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Passing test vs. lchauvin install error

作成日 9 か月前差分は期限切れになりません

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416 行

*******************************

* Welcome to SCT installation *

*******************************

Checking OS type and version...

Linux runnervmnfq8z 6.8.0-1036-azure #42~22.04.1-Ubuntu SMP Fri Sep 12 00:09:41 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux

Linux imaging-gpu-05 5.15.0-153-generic #163-Ubuntu SMP Thu Aug 7 16:37:18 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux

Checking requirements...

OK!

Source files not present. Downloading source files (@ master) to /tmp/tmp.zRQSjifCZQ/spinalcordtoolbox.

Cloning into '/tmp/tmp.zRQSjifCZQ/spinalcordtoolbox'...

SCT version ......... 7.2.dev0

Installation type ... package

Installation type ... in-place

Operating system .... linux (unknown)

Shell config ........ /home/runner/.bashrc

Shell config ........ /home/lchauvin/.bashrc

Checking permissions on required file /home/runner/.bashrc:

Checking permissions on required file /home/lchauvin/.bashrc:

- File exists: True

- File ownership: True

- Read permissions: True

- Write permissions: True

SCT will be installed here: [/home/runner/sct_7.2.dev0]

WARNING: Directory already exists. Files will be overwritten.

Copying source files from /tmp/tmp.zRQSjifCZQ/spinalcordtoolbox to /home/runner/sct_7.2.dev0

SCT will be installed here: [/scratch/02/lchauvin/workspace/projects/spinalcordtoolbox]

...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

Skipping copy of source files (source and destination folders are the same)

Downloading Miniforge...

wget -nv -O /tmp/tmp.zRQSjifCZQ/miniforge.sh https://github.com/conda-forge/miniforge/releases/download/24.11.2-1/Miniforge3-Linux-x86_64.sh

wget -nv -O /tmp/tmp.fRYleHJK6d/miniforge.sh https://github.com/conda-forge/miniforge/releases/download/24.11.2-1/Miniforge3-Linux-x86_64.sh

2025-10-20 11:03:04 URL:https://release-assets.githubusercontent.com/github-production-release-asset/221584272/81e205c2-1911-4a2d-8b46-066d460f73d6?sp=r&sv=2018-11-09&sr=b&spr=https&se=2025-10-20T11%3A45%3A36Z&rscd=attachment%3B+filename%3DMiniforge3-Linux-x86_64.sh&rsct=application%2Foctet-stream&skoid=96c2d410-5711-43a1-aedd-ab1947aa7ab0&sktid=398a6654-997b-47e9-b12b-9515b896b4de&skt=2025-10-20T10%3A45%3A01Z&ske=2025-10-20T11%3A45%3A36Z&sks=b&skv=2018-11-09&sig=3z7Zh%2FIVP9koICUReSw9uG4idTwebqbqMPC75KwKobo%3D&jwt=*** [77972610/77972610] -> "/tmp/tmp.zRQSjifCZQ/miniforge.sh" [1]

2025-10-15 15:22:51 URL:https://release-assets.githubusercontent.com/github-production-release-asset/221584272/81e205c2-1911-4a2d-8b46-066d460f73d6?sp=r&sv=2018-11-09&sr=b&spr=https&se=2025-10-15T16%3A00%3A24Z&rscd=attachment%3B+filename%3DMiniforge3-Linux-x86_64.sh&rsct=application%2Foctet-stream&skoid=96c2d410-5711-43a1-aedd-ab1947aa7ab0&sktid=398a6654-997b-47e9-b12b-9515b896b4de&skt=2025-10-15T15%3A00%3A07Z&ske=2025-10-15T16%3A00%3A24Z&sks=b&skv=2018-11-09&sig=gZl9lbEIwMEc%2B3uSHIC9rlNA489O46ysRDfTJlg00Ww%3D&jwt=eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmVsZWFzZS1hc3NldHMuZ2l0aHVidXNlcmNvbnRlbnQuY29tIiwia2V5Ijoia2V5MSIsImV4cCI6MTc2MDU0MzU2NiwibmJmIjoxNzYwNTQxNzY2LCJwYXRoIjoicmVsZWFzZWFzc2V0cHJvZHVjdGlvbi5ibG9iLmNvcmUud2luZG93cy5uZXQifQ.Z6S8dSFr71LHeFj0Asow-z1IvznpiSk3ToCDSq6d0m4&response-content-disposition=attachment%3B%20filename%3DMiniforge3-Linux-x86_64.sh&response-content-type=application%2Foctet-stream [77972610/77972610] -> "/tmp/tmp.fRYleHJK6d/miniforge.sh" [1]

Installing Miniforge...

bash /tmp/tmp.zRQSjifCZQ/miniforge.sh -p /home/runner/sct_7.2.dev0/python -b -f

bash /tmp/tmp.fRYleHJK6d/miniforge.sh -p /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python -b -f

PREFIX=/home/runner/sct_7.2.dev0/python

PREFIX=/scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python

Unpacking payload ...

