Installation error with Julia 1.9.0

[JackDunnNZ]

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]

Also experiencing similar issues on 1.9 😕

[torfjelde]

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