Crashes using mamba on macOS Sonoma

[pauldmccarthy]

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

Howdy,

(Reporting here for posterity - I think the main issue is curl/curl#11893).

I have a couple of users reporting crashes when running mamba env update on macOS Sonoma. I don't have access to a Sonoma machine, so can only provide a few more details (if necessary), but I think the most relevant message that is emitted is:

*** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: '-[__NSCFString stringByStandardizingPath]: unrecognized selector sent to instance 0x600003af0050'

Searching around the internet, I stumbled across a recently fixed issue in curl.

So I suspect that this issue will be resolved with a new miniforge/mambaforge release that bundles the latest curl 8.4.0.

Judging by #511, it sounds like this is already on the cards, so hopefully this be resolved without any further effort.

Thanks!

Installed packages

Environment installed via [`Mambaforge-23.3.1-1-MacOSX-arm64.sh`](https://github.com/conda-forge/miniforge/releases/download/23.3.1-1/Mambaforge-23.3.1-1-MacOSX-arm64.sh)

Environment info

Environment installed via [`Mambaforge-23.3.1-1-MacOSX-arm64.sh`](https://github.com/conda-forge/miniforge/releases/download/23.3.1-1/Mambaforge-23.3.1-1-MacOSX-arm64.sh)

[victorlin]

Just came across this. It seems to affect any attempt to install a package using mamba. Here's relevant snippets of output from a simple command mamba create -n tmp python=3.10 --yes:

Output

  Package               Version  Build            Channel         Size
────────────────────────────────────────────────────────────────────────
  Install:
────────────────────────────────────────────────────────────────────────

  + bzip2                 1.0.8  h1de35cc_0       pkgs/main     Cached
  + ncurses                 6.4  hcec6c5f_0       pkgs/main     Cached
  + zlib                 1.2.13  h4dc903c_0       pkgs/main     Cached
  + libffi                3.4.4  hecd8cb5_0       pkgs/main     Cached
  + xz                    5.4.5  h6c40b1e_0       pkgs/main      374kB
  + ca-certificates  2023.08.22  hecd8cb5_0       pkgs/main     Cached
  + readline                8.2  hca72f7f_0       pkgs/main     Cached
  + tk                   8.6.12  h5d9f67b_0       pkgs/main     Cached
  + openssl              3.0.12  hca72f7f_0       pkgs/main     Cached
  + sqlite               3.41.2  h6c40b1e_0       pkgs/main     Cached
  + tzdata                2023c  h04d1e81_0       pkgs/main     Cached
  + python              3.10.13  h5ee71fb_0       pkgs/main       14MB
  + wheel                0.41.2  py310hecd8cb5_0  pkgs/main      113kB
  + setuptools           68.0.0  py310hecd8cb5_0  pkgs/main      978kB
  + pip                  23.3.1  py310hecd8cb5_0  pkgs/main        3MB

  Summary:

