Consistently hitting a malloc error when attempting to install python=3.13
#589
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type::bug
describes erroneous operation, use severity::* to classify the type
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travishathaway
added
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type::bug
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Thanks for the report. Can you post the logs with |
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This is happening to me to semi randomly. The same command worked a few times today and did not a few times. It's supposed to throw solver error that the requested versions are incompatible. |
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Here's a subset of |
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Thank you @AlbertDeFusco, can you also report your |
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I've seen issues when mixing defaults and conda-forge and I have usually blamed the way that python / python_abi is implemented differently. Still, a segfault is not great. |
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Here's and info |
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I see you are on libmambapy 1.5.6, but 1.5.11 is available, and I'd also like to know if this is something recent, possibly triggered by an unrelated update. An OS upgrade? Maybe something in |
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Same for you @travishathaway, the timing here is strange given that you both are using different versions of libmamba and conda-libmamba-solver; I assume there's a recent update in the dependency tree that is breaking something. So please let me know the output of your |
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Here's the output of Output of commandFWIW, I updated to the most recent version of macOS last weekend (15.2). I saw the same error before and after the update. |
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I could share the error logs with |
Even compressed?? I can usually upload them to the comment box after zipping them. I'm mostly interested in the 500-1000 lines before the segfault, though. |
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I see two recent updates:
You posted this on the 12th... before or after that update? Were you observing it before the 12th? Before the 10th? Trying to pin-point who's introducing the error. |
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I'll bring up the history information in a little bit. I was not experiencing this before the 12th. It started happening in my base env and another env with conda installed where I was developing an extension. They had slightly different versions of conda and libmamba. But both envs hadn't changed since the 10th, I believe. |
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I am beginning to suspect that there is an issue with the This causes the segfault but this does not |
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I started noticing this on the 12th. Also, the compressed error log is a little smaller (21MB 🙌). It's attached. |
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For me, this error goes away when I introduce the |
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I wonder if this has to do with the Given that the underlying libmamba versions did not change after the 12th, I assume it has to do with some specific metadata that has changed upstream (e.g. a hotfix, as referred above) or something else that forces libmamba 1.x to run into a code path that segfaults (possibly in the conflict reporting logic, which has been the source of some segfaults in the past). Also, libmamba 2.x is about to be packaged for |
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With some Docker images: I wonder if this is some issue with inconsistent repodata.json caches? Can you try the following?
