pyhd8ed1ab_0[md5=49bb0d9e60ce1db25e151780331bb5f3] - conda-forge/osx-arm64::cffi==1.15.1=py310h2399d43_3[md5=d0ae0fd0363f0baef9d485c857d1d421] - conda-forge/noarch::pip==23.0.1=pyhd8ed1ab_0[md5=8025ca83b8ba5430b640b83917c2a6f7] - conda-forge/osx-arm64::ruamel.yaml==0.17.21=py310h8e9501a_3[md5=01b456ee2ef99281ddd9e9f773993e00] - conda-forge/noarch::tqdm==4.65.0=pyhd8ed1ab_1[md5=ed792aff3acb977d09c7013358097f83] - conda-forge/osx-arm64::brotlipy==0.7.0=py310h8e9501a_1005[md5=0dfdc1c2e2fa6d9a1cee4798a9e9454d] - conda-forge/osx-arm64::cryptography==40.0.1=py310hfc83b78_0[md5=6f7258e4ab49a2de79a4e6a035af3edc] - conda-forge/osx-arm64::zstandard==0.19.0=py310had9512b_1[md5=12e7e195efb08cf15859c7d900fa8ace] - conda-forge/noarch::conda-package-streaming==0.7.0=pyhd8ed1ab_1[md5=1a2fa9e53cfbc2e4d9ab21990805a436] - conda-forge/noarch::pyopenssl==23.1.1=pyhd8ed1ab_0[md5=0b34aa3ab7e7ccb1765a03dd9ed29938] - conda-forge/noarch::conda-package-handling==2.0.2=pyh38be061_0[md5=44800e9bd13143292097c65e57323038] - conda-forge/noarch::urllib3==1.26.15=pyhd8ed1ab_0[md5=27db656619a55d727eaf5a6ece3d2fd6] - conda-forge/noarch::requests==2.28.2=pyhd8ed1ab_1[md5=3bfbd6ead1d7299ed46dab3a7bf0bc8c] - conda-forge/osx-arm64::conda==23.1.0=py310hbe9552e_0[md5=6cda664b1e5a8047103dad825a30e2e2] Package Version Build Channel Size ──────────────────────────────────────────────────────────────────────────────────── Install: ──────────────────────────────────────────────────────────────────────────────────── + brotlipy 0.7.0 py310h8e9501a_1005 conda-forge Cached + bzip2 1.0.8 h3422bc3_4 conda-forge Cached + ca-certificates 2022.12.7 h4653dfc_0 conda-forge Cached + certifi 2022.12.7 pyhd8ed1ab_0 conda-forge Cached + cffi 1.15.1 py310h2399d43_3 conda-forge Cached + charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge Cached + colorama 0.4.6 pyhd8ed1ab_0 conda-forge Cached + conda 23.1.0 py310hbe9552e_0 conda-forge Cached + conda-package-handling 2.0.2 pyh38be061_0 conda-forge Cached + conda-package-streaming 0.7.0 pyhd8ed1ab_1 conda-forge Cached + cryptography 40.0.1 py310hfc83b78_0 conda-forge Cached + idna 3.4 pyhd8ed1ab_0 conda-forge Cached + libcxx 16.0.0 h75e25f2_0 conda-forge Cached + libffi 3.4.2 h3422bc3_5 conda-forge Cached + libsqlite 3.40.0 h76d750c_0 conda-forge Cached + libzlib 1.2.13 h03a7124_4 conda-forge Cached + ncurses 6.3 h07bb92c_1 conda-forge Cached + openssl 3.1.0 h03a7124_0 conda-forge Cached + pip 23.0.1 pyhd8ed1ab_0 conda-forge Cached + pluggy 1.0.0 pyhd8ed1ab_5 conda-forge Cached + pycosat 0.6.4 py310h8e9501a_1 conda-forge Cached + pycparser 2.21 pyhd8ed1ab_0 conda-forge Cached + pyopenssl 23.1.1 pyhd8ed1ab_0 conda-forge Cached + pysocks 1.7.1 pyha2e5f31_6 conda-forge Cached + python 3.10.10 h3ba56d0_0_cpython conda-forge Cached + python_abi 3.10 3_cp310 conda-forge Cached + readline 8.2 h92ec313_1 conda-forge Cached + requests 2.28.2 pyhd8ed1ab_1 conda-forge Cached + ruamel.yaml 0.17.21 py310h8e9501a_3 conda-forge Cached + ruamel.yaml.clib 