  Install: 15 packages

  Total download: 18MB

────────────────────────────────────────────────────────────────────────


[+] 0.1s
Downloading  (5) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━  59.2kB /  18.1MB pip                        0.0s
Extracting       ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━       0 /       5                            0.0s*** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: '-[__NSCFString stringByStandardizingPath]: unrecognized selector sent to instance 0x600000dac680'
*** First throw call stack:
(
	0   CoreFoundation                      0x00007ff807dadaae __exceptionPreprocess + 242
	1   libobjc.A.dylib                     0x00007ff8078a45ff objc_exception_throw + 48
	2   CoreFoundation                      0x00007ff807e529dd -[NSObject(NSObject) __retain_OA] + 0
	3   CoreFoundation                      0x00007ff807d1bff8 ___forwarding___ + 1379
	4   CoreFoundation                      0x00007ff807d1ba08 _CF_forwarding_prep_0 + 120
	5   Foundation                          0x00007ff808be0b8f -[NSProcessInfo arguments] + 203
	6   CoreFoundation                      0x00007ff807e20572 __getDefaultArguments_block_invoke + 101
	7   libdispatch.dylib                   0x00007ff807ab959a _dispatch_client_callout + 8
	8   libdispatch.dylib                   0x00007ff807aba7cb _dispatch_once_callout + 20
	9   CoreFoundation                      0x00007ff807e1ff83 _addBackstopValuesForIdentifierAndSource + 626
	10  CoreFoundation                      0x00007ff807ce7fc4 __81-[_CFXPreferences(SourceAdditions) withNamedVolatileSourceForIdentifier:perform:]_block_invoke + 151
	11  CoreFoundation                      0x00007ff807e1fc4c -[_CFXPreferences withNamedVolatileSourceForIdentifier:perform:] + 241
	12  CoreFoundation                      0x00007ff807ceec00 -[CFPrefsSearchListSource addNamedVolatileSourceForIdentifier:] + 98
	13  CoreFoundation                      0x00007ff807e5a479 __108-[_CFXPreferences(SearchListAdditions) withSearchListForIdentifier:container:cloudConfigurationURL:perform:]_block_invoke.160 + 310
	14  CoreFoundation                      0x00007ff807e5a146 -[_CFXPreferences withSearchLists:] + 60
	15  CoreFoundation                      0x00007ff807ce95e6 __108-[_CFXPreferences(SearchListAdditions) withSearchListForIdentifier:container:cloudConfigurationURL:perform:]_block_invoke + 278
	16  CoreFoundation                      0x00007ff807e5a2be -[_CFXPreferences withSearchListForIdentifier:container:cloudConfigurationURL:perform:] + 349
	17  CoreFoundation                      0x00007ff807ce906b -[_CFXPreferences copyAppValueForKey:identifier:container:configurationURL:] + 124
	18  CoreFoundation                      0x00007ff807ce8fb5 _CFPreferencesCopyAppValueWithContainerAndConfiguration + 101
	19  SystemConfiguration                 0x00007ff8088978bb SCDynamicStoreCopyProxiesWithOptions + 155
	20  libcurl.4.dylib                     0x000000010e4aa34b Curl_macos_init + 11
	21  libcurl.4.dylib                     0x000000010e487d31 global_init + 145
	22  libcurl.4.dylib                     0x000000010e487c88 curl_global_init + 56
	23  libmamba.2.0.0.dylib                0x000000010d872b31 _GLOBAL__sub_I_singletons.cpp + 17
	24  dyld                                0x0000000204a7ffea ___ZZNK5dyld46Loader25findAndRunAllInitializersERNS_12RuntimeStateEENK3$_0clEv_block_invoke + 182
	25  dyld                                0x0000000204ac15d4 ___ZNK5dyld313MachOAnalyzer18forEachInitializerER11DiagnosticsRKNS0_15VMAddrConverterEU13block_pointerFvjEPKv_block_invoke.175 + 133
	26  dyld                                0x0000000204ab5963 ___ZNK5dyld39MachOFile14forEachSectionEU13block_pointerFvRKNS0_11SectionInfoEbRbE_block_invoke + 543
	27  dyld                                0x0000000204a6307f _ZNK5dyld39MachOFile18forEachLoadCommandER11DiagnosticsU13block_pointerFvPK12load_commandRbE + 249
	28  dyld                                0x0000000204ab4b2c _ZNK5dyld39MachOFile14forEachSectionEU13block_pointerFvRKNS0_11SectionInfoEbRbE + 176
	29  dyld                                0x0000000204ab7154 _ZNK5dyld39MachOFile32forEachInitializerPointerSectionER11DiagnosticsU13block_pointerFvjjRbE + 116
	30  dyld                                0x0000000204ac130a _ZNK5dyld313MachOAnalyzer18forEachInitializerER11DiagnosticsRKNS0_15VMAddrConverterEU13block_pointerFvjEPKv + 390
	31  dyld                                0x0000000204a7cd1c _ZNK5dyld46Loader25findAndRunAllInitializersERNS_12RuntimeStateE + 222
	32  dyld                                0x0000000204a825eb _ZNK5dyld416JustInTimeLoader15runInitializersERNS_12RuntimeStateE + 21
	33  dyld                                0x0000000204a7cf11 _ZNK5dyld46Loader23runInitializersBottomUpERNS_12RuntimeStateERN5dyld35ArrayIPKS0_EE + 181
	34  dyld                                0x0000000204a7cef3 _ZNK5dyld46Loader23runInitializersBottomUpERNS_12RuntimeStateERN5dyld35ArrayIPKS0_EE + 151
	35  dyld                                0x0000000204a80060 _ZZNK5dyld46Loader38runInitializersBottomUpPlusUpwardLinksERNS_12RuntimeStateEENK3$_1clEv + 98
	36  dyld                                0x0000000204a7cfa7 _ZNK5dyld46Loader38runInitializersBottomUpPlusUpwardLinksERNS_12RuntimeStateE + 93
	37  dyld                                0x0000000204a9e9ad _ZN5dyld44APIs25runAllInitializersForMainEv + 317
	38  dyld                                0x0000000204a68261 _ZN5dyld4L7prepareERNS_4APIsEPKN5dyld313MachOAnalyzerE + 3397
	39  dyld                                0x0000000204a6733f start + 1839
)
libc++abi: terminating due to uncaught exception of type NSException
xz                                                 374.4kB @   2.5MB/s  0.2s
wheel                                              112.7kB @ 587.6kB/s  0.2s
xz-5.4.5-h6c40b1e_0.conda extraction failed
[+] 0.2s