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Clearing the repodata.json cache didn't work for me ☹ Following from what you were saying about libarchive, I was able to get this error to go away by manually updating libmambapy=1.5.11 from build version Here's the install plan: I think this confirms you hunch. |
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Awesome! |
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I'll give it a try. Also, I haven't encountered the problem for the past two days. |
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What happened?
When I attempt to install
python=3.13into my base environment, I consistently come across the following error:This happens even after clearing cache.
Conda Info
conda info active environment : base active env location : /Users/username/miniconda3 shell level : 1 user config file : /Users/username/.condarc populated config files : /Users/username/.condarc conda version : 24.11.1 conda-build version : not installed python version : 3.12.7.final.0 solver : libmamba (default) virtual packages : __archspec=1=m1 __conda=24.11.1=0 __osx=14.4.1=0 __unix=0=0 base environment : /Users/username/miniconda3 (writable) conda av data dir : /Users/username/miniconda3/etc/conda conda av metadata url : None channel URLs : https://repo.anaconda.com/pkgs/main/osx-arm64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/osx-arm64 https://repo.anaconda.com/pkgs/r/noarch package cache : /Users/username/miniconda3/pkgs /Users/username/.conda/pkgs envs directories : /Users/username/miniconda3/envs /Users/username/.conda/envs platform : osx-arm64 user-agent : conda/24.11.1 requests/2.32.3 CPython/3.12.7 Darwin/23.4.0 OSX/14.4.1 solver/libmamba conda-libmamba-solver/24.9.0 libmambapy/1.5.11 UID:GID : 501:20 netrc file : None offline mode : FalseConda Config
Conda list
# Name Version Build Channel anaconda-cli-base 0.4.1 py312hca03da5_1 defaults anaconda-cloud-auth 0.7.2 py312hca03da5_0 defaults annotated-types 0.6.0 py312hca03da5_0 defaults appdirs 1.4.4 pyhd3eb1b0_0 defaults appnope 0.1.3 py312hca03da5_1001 defaults archspec 0.2.3 pyhd3eb1b0_0 defaults asttokens 2.0.5 pyhd3eb1b0_0 defaults backcall 0.2.0 pyhd3eb1b0_0 defaults boltons 23.0.0 py312hca03da5_0 defaults brotli-python 1.0.9 py312h313beb8_8 defaults bzip2 1.0.8 h80987f9_6 defaults c-ares 1.19.1 h80987f9_0 defaults ca-certificates 2024.11.26 hca03da5_0 defaults cachecontrol 0.14.0 py312hca03da5_1 defaults cachecontrol-with-filecache 0.14.0 py312hca03da5_1 defaults cachy 0.3.0 pyhd3eb1b0_0 defaults certifi 2024.8.30 py312hca03da5_0 defaults cffi 1.17.1 py312h3eb5a62_0 defaults charset-normalizer 3.3.2 pyhd3eb1b0_0 defaults click 8.1.7 py312hca03da5_0 defaults click-default-group 1.2.2 py312hca03da5_0 defaults clikit 0.6.2 py_0 defaults colorama 0.4.6 py312hca03da5_0 defaults conda 24.11.1 py312hca03da5_0 defaults conda-anaconda-telemetry 0.1.0.7_gb44023c py_0 distribution-plugins/label/dev conda-content-trust 0.2.0+92_gac0add6 py_0 conda-canary/label/dev conda-libmamba-solver 24.9.0 pyhd3eb1b0_0 defaults conda-lock 2.5.6 py312hca03da5_0 defaults conda-package-handling 2.4.0 py312hca03da5_0 defaults conda-package-streaming 0.11.0 py312hca03da5_0 defaults conda-token 0.5.0 pyhd3eb1b0_0 defaults conda-tree 1.1.1 pyhff2d567_0 conda-forge crashtest 0.3.1 pyhd3eb1b0_1 defaults cryptography 43.0.3 py312h8026fc7_1 defaults decorator 5.1.1 pyhd3eb1b0_0 defaults distlib 0.3.8 py312hca03da5_0 defaults distro 1.9.0 py312hca03da5_0 defaults ensureconda 1.4.4 py312hca03da5_1 defaults exceptiongroup 1.2.0 py312hca03da5_0 defaults executing 0.8.3 pyhd3eb1b0_0 defaults expat 2.6.3 h313beb8_0 defaults filelock 3.13.1 py312hca03da5_0 defaults fmt 9.1.0 h48ca7d4_1 defaults frozendict 2.4.2 py312hca03da5_0 defaults gitdb 4.0.7 pyhd3eb1b0_0 defaults gitpython 3.1.43 py312hca03da5_0 defaults html5lib 1.1 pyhd3eb1b0_0 defaults icu 73.1 h313beb8_0 defaults idna 3.7 py312hca03da5_0 defaults importlib-metadata 8.5.0 