Extracting _libgcc_mutex-0.1-conda_forge.tar.bz2

Extracting ca-certificates-2024.12.14-hbcca054_0.conda

Extracting ld_impl_linux-64-2.43-h712a8e2_2.conda

Extracting pybind11-abi-4-hd8ed1ab_3.tar.bz2

Extracting python_abi-3.12-5_cp312.conda

Extracting tzdata-2024b-hc8b5060_0.conda

Extracting libgomp-14.2.0-h77fa898_1.conda

Extracting _openmp_mutex-4.5-2_gnu.tar.bz2

Extracting libgcc-14.2.0-h77fa898_1.conda

Extracting c-ares-1.34.4-hb9d3cd8_0.conda

Extracting libexpat-2.6.4-h5888daf_0.conda

Extracting libgcc-ng-14.2.0-h69a702a_1.conda

Extracting liblzma-5.6.3-hb9d3cd8_1.conda

Extracting libstdcxx-14.2.0-hc0a3c3a_1.conda

Extracting libzlib-1.3.1-hb9d3cd8_2.conda

Extracting openssl-3.4.0-hb9d3cd8_0.conda

Extracting reproc-14.2.5.post0-hb9d3cd8_0.conda

Extracting bzip2-1.0.8-h4bc722e_7.conda

Extracting keyutils-1.6.1-h166bdaf_0.tar.bz2

Extracting libev-4.33-hd590300_2.conda

Extracting libffi-3.4.2-h7f98852_5.tar.bz2

Extracting libiconv-1.17-hd590300_2.conda

Extracting libnsl-2.0.1-hd590300_0.conda

Extracting libsqlite-3.47.2-hee588c1_0.conda

Extracting libssh2-1.11.1-hf672d98_0.conda

Extracting libstdcxx-ng-14.2.0-h4852527_1.conda

Extracting libuuid-2.38.1-h0b41bf4_0.conda

Extracting libxcrypt-4.4.36-hd590300_1.conda

Extracting lz4-c-1.10.0-h5888daf_1.conda

Extracting lzo-2.10-hd590300_1001.conda

Extracting ncurses-6.5-he02047a_1.conda

Extracting reproc-cpp-14.2.5.post0-h5888daf_0.conda

Extracting tk-8.6.13-noxft_h4845f30_101.conda

Extracting fmt-11.0.2-h434a139_0.conda

Extracting libedit-3.1.20191231-he28a2e2_2.tar.bz2

Extracting libnghttp2-1.64.0-h161d5f1_0.conda

Extracting libsolv-0.7.30-h3509ff9_0.conda

Extracting libxml2-2.13.5-h0d44e9d_1.conda

Extracting readline-8.2-h8228510_1.conda

Extracting yaml-cpp-0.8.0-h59595ed_0.conda

Extracting zstd-1.5.6-ha6fb4c9_0.conda

Extracting krb5-1.21.3-h659f571_0.conda

Extracting libarchive-3.7.7-h4585015_3.conda

Extracting python-3.12.8-h9e4cc4f_1_cpython.conda

Extracting libcurl-8.11.1-h332b0f4_0.conda

Extracting menuinst-2.2.0-py312h7900ff3_0.conda

Extracting archspec-0.2.3-pyhd8ed1ab_0.conda

Extracting boltons-24.0.0-pyhd8ed1ab_1.conda

Extracting brotli-python-1.1.0-py312h2ec8cdc_2.conda

Extracting certifi-2024.12.14-pyhd8ed1ab_0.conda

Extracting charset-normalizer-3.4.1-pyhd8ed1ab_0.conda

Extracting colorama-0.4.6-pyhd8ed1ab_1.conda

Extracting distro-1.9.0-pyhd8ed1ab_1.conda

Extracting frozendict-2.4.6-py312h66e93f0_0.conda

Extracting hpack-4.0.0-pyhd8ed1ab_1.conda

Extracting hyperframe-6.0.1-pyhd8ed1ab_1.conda

Extracting idna-3.10-pyhd8ed1ab_1.conda

Extracting jsonpointer-3.0.0-py312h7900ff3_1.conda

Extracting libmamba-1.5.12-h49b8a8d_0.conda

Extracting packaging-24.2-pyhd8ed1ab_2.conda

Extracting platformdirs-4.3.6-pyhd8ed1ab_1.conda

Extracting pluggy-1.5.0-pyhd8ed1ab_1.conda

Extracting pycosat-0.6.6-py312h66e93f0_2.conda

Extracting pycparser-2.22-pyh29332c3_1.conda

Extracting pysocks-1.7.1-pyha55dd90_7.conda

Extracting ruamel.yaml.clib-0.2.8-py312h66e93f0_1.conda

Extracting setuptools-75.6.0-pyhff2d567_1.conda

Extracting truststore-0.10.0-pyhd8ed1ab_0.conda

Extracting wheel-0.45.1-pyhd8ed1ab_1.conda

Extracting cffi-1.17.1-py312h06ac9bb_0.conda

Extracting h2-4.1.0-pyhd8ed1ab_1.conda

Extracting jsonpatch-1.33-pyhd8ed1ab_1.conda

Extracting libmambapy-1.5.12-py312hbaee817_0.conda

Extracting pip-24.3.1-pyh8b19718_2.conda

Extracting ruamel.yaml-0.18.8-py312h66e93f0_0.conda

Extracting tqdm-4.67.1-pyhd8ed1ab_1.conda

Extracting zstandard-0.23.0-py312hef9b889_1.conda

Extracting conda-package-streaming-0.11.0-pyhd8ed1ab_0.conda

Extracting urllib3-2.3.0-pyhd8ed1ab_0.conda

Extracting conda-package-handling-2.4.0-pyha770c72_1.conda

Extracting requests-2.32.3-pyhd8ed1ab_1.conda

Extracting conda-24.11.2-py312h7900ff3_1.conda

Extracting conda-libmamba-solver-24.9.0-pyhd8ed1ab_0.conda

Extracting mamba-1.5.12-py312h9460a1c_0.conda

Installing base environment...

Transaction

Prefix: /home/runner/sct_7.2.dev0/python

Prefix: /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python

Updating specs:

- conda-forge/linux-64::_libgcc_mutex==0.1=conda_forge[md5=d7c89558ba9fa0495403155b64376d81]

- conda-forge/linux-64::ca-certificates==2024.12.14=hbcca054_0[md5=720523eb0d6a9b0f6120c16b2aa4e7de]

- conda-forge/linux-64::ld_impl_linux-64==2.43=h712a8e2_2[md5=048b02e3962f066da18efe3a21b77672]

- conda-forge/noarch::pybind11-abi==4=hd8ed1ab_3[md5=878f923dd6acc8aeb47a75da6c4098be]

- conda-forge/linux-64::python_abi==3.12=5_cp312[md5=0424ae29b104430108f5218a66db7260]

- conda-forge/noarch::tzdata==2024b=hc8b5060_0[md5=8ac3367aafb1cc0a068483c580af8015]

- conda-forge/linux-64::libgomp==14.2.0=h77fa898_1[md5=cc3573974587f12dda90d96e3e55a702]

- conda-forge/linux-64::_openmp_mutex==4.5=2_gnu[md5=73aaf86a425cc6e73fcf236a5a46396d]

- conda-forge/linux-64::libgcc==14.2.0=h77fa898_1[md5=3cb76c3f10d3bc7f1105b2fc9db984df]

- conda-forge/linux-64::c-ares==1.34.4=hb9d3cd8_0[md5=e2775acf57efd5af15b8e3d1d74d72d3]

- conda-forge/linux-64::libexpat==2.6.4=h5888daf_0[md5=db833e03127376d461e1e13e76f09b6c]

- conda-forge/linux-64::libgcc-ng==14.2.0=h69a702a_1[md5=e39480b9ca41323497b05492a63bc35b]

- conda-forge/linux-64::liblzma==5.6.3=hb9d3cd8_1[md5=2ecf2f1c7e4e21fcfe6423a51a992d84]

- conda-forge/linux-64::libstdcxx==14.2.0=hc0a3c3a_1[md5=234a5554c53625688d51062645337328]