# the above error is repeated for a few packages
# - victorlin


libc++abi: terminating due to uncaught exception of type NSException
python-3.10.13-h5ee71fb_0.conda extraction failed
Found incorrect download: xz. Aborting

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/Users/victor/miniconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 17, in __call__
        return func(*args, **kwargs)
               ^^^^^^^^^^^^^^^^^^^^^
      File "/Users/victor/miniconda3/lib/python3.11/site-packages/mamba/mamba.py", line 956, in exception_converter
        raise e
      File "/Users/victor/miniconda3/lib/python3.11/site-packages/mamba/mamba.py", line 949, in exception_converter
        exit_code = _wrapped_main(*args, **kwargs)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/Users/victor/miniconda3/lib/python3.11/site-packages/mamba/mamba.py", line 895, in _wrapped_main
        result = do_call(parsed_args, p)
                 ^^^^^^^^^^^^^^^^^^^^^^^
      File "/Users/victor/miniconda3/lib/python3.11/site-packages/mamba/mamba.py", line 764, in do_call
        exit_code = create(args, parser)
                    ^^^^^^^^^^^^^^^^^^^^
      File "/Users/victor/miniconda3/lib/python3.11/site-packages/mamba/mamba.py", line 602, in create
        return install(args, parser, "create")
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/Users/victor/miniconda3/lib/python3.11/site-packages/mamba/mamba.py", line 558, in install
        transaction.fetch_extract_packages()
    RuntimeError: Found incorrect download: xz. Aborting

