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RuntimeError: filesystem error: cannot copy symlink: Invalid argument

Open ReimarBauer opened this issue 2 years ago • 1 comments

We run into a problem on a linux ubuntu VM qemu img with boa build . In comparision mamba build . works there

The same repo works with boa build . on another "real" computer. It has likly something to do with the disk image used.

boa build .

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Loading config files:

Updating build index: /home/mss-mscolab/mambaforge/conda-bld

No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 Recipe validation OK Found 1 recipe

  • msstesting

Assembling all recipes and variants

      Output: msstesting

┏━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━┓ ┃ Package ┃ Variant versions ┃ ┡━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━┩ │ target_platform │ linux-64 │ │ python │ 3.10 │ └─────────────────┴──────────────────┘

Initializing mamba solver

Downloading source

Copying /home/mss-mscolab/src/nilupul/MSS to /home/mss-mscolab/mambaforge/conda-bld/msstesting-0_1698153297756/work/

Preparing environment for msstesting

Finalizing build for msstesting conda-forge/linux-64 Using cache conda-forge/noarch Using cache pkgs/r/noarch No change pkgs/main/linux-64 No change pkgs/r/linux-64 No change pkgs/main/noarch No change Reloading output folder: /home/mss-mscolab/mambaforge/conda-bld home/mss-mscolab/mambaforge/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s home/mss-mscolab/mambaforge/conda-bld/noarch 127.0 B @ 5.3MB/s 0.0s Finalizing host for msstesting Finalizing run for msstesting Transaction

Prefix: /home/mss-mscolab/mambaforge/conda-bld/msstesting-0_1698153297756/_build_env

Updating specs:

  • python=3.10
  • pip
  • setuptools

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

  • _libgcc_mutex 0.1 conda_forge conda-forge/linux-64 Cached
  • _openmp_mutex 4.5 2_gnu conda-forge/linux-64 Cached
  • bzip2 1.0.8 h7f98852_4 conda-forge/linux-64 Cached
  • ca-certificates 2023.7.22 hbcca054_0 conda-forge/linux-64 Cached
  • ld_impl_linux-64 2.40 h41732ed_0 conda-forge/linux-64 Cached
  • libffi 3.4.2 h7f98852_5 conda-forge/linux-64 Cached
  • libgcc-ng 13.2.0 h807b86a_2 conda-forge/linux-64 Cached
  • libgomp 13.2.0 h807b86a_2 conda-forge/linux-64 Cached
  • libnsl 2.0.1 hd590300_0 conda-forge/linux-64 Cached
  • libsqlite 3.43.2 h2797004_0 conda-forge/linux-64 Cached
  • libuuid 2.38.1 h0b41bf4_0 conda-forge/linux-64 Cached
  • libzlib 1.2.13 hd590300_5 conda-forge/linux-64 Cached
  • ncurses 6.4 hcb278e6_0 conda-forge/linux-64 Cached
  • openssl 3.1.3 hd590300_0 conda-forge/linux-64 Cached
  • pip 23.3.1 pyhd8ed1ab_0 conda-forge/noarch Cached
  • python 3.10.12 hd12c33a_0_cpython conda-forge/linux-64 Cached
  • readline 8.2 h8228510_1 conda-forge/linux-64 Cached
  • setuptools 68.2.2 pyhd8ed1ab_0 conda-forge/noarch Cached
  • tk 8.6.13 h2797004_0 conda-forge/linux-64 Cached
  • tzdata 2023c h71feb2d_0 conda-forge/noarch Cached
  • wheel 0.41.2 pyhd8ed1ab_0 conda-forge/noarch Cached
  • xz 5.2.6 h166bdaf_0 conda-forge/linux-64 Cached

Summary:

Install: 22 packages

Total download: 0 B

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

Transaction starting Linking ld_impl_linux-64-2.40-h41732ed_0 Could not instantiate build environment Transaction