- conda-forge/linux-64::libzlib==1.3.1=hb9d3cd8_2[md5=edb0dca6bc32e4f4789199455a1dbeb8]

- conda-forge/linux-64::openssl==3.4.0=hb9d3cd8_0[md5=23cc74f77eb99315c0360ec3533147a9]

- conda-forge/linux-64::reproc==14.2.5.post0=hb9d3cd8_0[md5=69fbc0a9e42eb5fe6733d2d60d818822]

- conda-forge/linux-64::bzip2==1.0.8=h4bc722e_7[md5=62ee74e96c5ebb0af99386de58cf9553]

- conda-forge/linux-64::keyutils==1.6.1=h166bdaf_0[md5=30186d27e2c9fa62b45fb1476b7200e3]

- conda-forge/linux-64::libev==4.33=hd590300_2[md5=172bf1cd1ff8629f2b1179945ed45055]

- conda-forge/linux-64::libffi==3.4.2=h7f98852_5[md5=d645c6d2ac96843a2bfaccd2d62b3ac3]

- conda-forge/linux-64::libiconv==1.17=hd590300_2[md5=d66573916ffcf376178462f1b61c941e]

- conda-forge/linux-64::libnsl==2.0.1=hd590300_0[md5=30fd6e37fe21f86f4bd26d6ee73eeec7]

- conda-forge/linux-64::libsqlite==3.47.2=hee588c1_0[md5=b58da17db24b6e08bcbf8fed2fb8c915]

- conda-forge/linux-64::libssh2==1.11.1=hf672d98_0[md5=be2de152d8073ef1c01b7728475f2fe7]

- conda-forge/linux-64::libstdcxx-ng==14.2.0=h4852527_1[md5=8371ac6457591af2cf6159439c1fd051]

- conda-forge/linux-64::libuuid==2.38.1=h0b41bf4_0[md5=40b61aab5c7ba9ff276c41cfffe6b80b]

- conda-forge/linux-64::libxcrypt==4.4.36=hd590300_1[md5=5aa797f8787fe7a17d1b0821485b5adc]

- conda-forge/linux-64::lz4-c==1.10.0=h5888daf_1[md5=9de5350a85c4a20c685259b889aa6393]

- conda-forge/linux-64::lzo==2.10=hd590300_1001[md5=ec7398d21e2651e0dcb0044d03b9a339]

- conda-forge/linux-64::ncurses==6.5=he02047a_1[md5=70caf8bb6cf39a0b6b7efc885f51c0fe]

- conda-forge/linux-64::reproc-cpp==14.2.5.post0=h5888daf_0[md5=828302fca535f9cfeb598d5f7c204323]

- conda-forge/linux-64::tk==8.6.13=noxft_h4845f30_101[md5=d453b98d9c83e71da0741bb0ff4d76bc]

- conda-forge/linux-64::fmt==11.0.2=h434a139_0[md5=995f7e13598497691c1dc476d889bc04]

- conda-forge/linux-64::libedit==3.1.20191231=he28a2e2_2[md5=4d331e44109e3f0e19b4cb8f9b82f3e1]

- conda-forge/linux-64::libnghttp2==1.64.0=h161d5f1_0[md5=19e57602824042dfd0446292ef90488b]

- conda-forge/linux-64::libsolv==0.7.30=h3509ff9_0[md5=02539b77d25aa4f65b20246549e256c3]

- conda-forge/linux-64::libxml2==2.13.5=h0d44e9d_1[md5=f5b05674697ae7d2c5932766695945e1]

- conda-forge/linux-64::readline==8.2=h8228510_1[md5=47d31b792659ce70f470b5c82fdfb7a4]

- conda-forge/linux-64::yaml-cpp==0.8.0=h59595ed_0[md5=965eaacd7c18eb8361fd12bb9e7a57d7]

- conda-forge/linux-64::zstd==1.5.6=ha6fb4c9_0[md5=4d056880988120e29d75bfff282e0f45]

- conda-forge/linux-64::krb5==1.21.3=h659f571_0[md5=3f43953b7d3fb3aaa1d0d0723d91e368]

- conda-forge/linux-64::libarchive==3.7.7=h4585015_3[md5=a28808eae584c7f519943719b2a2b386]

- conda-forge/linux-64::python==3.12.8=h9e4cc4f_1_cpython[md5=7fd2fd79436d9b473812f14e86746844]

- conda-forge/linux-64::libcurl==8.11.1=h332b0f4_0[md5=2b3e0081006dc21e8bf53a91c83a055c]

- conda-forge/linux-64::menuinst==2.2.0=py312h7900ff3_0[md5=f22f8e77b36e67297feffe03eefd5375]

- conda-forge/noarch::archspec==0.2.3=pyhd8ed1ab_0[md5=192278292e20704f663b9c766909d67b]

- conda-forge/noarch::boltons==24.0.0=pyhd8ed1ab_1[md5=d88c38e66d85ecc9c7e2c4110676bbf4]

- conda-forge/linux-64::brotli-python==1.1.0=py312h2ec8cdc_2[md5=b0b867af6fc74b2a0aa206da29c0f3cf]

- conda-forge/noarch::certifi==2024.12.14=pyhd8ed1ab_0[md5=6feb87357ecd66733be3279f16a8c400]

- conda-forge/noarch::charset-normalizer==3.4.1=pyhd8ed1ab_0[md5=e83a31202d1c0a000fce3e9cf3825875]

- conda-forge/noarch::colorama==0.4.6=pyhd8ed1ab_1[md5=962b9857ee8e7018c22f2776ffa0b2d7]

- conda-forge/noarch::distro==1.9.0=pyhd8ed1ab_1[md5=0a2014fd9860f8b1eaa0b1f3d3771a08]

- conda-forge/linux-64::frozendict==2.4.6=py312h66e93f0_0[md5=9fa8408745a0621314b7751d11fecc18]

- conda-forge/noarch::hpack==4.0.0=pyhd8ed1ab_1[md5=2aa5ff7fa34a81b9196532c84c10d865]

- conda-forge/noarch::hyperframe==6.0.1=pyhd8ed1ab_1[md5=566e75c90c1d0c8c459eb0ad9833dc7a]

- conda-forge/noarch::idna==3.10=pyhd8ed1ab_1[md5=39a4f67be3286c86d696df570b1201b7]

- conda-forge/linux-64::jsonpointer==3.0.0=py312h7900ff3_1[md5=6b51f7459ea4073eeb5057207e2e1e3d]

- conda-forge/linux-64::libmamba==1.5.12=h49b8a8d_0[md5=d6aec145c4f2473c09c2699d74f6dfc0]