`$ /Users/victor/miniconda3/bin/mamba create -n tmp python=3.10 --yes`

  environment variables:
                 CIO_TEST=<not set>
        CONDA_DEFAULT_ENV=base
                CONDA_EXE=/Users/victor/miniconda3/bin/conda
             CONDA_PREFIX=/Users/victor/miniconda3
    CONDA_PROMPT_MODIFIER=(base)
         CONDA_PYTHON_EXE=/Users/victor/miniconda3/bin/python
               CONDA_ROOT=/Users/victor/miniconda3
              CONDA_SHLVL=1
           CURL_CA_BUNDLE=<not set>
                 GEM_PATH=/Users/victor/.gem/ruby/3.1.3:/Users/victor/.rubies/ruby-
                          3.1.3/lib/ruby/gems/3.1.0
                 INFOPATH=/opt/homebrew/share/info:
               LD_PRELOAD=<not set>
                  MANPATH=/opt/homebrew/share/man::
                     PATH=/Users/victor/miniconda3/bin:/Users/victor/.micromamba/condabin:/Users
                          /victor/.gem/ruby/3.1.3/bin:/Users/victor/.rubies/ruby-
                          3.1.3/lib/ruby/gems/3.1.0/bin:/Users/victor/.rubies/ruby-
                          3.1.3/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/Users/victor/.bin:/usr
                          /local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin
                          :/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local
                          /bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/b
                          in:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/app
                          leinternal/bin:/Library/Apple/usr/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : base
    active env location : /Users/victor/miniconda3
            shell level : 1
       user config file : /Users/victor/.condarc
 populated config files : 
          conda version : 23.11.0
    conda-build version : not installed
         python version : 3.11.5.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=m1
                          __conda=23.11.0=0
                          __osx=10.16=0
                          __unix=0=0
       base environment : /Users/victor/miniconda3  (writable)
      conda av data dir : /Users/victor/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/victor/miniconda3/pkgs
                          /Users/victor/.conda/pkgs
       envs directories : /Users/victor/miniconda3/envs
                          /Users/victor/.conda/envs
               platform : osx-64
             user-agent : conda/23.11.0 requests/2.31.0 CPython/3.11.5 Darwin/23.1.0 OSX/10.16 solver/libmamba conda-libmamba-solver/23.11.1 libmambapy/1.5.4
                UID:GID : 501:20
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.
If you suspect this error is being caused by a malfunctioning plugin,
consider using the --no-plugins option to turn off plugins.

Example: conda --no-plugins install <package>

Alternatively, you can set the CONDA_NO_PLUGINS environment variable on
the command line to run the command without plugins enabled.

Example: CONDA_NO_PLUGINS=true conda install <package>

[sorenwacker]

Same problem.

[fxcoudert]

This crash is typically because some library loaded (here, probably curl) should link to CoreServices but doesn't. This was fixed in Curl in this commit: curl/curl@6ab7e19

So this should be fixed by moving to curl >= 8.4.0

[jaimergp]

Does it work with conda too? With the new solver, it should be more or less the same result, but the download happens via a Python code path, so maybe it's not affected.

This should be the same (--solver libmamba not needed, just added for clarity):

$ conda create -n tmp python=3.10 --yes --solver=libmamba

[pauldmccarthy]

I'm afraid I don't have access to a Sonoma machine, so cannot be of much use. However I am still getting reports of this occurring with the latest Mambaforge (23.11.0). Confusingly I am also getting reports of successful installations on Sonoma, so there is another factor at play somewhere.

We have solved this issue in our system by switching to the latest Miniconda release (also versioned 23.11.0), and calling conda rather than mamba (which as @jaimergp points out is likely to be using libmamba under the hood).

For what it's worth, here is a log file of our installer script which uses mambaforge to set up a conda environment containing our software, in which the error has occurred. The installer does the following:

1. Downloads and installs Mambaforge-23.11.0-0-MacOSX-arm64.sh
2. Downloads our environment specification
3. Runs $PREFIX/bin/mamba env update -p $PREFIX -f <env>.yml (We're aware that installing directly into the base environment is discouraged, but it has worked well for us in practice so far).

Note that our installer script is written in Python, and so a separate Python interpreter is required to run our script and to bootstrap the installation. One common theme amongst all of the reports I have received are that the Python interpreter used for running the installer script is an Anaconda installation (e.g. /Users/<username>/anaconda3/bin/python).

I had a wild theory that perhaps the Anaconda installation has an out-dated libcurl library, and that this library is somehow magically being loaded by the mambaforge Python interpreter, instead of the one installed into the mambaforge base environment. I asked a colleague of mine (with a M1 mac running Sonoma) to test this theory (install an old version of Anaconda with a broken libcurl, then use it to run our installer), but he wasn't able to reproduce the error.

So I'm kind of stumped. But as I mentioned, this is not a problem for us, as with the switch to miniconda our users are no longer experiencing the error.