RuntimeError: filesystem error: cannot copy symlink: Invalid argument

[ReimarBauer]

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]

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