- conda-forge/noarch::packaging==24.2=pyhd8ed1ab_2[md5=3bfed7e6228ebf2f7b9eaa47f1b4e2aa]

- conda-forge/noarch::platformdirs==4.3.6=pyhd8ed1ab_1[md5=577852c7e53901ddccc7e6a9959ddebe]

- conda-forge/noarch::pluggy==1.5.0=pyhd8ed1ab_1[md5=e9dcbce5f45f9ee500e728ae58b605b6]

- conda-forge/linux-64::pycosat==0.6.6=py312h66e93f0_2[md5=08223e6a73e0bca5ade16ec4cebebf23]

- conda-forge/noarch::pycparser==2.22=pyh29332c3_1[md5=12c566707c80111f9799308d9e265aef]

- conda-forge/noarch::pysocks==1.7.1=pyha55dd90_7[md5=461219d1a5bd61342293efa2c0c90eac]

- conda-forge/linux-64::ruamel.yaml.clib==0.2.8=py312h66e93f0_1[md5=532c3e5d0280be4fea52396ec1fa7d5d]

- conda-forge/noarch::setuptools==75.6.0=pyhff2d567_1[md5=fc80f7995e396cbaeabd23cf46c413dc]

- conda-forge/noarch::truststore==0.10.0=pyhd8ed1ab_0[md5=ad1c20cd193e3044bcf17798c33b9d67]

- conda-forge/noarch::wheel==0.45.1=pyhd8ed1ab_1[md5=75cb7132eb58d97896e173ef12ac9986]

- conda-forge/linux-64::cffi==1.17.1=py312h06ac9bb_0[md5=a861504bbea4161a9170b85d4d2be840]

- conda-forge/noarch::h2==4.1.0=pyhd8ed1ab_1[md5=825927dc7b0f287ef8d4d0011bb113b1]

- conda-forge/noarch::jsonpatch==1.33=pyhd8ed1ab_1[md5=cb60ae9cf02b9fcb8004dec4089e5691]

- conda-forge/linux-64::libmambapy==1.5.12=py312hbaee817_0[md5=88dd983e44c86cdde2817ecfa7d84d5a]

- conda-forge/noarch::pip==24.3.1=pyh8b19718_2[md5=04e691b9fadd93a8a9fad87a81d4fd8f]

- conda-forge/linux-64::ruamel.yaml==0.18.8=py312h66e93f0_0[md5=b77952bccd6b8d5c46e2f54354b4296b]

- conda-forge/noarch::tqdm==4.67.1=pyhd8ed1ab_1[md5=9efbfdc37242619130ea42b1cc4ed861]

- conda-forge/linux-64::zstandard==0.23.0=py312hef9b889_1[md5=8b7069e9792ee4e5b4919a7a306d2e67]

- conda-forge/noarch::conda-package-streaming==0.11.0=pyhd8ed1ab_0[md5=bc9533d8616a97551ed144789bf9c1cd]

- conda-forge/noarch::urllib3==2.3.0=pyhd8ed1ab_0[md5=32674f8dbfb7b26410ed580dd3c10a29]

- conda-forge/noarch::conda-package-handling==2.4.0=pyha770c72_1[md5=28b86d110bda4ef40e680d1afa9ddb1d]

- conda-forge/noarch::requests==2.32.3=pyhd8ed1ab_1[md5=a9b9368f3701a417eac9edbcae7cb737]

- conda-forge/linux-64::conda==24.11.2=py312h7900ff3_1[md5=2dff8a88fb65b9c99f6c28aad1126c66]

- conda-forge/noarch::conda-libmamba-solver==24.9.0=pyhd8ed1ab_0[md5=45378d089c5f72c9c0d63d58414c645d]

- conda-forge/linux-64::mamba==1.5.12=py312h9460a1c_0[md5=59a9360536caad98732fdfdc320e41dc]

Package Version Build Channel Size

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

Install:

+ _libgcc_mutex 0.1 conda_forge conda-forge

+ ca-certificates 2024.12.14 hbcca054_0 conda-forge

+ ld_impl_linux-64 2.43 h712a8e2_2 conda-forge

+ pybind11-abi 4 hd8ed1ab_3 conda-forge

+ python_abi 3.12 5_cp312 conda-forge

+ tzdata 2024b hc8b5060_0 conda-forge

+ libgomp 14.2.0 h77fa898_1 conda-forge

+ _openmp_mutex 4.5 2_gnu conda-forge

+ libgcc 14.2.0 h77fa898_1 conda-forge

+ c-ares 1.34.4 hb9d3cd8_0 conda-forge

+ libexpat 2.6.4 h5888daf_0 conda-forge

+ libgcc-ng 14.2.0 h69a702a_1 conda-forge

+ liblzma 5.6.3 hb9d3cd8_1 conda-forge

+ libstdcxx 14.2.0 hc0a3c3a_1 conda-forge

+ libzlib 1.3.1 hb9d3cd8_2 conda-forge

+ openssl 3.4.0 hb9d3cd8_0 conda-forge

+ reproc 14.2.5.post0 hb9d3cd8_0 conda-forge

+ bzip2 1.0.8 h4bc722e_7 conda-forge

+ keyutils 1.6.1 h166bdaf_0 conda-forge

+ libev 4.33 hd590300_2 conda-forge

+ libffi 3.4.2 h7f98852_5 conda-forge

+ libiconv 1.17 hd590300_2 conda-forge

+ libnsl 2.0.1 hd590300_0 conda-forge

+ libsqlite 3.47.2 hee588c1_0 conda-forge

+ libssh2 1.11.1 hf672d98_0 conda-forge

+ libstdcxx-ng 14.2.0 h4852527_1 conda-forge

+ libuuid 2.38.1 h0b41bf4_0 conda-forge

+ libxcrypt 4.4.36 hd590300_1 conda-forge

+ lz4-c 1.10.0 h5888daf_1 conda-forge

+ lzo 2.10 hd590300_1001 conda-forge

+ ncurses 6.5 he02047a_1 conda-forge

+ reproc-cpp 14.2.5.post0 h5888daf_0 conda-forge

+ tk 8.6.13 noxft_h4845f30_101 conda-forge

+ fmt 11.0.2 h434a139_0 conda-forge

+ libedit 3.1.20191231 he28a2e2_2 conda-forge

+ libnghttp2 1.64.0 h161d5f1_0 conda-forge

+ libsolv 0.7.30 h3509ff9_0 conda-forge

+ libxml2 2.13.5 h0d44e9d_1 conda-forge

+ readline 8.2 h8228510_1 conda-forge

+ yaml-cpp 0.8.0 h59595ed_0 conda-forge

+ zstd 1.5.6 ha6fb4c9_0 conda-forge

+ krb5 1.21.3 h659f571_0 conda-forge

+ libarchive 3.7.7 h4585015_3 conda-forge

+ python 3.12.8 h9e4cc4f_1_cpython conda-forge

+ libcurl 8.11.1 h332b0f4_0 conda-forge

+ menuinst 2.2.0 py312h7900ff3_0 conda-forge

+ archspec 0.2.3 pyhd8ed1ab_0 conda-forge

+ boltons 24.0.0 pyhd8ed1ab_1 conda-forge

+ brotli-python 1.1.0 py312h2ec8cdc_2 conda-forge

+ certifi 2024.12.14 pyhd8ed1ab_0 conda-forge

+ charset-normalizer 3.4.1 pyhd8ed1ab_0 conda-forge

+ colorama 0.4.6 pyhd8ed1ab_1 conda-forge

+ distro 1.9.0 pyhd8ed1ab_1 conda-forge

+ frozendict 2.4.6 py312h66e93f0_0 conda-forge

+ hpack 4.0.0 pyhd8ed1ab_1 conda-forge

+ hyperframe 6.0.1 pyhd8ed1ab_1 conda-forge

+ idna 3.10 pyhd8ed1ab_1 conda-forge

+ jsonpointer 3.0.0 py312h7900ff3_1 conda-forge

+ libmamba 1.5.12 h49b8a8d_0 conda-forge

+ packaging 24.2 pyhd8ed1ab_2 conda-forge

+ platformdirs 4.3.6 pyhd8ed1ab_1 conda-forge

+ pluggy 1.5.0 pyhd8ed1ab_1 conda-forge

+ pycosat 0.6.6 py312h66e93f0_2 conda-forge

+ pycparser 2.22 pyh29332c3_1 conda-forge

+ pysocks 1.7.1 pyha55dd90_7 conda-forge

+ ruamel.yaml.clib 0.2.8 py312h66e93f0_1 conda-forge

+ setuptools 75.6.0 pyhff2d567_1 conda-forge

+ truststore 0.10.0 pyhd8ed1ab_0 conda-forge

+ wheel 0.45.1 pyhd8ed1ab_1 conda-forge

+ cffi 1.17.1 py312h06ac9bb_0 conda-forge

+ h2 4.1.0 pyhd8ed1ab_1 conda-forge

+ jsonpatch 1.33 pyhd8ed1ab_1 conda-forge

+ libmambapy 1.5.12 py312hbaee817_0 conda-forge

+ pip 24.3.1 pyh8b19718_2 conda-forge

+ ruamel.yaml 0.18.8 py312h66e93f0_0 conda-forge

+ tqdm 4.67.1 pyhd8ed1ab_1 conda-forge

+ zstandard 0.23.0 py312hef9b889_1 conda-forge

+ conda-package-streaming 0.11.0 pyhd8ed1ab_0 conda-forge

+ urllib3 2.3.0 pyhd8ed1ab_0 conda-forge

+ conda-package-handling 2.4.0 pyha770c72_1 conda-forge

+ requests 2.32.3 pyhd8ed1ab_1 conda-forge

+ conda 24.11.2 py312h7900ff3_1 conda-forge

+ conda-libmamba-solver 24.9.0 pyhd8ed1ab_0 conda-forge

+ mamba 1.5.12 py312h9460a1c_0 conda-forge

Summary:

Install: 84 packages

Total download: 0 B

Transaction starting

Transaction finished

To activate this environment, use:

micromamba activate /home/runner/sct_7.2.dev0/python

micromamba activate /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python

Or to execute a single command in this environment, use:

micromamba run -p /home/runner/sct_7.2.dev0/python mycommand

micromamba run -p /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python mycommand

installation finished.

Creating conda environment...

Channels:

- defaults

- conda-forge

- nodefaults

Platform: linux-64

Collecting package metadata (repodata.json): ...working... done

Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==

current version: 24.11.2

latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /home/runner/sct_7.2.dev0/python/envs/venv_sct

environment location: /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct

added / updated specs:

- python=3.10

The following packages will be downloaded:

package | build

---------------------------|-----------------

bzip2-1.0.8 | hda65f42_8 254 KB conda-forge

_libgcc_mutex-0.1 | main 3 KB

ca-certificates-2025.10.5 | hbd8a1cb_0 152 KB conda-forge

_openmp_mutex-5.1 | 1_gnu 21 KB

ld_impl_linux-64-2.44 | ha97dd6f_2 730 KB conda-forge

bzip2-1.0.8 | h5eee18b_6 262 KB

libexpat-2.7.1 | hecca717_0 73 KB conda-forge

ca-certificates-2025.9.9 | h06a4308_0 127 KB

libffi-3.5.2 | h9ec8514_0 56 KB conda-forge

expat-2.7.1 | h6a678d5_0 182 KB

libgcc-15.2.0 | h767d61c_7 803 KB conda-forge

ld_impl_linux-64-2.44 | h153f514_2 672 KB

libgcc-ng-15.2.0 | h69a702a_7 29 KB conda-forge

libffi-3.4.4 | h6a678d5_1 141 KB

libgomp-15.2.0 | h767d61c_7 437 KB conda-forge

libgcc-ng-11.2.0 | h1234567_1 5.3 MB

liblzma-5.8.1 | hb9d3cd8_2 110 KB conda-forge

libgomp-11.2.0 | h1234567_1 474 KB

libnsl-2.0.1 | hb9d3cd8_1 33 KB conda-forge

libstdcxx-ng-11.2.0 | h1234567_1 4.7 MB

libsqlite-3.50.4 | h0c1763c_0 911 KB conda-forge

libuuid-1.41.5 | h5eee18b_0 27 KB

libuuid-2.41.2 | he9a06e4_0 36 KB conda-forge

libxcb-1.17.0 | h9b100fa_0 430 KB

ncurses-6.5 | h2d0b736_3 871 KB conda-forge

libzlib-1.3.1 | hb25bd0a_0 59 KB

openssl-3.5.4 | h26f9b46_0 3.0 MB conda-forge

ncurses-6.5 | h7934f7d_0 1.1 MB

pip-25.2 | pyh8b19718_0 1.1 MB conda-forge

openssl-3.0.18 | hd6dcaed_0 4.5 MB

python-3.10.19 |hd994cfb_1_cpython 24.2 MB conda-forge

pip-25.2 | pyhc872135_0 1.2 MB

readline-8.2 | h8c095d6_2 276 KB conda-forge

pthread-stubs-0.3 | h0ce48e5_1 5 KB

setuptools-80.9.0 | pyhff2d567_0 731 KB conda-forge

python-3.10.18 | h1a3bd86_0 26.5 MB

tk-8.6.13 |noxft_hd72426e_102 3.1 MB conda-forge

readline-8.3 | hc2a1206_0 471 KB

tzdata-2025b | h78e105d_0 120 KB conda-forge

setuptools-80.9.0 | py310h06a4308_0 1.4 MB

sqlite-3.50.2 | hb25bd0a_1 1.1 MB

tk-8.6.15 | h54e0aa7_0 3.4 MB

tzdata-2025b | h04d1e81_0 116 KB

wheel-0.45.1 | py310h06a4308_0 115 KB

xorg-libx11-1.8.12 | h9b100fa_1 895 KB

xorg-libxau-1.0.12 | h9b100fa_0 13 KB

xorg-libxdmcp-1.1.5 | h9b100fa_0 19 KB

xorg-xorgproto-2024.1 | h5eee18b_1 580 KB

xz-5.6.4 | h5eee18b_1 567 KB

zlib-1.3.1 | hb25bd0a_0 96 KB

------------------------------------------------------------

Total: 36.9 MB

Total: 54.5 MB

The following NEW packages will be INSTALLED:

_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge

_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main

_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu

_openmp_mutex pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu

bzip2 conda-forge/linux-64::bzip2-1.0.8-hda65f42_8

bzip2 pkgs/main/linux-64::bzip2-1.0.8-h5eee18b_6

ca-certificates conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0

ca-certificates pkgs/main/linux-64::ca-certifica

ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.44-ha97dd6f_2

libexpat conda-forge/linux-64::libexpat-2.7.1-hecca717_0

libffi conda-forge/linux-64::libffi-3.5.2-h9ec8514_0

libgcc conda-forge/linux-64::libgcc-15.2.0-h767d61c_7

libgcc-ng conda-forge/linux-64::libg

保存された差分

原文

ファイルを開く

*******************************
* Welcome to SCT installation *
*******************************

Checking OS type and version...

Linux runnervmnfq8z 6.8.0-1036-azure #42~22.04.1-Ubuntu SMP Fri Sep 12 00:09:41 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux

Checking requirements...

OK!

Source files not present. Downloading source files (@ master) to /tmp/tmp.zRQSjifCZQ/spinalcordtoolbox.
Cloning into '/tmp/tmp.zRQSjifCZQ/spinalcordtoolbox'...

SCT version ......... 7.2.dev0
Installation type ... package
Operating system .... linux (unknown)
Shell config ........ /home/runner/.bashrc

Checking permissions on required file /home/runner/.bashrc:
  - File exists: True
  - File ownership: True
  - Read permissions: True
  - Write permissions: True

SCT will be installed here: [/home/runner/sct_7.2.dev0]

Copying source files from /tmp/tmp.zRQSjifCZQ/spinalcordtoolbox to /home/runner/sct_7.2.dev0

wget -nv -O /tmp/tmp.zRQSjifCZQ/miniforge.sh https://github.com/conda-forge/miniforge/releases/download/24.11.2-1/Miniforge3-Linux-x86_64.sh