Prefix: /home/mss-mscolab/mambaforge/conda-bld/msstesting-0_1698153297756/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl

Updating specs:

  • python=3.10
  • setuptools
  • pip
  • future
  • python_abi=3.10[build=*_cp310]

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

  • _libgcc_mutex 0.1 conda_forge conda-forge/linux-64 Cached
  • _openmp_mutex 4.5 2_gnu conda-forge/linux-64 Cached
  • bzip2 1.0.8 h7f98852_4 conda-forge/linux-64 Cached
  • ca-certificates 2023.7.22 hbcca054_0 conda-forge/linux-64 Cached
  • future 0.18.3 pyhd8ed1ab_0 conda-forge/noarch Cached
  • ld_impl_linux-64 2.40 h41732ed_0 conda-forge/linux-64 Cached
  • libffi 3.4.2 h7f98852_5 conda-forge/linux-64 Cached
  • libgcc-ng 13.2.0 h807b86a_2 conda-forge/linux-64 Cached
  • libgomp 13.2.0 h807b86a_2 conda-forge/linux-64 Cached
  • libnsl 2.0.1 hd590300_0 conda-forge/linux-64 Cached
  • libsqlite 3.43.2 h2797004_0 conda-forge/linux-64 Cached
  • libuuid 2.38.1 h0b41bf4_0 conda-forge/linux-64 Cached
  • libzlib 1.2.13 hd590300_5 conda-forge/linux-64 Cached
  • ncurses 6.4 hcb278e6_0 conda-forge/linux-64 Cached
  • openssl 3.1.3 hd590300_0 conda-forge/linux-64 Cached
  • pip 23.3.1 pyhd8ed1ab_0 conda-forge/noarch Cached
  • python 3.10.12 hd12c33a_0_cpython conda-forge/linux-64 Cached
  • python_abi 3.10 4_cp310 conda-forge/linux-64 Cached
  • readline 8.2 h8228510_1 conda-forge/linux-64 Cached
  • setuptools 68.2.2 pyhd8ed1ab_0 conda-forge/noarch Cached
  • tk 8.6.13 h2797004_0 conda-forge/linux-64 Cached
  • tzdata 2023c h71feb2d_0 conda-forge/noarch Cached
  • wheel 0.41.2 pyhd8ed1ab_0 conda-forge/noarch Cached
  • xz 5.2.6 h166bdaf_0 conda-forge/linux-64 Cached

Summary:

Install: 24 packages

Total download: 0 B

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

Transaction starting Linking python_abi-3.10-4_cp310 Linking ld_impl_linux-64-2.40-h41732ed_0 ╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮ │ /home/mss-mscolab/mambaforge/lib/python3.10/site-packages/boa/core/run_build.py:349 in │ │ build_recipe │ │ │ │ 346 │ │ │ │ mkdir_p(os.path.join(o.config.host_prefix, "conda-meta")) │ │ 347 │ │ │ │ MambaContext().target_prefix = o.config.host_prefix │ │ 348 │ │ │ │ o.transactions["host"]["transaction"].print() │ │ ❱ 349 │ │ │ │ o.transactions["host"]["transaction"].execute( │ │ 350 │ │ │ │ │ PrefixData(o.config.host_prefix) │ │ 351 │ │ │ │ ) │ │ 352 │ ╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ RuntimeError: filesystem error: cannot copy symlink: Invalid argument [/home/mss-mscolab/mambaforge/pkgs/ld_impl_linux-64-2.40-h41732ed_0/bin/x86_64-conda_cos6-linux-gnu-ld] [/home/mss-mscolab/mambaforge/conda-bld/msstesting-0_1698153297756/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_pl acehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/bin/x86_64-cond a_cos6-linux-gnu-ld]

ReimarBauer avatar Oct 24 '23 13:10 ReimarBauer

the much slower mamba build . is able to build the package

ReimarBauer avatar Oct 26 '23 07:10 ReimarBauer