py312hca03da5_0 defaults importlib_metadata 8.5.0 hd3eb1b0_0 defaults ipython 8.27.0 py312hca03da5_0 defaults jaraco.classes 3.2.1 pyhd3eb1b0_0 defaults jedi 0.19.1 py312hca03da5_0 defaults jinja2 3.1.4 py312hca03da5_1 defaults jsonpatch 1.33 py312hca03da5_1 defaults jsonpointer 2.1 pyhd3eb1b0_0 defaults keyring 24.3.1 py312hca03da5_0 defaults krb5 1.20.1 hf3e1bf2_1 defaults libarchive 3.7.4 h8f13d7a_0 defaults libcurl 8.9.1 h3e2b118_0 defaults libcxx 14.0.6 h848a8c0_0 defaults libedit 3.1.20230828 h80987f9_0 defaults libev 4.33 h1a28f6b_1 defaults libffi 3.4.4 hca03da5_1 defaults libiconv 1.16 h80987f9_3 defaults libmamba 1.5.11 haeffa04_0 defaults libmambapy 1.5.11 py312h15e39b3_0 defaults libnghttp2 1.57.0 h62f6fdd_0 defaults libsolv 0.7.24 h514c7bf_1 defaults libssh2 1.11.1 h3e2b118_0 defaults libxml2 2.13.5 h0b34f26_0 defaults lz4-c 1.9.4 h313beb8_1 defaults markdown-it-py 2.2.0 py312hca03da5_1 defaults markupsafe 2.1.3 py312h80987f9_0 defaults matplotlib-inline 0.1.6 py312hca03da5_0 defaults mdurl 0.1.0 py312hca03da5_0 defaults menuinst 2.2.0 py312hca03da5_0 defaults more-itertools 10.3.0 py312hca03da5_0 defaults msgpack-python 1.0.3 py312h48ca7d4_0 defaults ncurses 6.4 h313beb8_0 defaults networkx 3.3 py312hca03da5_0 defaults openssl 3.0.15 h80987f9_0 defaults packaging 24.1 py312hca03da5_0 defaults parso 0.8.3 pyhd3eb1b0_0 defaults pastel 0.2.1 py_0 defaults pcre2 10.42 hb066dcc_1 defaults pexpect 4.8.0 pyhd3eb1b0_3 defaults pickleshare 0.7.5 pyhd3eb1b0_1003 defaults pip 24.2 py312hca03da5_0 defaults pkce 1.0.3 py312hca03da5_0 defaults pkginfo 1.11.2 py312hca03da5_0 defaults platformdirs 3.10.0 py312hca03da5_0 defaults pluggy 1.5.0 py312hca03da5_0 defaults prompt-toolkit 3.0.43 py312hca03da5_0 defaults prompt_toolkit 3.0.43 hd3eb1b0_0 defaults ptyprocess 0.7.0 pyhd3eb1b0_2 defaults pure_eval 0.2.2 pyhd3eb1b0_0 defaults pybind11-abi 5 hd3eb1b0_0 defaults pycosat 0.6.6 py312h80987f9_1 defaults pycparser 2.21 pyhd3eb1b0_0 defaults pydantic 2.8.2 py312hca03da5_0 defaults pydantic-core 2.20.1 py312hf0e4da2_0 defaults pydantic-settings 2.6.1 py312hca03da5_0 defaults pygments 2.15.1 py312hca03da5_1 defaults pyjwt 2.9.0 py312hca03da5_0 defaults pylev 1.3.0 py_0 defaults pyopenssl 24.2.1 py312hca03da5_0 defaults pysocks 1.7.1 py312hca03da5_0 defaults python 3.12.7 h99e199e_0 defaults python-dotenv 0.21.0 py312hca03da5_0 defaults python.app 3 py312h80987f9_1 defaults pyyaml 6.0.2 py312h80987f9_0 defaults readchar 4.0.5 py312hca03da5_0 defaults readline 8.2 h1a28f6b_0 defaults reproc 14.2.4 h313beb8_2 defaults reproc-cpp 14.2.4 h313beb8_2 defaults requests 2.32.3 py312hca03da5_1 defaults rich 13.9.4 py312hca03da5_0 defaults ruamel.yaml 0.18.6 py312h80987f9_0 defaults ruamel.yaml.clib 0.2.8 py312h80987f9_0 defaults semver 3.0.2 py312hca03da5_0 defaults setuptools 75.1.0 py312hca03da5_0 defaults shellingham 1.5.0 py312hca03da5_0 defaults six 1.16.0 pyhd3eb1b0_1 defaults smmap 4.0.0 pyhd3eb1b0_0 defaults sqlite 3.45.3 h80987f9_0 defaults stack_data 0.2.0 pyhd3eb1b0_0 defaults tk 8.6.14 h6ba3021_0 defaults tomli 2.0.1 py312hca03da5_1 defaults tomlkit 0.13.2 py312hca03da5_0 defaults toolz 0.12.0 py312hca03da5_0 defaults tqdm 4.66.5 py312h989b03a_0 defaults traitlets 5.14.3 py312hca03da5_0 defaults truststore 0.8.0 py312hca03da5_0 defaults typer 0.9.0 py312hca03da5_0 defaults typing-extensions 4.11.0 py312hca03da5_0 defaults typing_extensions 4.11.0 py312hca03da5_0 defaults tzdata 2024b h04d1e81_0 defaults urllib3 1.26.19 py312hca03da5_0 defaults virtualenv 20.28.0 py312hca03da5_0 defaults wcwidth 0.2.5 pyhd3eb1b0_0 defaults webencodings 0.5.1 py312hca03da5_2 defaults wheel 0.44.0 py312hca03da5_0 defaults xz 5.4.6 h80987f9_1 defaults yaml 0.2.5 h1a28f6b_0 defaults yaml-cpp 0.8.0 h313beb8_1 defaults zipp 3.21.0 py312hca03da5_0 defaults zlib 1.2.13 h18a0788_1 defaults zstandard 0.23.0 py312h1a4646a_1 defaults zstd 1.5.6 hfb09047_0 defaultsAdditional Context
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