Installing Miniforge...

bash /tmp/tmp.zRQSjifCZQ/miniforge.sh -p /home/runner/sct_7.2.dev0/python -b -f

PREFIX=/home/runner/sct_7.2.dev0/python
Unpacking payload ...
Extracting _libgcc_mutex-0.1-conda_forge.tar.bz2
Extracting ca-certificates-2024.12.14-hbcca054_0.conda
Extracting ld_impl_linux-64-2.43-h712a8e2_2.conda
Extracting pybind11-abi-4-hd8ed1ab_3.tar.bz2
Extracting python_abi-3.12-5_cp312.conda
Extracting tzdata-2024b-hc8b5060_0.conda
Extracting libgomp-14.2.0-h77fa898_1.conda
Extracting _openmp_mutex-4.5-2_gnu.tar.bz2
Extracting libgcc-14.2.0-h77fa898_1.conda
Extracting c-ares-1.34.4-hb9d3cd8_0.conda
Extracting libexpat-2.6.4-h5888daf_0.conda
Extracting libgcc-ng-14.2.0-h69a702a_1.conda
Extracting liblzma-5.6.3-hb9d3cd8_1.conda
Extracting libstdcxx-14.2.0-hc0a3c3a_1.conda
Extracting libzlib-1.3.1-hb9d3cd8_2.conda
Extracting openssl-3.4.0-hb9d3cd8_0.conda
Extracting reproc-14.2.5.post0-hb9d3cd8_0.conda
Extracting bzip2-1.0.8-h4bc722e_7.conda
Extracting keyutils-1.6.1-h166bdaf_0.tar.bz2
Extracting libev-4.33-hd590300_2.conda
Extracting libffi-3.4.2-h7f98852_5.tar.bz2
Extracting libiconv-1.17-hd590300_2.conda
Extracting libnsl-2.0.1-hd590300_0.conda
Extracting libsqlite-3.47.2-hee588c1_0.conda
Extracting libssh2-1.11.1-hf672d98_0.conda
Extracting libstdcxx-ng-14.2.0-h4852527_1.conda
Extracting libuuid-2.38.1-h0b41bf4_0.conda
Extracting libxcrypt-4.4.36-hd590300_1.conda
Extracting lz4-c-1.10.0-h5888daf_1.conda
Extracting lzo-2.10-hd590300_1001.conda
Extracting ncurses-6.5-he02047a_1.conda
Extracting reproc-cpp-14.2.5.post0-h5888daf_0.conda
Extracting tk-8.6.13-noxft_h4845f30_101.conda
Extracting fmt-11.0.2-h434a139_0.conda
Extracting libedit-3.1.20191231-he28a2e2_2.tar.bz2
Extracting libnghttp2-1.64.0-h161d5f1_0.conda
Extracting libsolv-0.7.30-h3509ff9_0.conda
Extracting libxml2-2.13.5-h0d44e9d_1.conda
Extracting readline-8.2-h8228510_1.conda
Extracting yaml-cpp-0.8.0-h59595ed_0.conda
Extracting zstd-1.5.6-ha6fb4c9_0.conda
Extracting krb5-1.21.3-h659f571_0.conda
Extracting libarchive-3.7.7-h4585015_3.conda
Extracting python-3.12.8-h9e4cc4f_1_cpython.conda
Extracting libcurl-8.11.1-h332b0f4_0.conda
Extracting menuinst-2.2.0-py312h7900ff3_0.conda
Extracting archspec-0.2.3-pyhd8ed1ab_0.conda
Extracting boltons-24.0.0-pyhd8ed1ab_1.conda
Extracting brotli-python-1.1.0-py312h2ec8cdc_2.conda
Extracting certifi-2024.12.14-pyhd8ed1ab_0.conda
Extracting charset-normalizer-3.4.1-pyhd8ed1ab_0.conda
Extracting colorama-0.4.6-pyhd8ed1ab_1.conda
Extracting distro-1.9.0-pyhd8ed1ab_1.conda
Extracting frozendict-2.4.6-py312h66e93f0_0.conda
Extracting hpack-4.0.0-pyhd8ed1ab_1.conda
Extracting hyperframe-6.0.1-pyhd8ed1ab_1.conda
Extracting idna-3.10-pyhd8ed1ab_1.conda
Extracting jsonpointer-3.0.0-py312h7900ff3_1.conda
Extracting libmamba-1.5.12-h49b8a8d_0.conda
Extracting packaging-24.2-pyhd8ed1ab_2.conda
Extracting platformdirs-4.3.6-pyhd8ed1ab_1.conda
Extracting pluggy-1.5.0-pyhd8ed1ab_1.conda
Extracting pycosat-0.6.6-py312h66e93f0_2.conda
Extracting pycparser-2.22-pyh29332c3_1.conda
Extracting pysocks-1.7.1-pyha55dd90_7.conda
Extracting ruamel.yaml.clib-0.2.8-py312h66e93f0_1.conda
Extracting setuptools-75.6.0-pyhff2d567_1.conda
Extracting truststore-0.10.0-pyhd8ed1ab_0.conda
Extracting wheel-0.45.1-pyhd8ed1ab_1.conda
Extracting cffi-1.17.1-py312h06ac9bb_0.conda
Extracting h2-4.1.0-pyhd8ed1ab_1.conda
Extracting jsonpatch-1.33-pyhd8ed1ab_1.conda
Extracting libmambapy-1.5.12-py312hbaee817_0.conda
Extracting pip-24.3.1-pyh8b19718_2.conda
Extracting ruamel.yaml-0.18.8-py312h66e93f0_0.conda
Extracting tqdm-4.67.1-pyhd8ed1ab_1.conda
Extracting zstandard-0.23.0-py312hef9b889_1.conda
Extracting conda-package-streaming-0.11.0-pyhd8ed1ab_0.conda
Extracting urllib3-2.3.0-pyhd8ed1ab_0.conda
Extracting conda-package-handling-2.4.0-pyha770c72_1.conda
Extracting requests-2.32.3-pyhd8ed1ab_1.conda
Extracting conda-24.11.2-py312h7900ff3_1.conda
Extracting conda-libmamba-solver-24.9.0-pyhd8ed1ab_0.conda
Extracting mamba-1.5.12-py312h9460a1c_0.conda