0.2.7 py310h8e9501a_1 conda-forge Cached + setuptools 65.6.3 pyhd8ed1ab_0 conda-forge Cached + tk 8.6.12 he1e0b03_0 conda-forge Cached + toolz 0.12.0 pyhd8ed1ab_0 conda-forge Cached + tqdm 4.65.0 pyhd8ed1ab_1 conda-forge Cached + tzdata 2023c h71feb2d_0 conda-forge Cached + urllib3 1.26.15 pyhd8ed1ab_0 conda-forge Cached + wheel 0.40.0 pyhd8ed1ab_0 conda-forge Cached + xz 5.2.6 h57fd34a_0 conda-forge Cached + zstandard 0.19.0 py310had9512b_1 conda-forge Cached + zstd 1.5.2 hf913c23_6 conda-forge Cached Summary: Install: 40 packages Total download: 0 B ──────────────────────────────────────────────────────────────────────────────────── Transaction starting Linking bzip2-1.0.8-h3422bc3_4 Linking ca-certificates-2022.12.7-h4653dfc_0 Linking libcxx-16.0.0-h75e25f2_0 Linking libffi-3.4.2-h3422bc3_5 critical libmamba Could not codesign executable: Invalid argument ERROR: failed process: Process(`/var/folders/5y/x64z5hsx13bf0x35qdg_n2l80000gn/T/installer.sh -b -f -p /tmp/conda/.julia/conda/3/aarch64`, ProcessExited(1)) [1] Stacktrace: [1] pipeline_error @ ./process.jl:565 [inlined] [2] run(::Cmd; wait::Bool) @ Base ./process.jl:480 [3] run @ ./process.jl:477 [inlined] [4] _install_conda(env::String, force::Bool) @ Conda /tmp/conda/.julia/packages/Conda/kOnIE/src/Conda.jl:208 [5] _install_conda(env::String) @ Conda /tmp/conda/.julia/packages/Conda/kOnIE/src/Conda.jl:191 [6] runconda(args::Cmd, env::String) @ Conda /tmp/conda/.julia/packages/Conda/kOnIE/src/Conda.jl:126 [7] add(pkg::String, env::String; channel::String) @ Conda /tmp/conda/.julia/packages/Conda/kOnIE/src/Conda.jl:224 [8] add @ /tmp/conda/.julia/packages/Conda/kOnIE/src/Conda.jl:222 [inlined] [9] add(pkg::String) @ Conda /tmp/conda/.julia/packages/Conda/kOnIE/src/Conda.jl:222 [10] top-level scope @ REPL[3]:1 ```

If I run this failed process in shell mode within Julia, I get the same error:

shell> /var/folders/5y/x64z5hsx13bf0x35qdg_n2l80000gn/T/installer.sh -b -f -p /tmp/conda/.julia/conda/3/aarch64
...
Linking libffi-3.4.2-h3422bc3_5
critical libmamba Could not codesign executable: Invalid argument

However if I just run that command directly in a shell it works fine, and also works fine under Julia 1.8.5, so it seems like something about Julia 1.9 is causing the problem.

There's also a message in there: 

warning  libmamba Could not find macOS version by calling 'sw_vers -productVersion'
    Please file a bug report.
    Error: Invalid argument

But this command definitely works.

Like I said, I think this is probably a Julia 1.9 issue as everything works fine on the same machine in 1.8.5 but just wanted to report it here for reference. It didn't reproduce on any other OS, nor was I able to replicate on another M1 Mac I tried with.

torfjelde commented 1 year ago

Also experiencing similar issues on 1.9 :confused:

torfjelde commented 1 year ago

Okay, so what helped for me was deleting ~/.julia/conda and then rebuilding PyCall and Conda. Seems to have done the trick.