Installing base environment...

Transaction

Prefix: /home/runner/sct_7.2.dev0/python

Updating specs:

- conda-forge/linux-64::_libgcc_mutex==0.1=conda_forge[md5=d7c89558ba9fa0495403155b64376d81]
   - conda-forge/linux-64::ca-certificates==2024.12.14=hbcca054_0[md5=720523eb0d6a9b0f6120c16b2aa4e7de]
   - conda-forge/linux-64::ld_impl_linux-64==2.43=h712a8e2_2[md5=048b02e3962f066da18efe3a21b77672]
   - conda-forge/noarch::pybind11-abi==4=hd8ed1ab_3[md5=878f923dd6acc8aeb47a75da6c4098be]
   - conda-forge/linux-64::python_abi==3.12=5_cp312[md5=0424ae29b104430108f5218a66db7260]
   - conda-forge/noarch::tzdata==2024b=hc8b5060_0[md5=8ac3367aafb1cc0a068483c580af8015]
   - conda-forge/linux-64::libgomp==14.2.0=h77fa898_1[md5=cc3573974587f12dda90d96e3e55a702]
   - conda-forge/linux-64::_openmp_mutex==4.5=2_gnu[md5=73aaf86a425cc6e73fcf236a5a46396d]
   - conda-forge/linux-64::libgcc==14.2.0=h77fa898_1[md5=3cb76c3f10d3bc7f1105b2fc9db984df]
   - conda-forge/linux-64::c-ares==1.34.4=hb9d3cd8_0[md5=e2775acf57efd5af15b8e3d1d74d72d3]
   - conda-forge/linux-64::libexpat==2.6.4=h5888daf_0[md5=db833e03127376d461e1e13e76f09b6c]
   - conda-forge/linux-64::libgcc-ng==14.2.0=h69a702a_1[md5=e39480b9ca41323497b05492a63bc35b]
   - conda-forge/linux-64::liblzma==5.6.3=hb9d3cd8_1[md5=2ecf2f1c7e4e21fcfe6423a51a992d84]
   - conda-forge/linux-64::libstdcxx==14.2.0=hc0a3c3a_1[md5=234a5554c53625688d51062645337328]
   - conda-forge/linux-64::libzlib==1.3.1=hb9d3cd8_2[md5=edb0dca6bc32e4f4789199455a1dbeb8]
   - conda-forge/linux-64::openssl==3.4.0=hb9d3cd8_0[md5=23cc74f77eb99315c0360ec3533147a9]
   - conda-forge/linux-64::reproc==14.2.5.post0=hb9d3cd8_0[md5=69fbc0a9e42eb5fe6733d2d60d818822]
   - conda-forge/linux-64::bzip2==1.0.8=h4bc722e_7[md5=62ee74e96c5ebb0af99386de58cf9553]
   - conda-forge/linux-64::keyutils==1.6.1=h166bdaf_0[md5=30186d27e2c9fa62b45fb1476b7200e3]
   - conda-forge/linux-64::libev==4.33=hd590300_2[md5=172bf1cd1ff8629f2b1179945ed45055]
   - conda-forge/linux-64::libffi==3.4.2=h7f98852_5[md5=d645c6d2ac96843a2bfaccd2d62b3ac3]
   - conda-forge/linux-64::libiconv==1.17=hd590300_2[md5=d66573916ffcf376178462f1b61c941e]
   - conda-forge/linux-64::libnsl==2.0.1=hd590300_0[md5=30fd6e37fe21f86f4bd26d6ee73eeec7]
   - conda-forge/linux-64::libsqlite==3.47.2=hee588c1_0[md5=b58da17db24b6e08bcbf8fed2fb8c915]
   - conda-forge/linux-64::libssh2==1.11.1=hf672d98_0[md5=be2de152d8073ef1c01b7728475f2fe7]
   - conda-forge/linux-64::libstdcxx-ng==14.2.0=h4852527_1[md5=8371ac6457591af2cf6159439c1fd051]
   - conda-forge/linux-64::libuuid==2.38.1=h0b41bf4_0[md5=40b61aab5c7ba9ff276c41cfffe6b80b]
   - conda-forge/linux-64::libxcrypt==4.4.36=hd590300_1[md5=5aa797f8787fe7a17d1b0821485b5adc]
   - conda-forge/linux-64::lz4-c==1.10.0=h5888daf_1[md5=9de5350a85c4a20c685259b889aa6393]
   - conda-forge/linux-64::lzo==2.10=hd590300_1001[md5=ec7398d21e2651e0dcb0044d03b9a339]
   - conda-forge/linux-64::ncurses==6.5=he02047a_1[md5=70caf8bb6cf39a0b6b7efc885f51c0fe]
   - conda-forge/linux-64::reproc-cpp==14.2.5.post0=h5888daf_0[md5=828302fca535f9cfeb598d5f7c204323]
   - conda-forge/linux-64::tk==8.6.13=noxft_h4845f30_101[md5=d453b98d9c83e71da0741bb0ff4d76bc]
   - conda-forge/linux-64::fmt==11.0.2=h434a139_0[md5=995f7e13598497691c1dc476d889bc04]
   - conda-forge/linux-64::libedit==3.1.20191231=he28a2e2_2[md5=4d331e44109e3f0e19b4cb8f9b82f3e1]
   - conda-forge/linux-64::libnghttp2==1.64.0=h161d5f1_0[md5=19e57602824042dfd0446292ef90488b]
   - conda-forge/linux-64::libsolv==0.7.30=h3509ff9_0[md5=02539b77d25aa4f65b20246549e256c3]
   - conda-forge/linux-64::libxml2==2.13.5=h0d44e9d_1[md5=f5b05674697ae7d2c5932766695945e1]
   - conda-forge/linux-64::readline==8.2=h8228510_1[md5=47d31b792659ce70f470b5c82fdfb7a4]
   - conda-forge/linux-64::yaml-cpp==0.8.0=h59595ed_0[md5=965eaacd7c18eb8361fd12bb9e7a57d7]
   - conda-forge/linux-64::zstd==1.5.6=ha6fb4c9_0[md5=4d056880988120e29d75bfff282e0f45]
   - conda-forge/linux-64::krb5==1.21.3=h659f571_0[md5=3f43953b7d3fb3aaa1d0d0723d91e368]
   - conda-forge/linux-64::libarchive==3.7.7=h4585015_3[md5=a28808eae584c7f519943719b2a2b386]
   - conda-forge/linux-64::python==3.12.8=h9e4cc4f_1_cpython[md5=7fd2fd79436d9b473812f14e86746844]
   - conda-forge/linux-64::libcurl==8.11.1=h332b0f4_0[md5=2b3e0081006dc21e8bf53a91c83a055c]
   - conda-forge/linux-64::menuinst==2.2.0=py312h7900ff3_0[md5=f22f8e77b36e67297feffe03eefd5375]
   - conda-forge/noarch::archspec==0.2.3=pyhd8ed1ab_0[md5=192278292e20704f663b9c766909d67b]
   - conda-forge/noarch::boltons==24.0.0=pyhd8ed1ab_1[md5=d88c38e66d85ecc9c7e2c4110676bbf4]
   - conda-forge/linux-64::brotli-python==1.1.0=py312h2ec8cdc_2[md5=b0b867af6fc74b2a0aa206da29c0f3cf]
   - conda-forge/noarch::certifi==2024.12.14=pyhd8ed1ab_0[md5=6feb87357ecd66733be3279f16a8c400]
   - conda-forge/noarch::charset-normalizer==3.4.1=pyhd8ed1ab_0[md5=e83a31202d1c0a000fce3e9cf3825875]
   - conda-forge/noarch::colorama==0.4.6=pyhd8ed1ab_1[md5=962b9857ee8e7018c22f2776ffa0b2d7]
   - conda-forge/noarch::distro==1.9.0=pyhd8ed1ab_1[md5=0a2014fd9860f8b1eaa0b1f3d3771a08]
   - conda-forge/linux-64::frozendict==2.4.6=py312h66e93f0_0[md5=9fa8408745a0621314b7751d11fecc18]
   - conda-forge/noarch::hpack==4.0.0=pyhd8ed1ab_1[md5=2aa5ff7fa34a81b9196532c84c10d865]
   - conda-forge/noarch::hyperframe==6.0.1=pyhd8ed1ab_1[md5=566e75c90c1d0c8c459eb0ad9833dc7a]
   - conda-forge/noarch::idna==3.10=pyhd8ed1ab_1[md5=39a4f67be3286c86d696df570b1201b7]
   - conda-forge/linux-64::jsonpointer==3.0.0=py312h7900ff3_1[md5=6b51f7459ea4073eeb5057207e2e1e3d]
   - conda-forge/linux-64::libmamba==1.5.12=h49b8a8d_0[md5=d6aec145c4f2473c09c2699d74f6dfc0]
   - conda-forge/noarch::packaging==24.2=pyhd8ed1ab_2[md5=3bfed7e6228ebf2f7b9eaa47f1b4e2aa]
   - conda-forge/noarch::platformdirs==4.3.6=pyhd8ed1ab_1[md5=577852c7e53901ddccc7e6a9959ddebe]
   - conda-forge/noarch::pluggy==1.5.0=pyhd8ed1ab_1[md5=e9dcbce5f45f9ee500e728ae58b605b6]
   - conda-forge/linux-64::pycosat==0.6.6=py312h66e93f0_2[md5=08223e6a73e0bca5ade16ec4cebebf23]
   - conda-forge/noarch::pycparser==2.22=pyh29332c3_1[md5=12c566707c80111f9799308d9e265aef]
   - conda-forge/noarch::pysocks==1.7.1=pyha55dd90_7[md5=461219d1a5bd61342293efa2c0c90eac]
   - conda-forge/linux-64::ruamel.yaml.clib==0.2.8=py312h66e93f0_1[md5=532c3e5d0280be4fea52396ec1fa7d5d]
   - conda-forge/noarch::setuptools==75.6.0=pyhff2d567_1[md5=fc80f7995e396cbaeabd23cf46c413dc]
   - conda-forge/noarch::truststore==0.10.0=pyhd8ed1ab_0[md5=ad1c20cd193e3044bcf17798c33b9d67]
   - conda-forge/noarch::wheel==0.45.1=pyhd8ed1ab_1[md5=75cb7132eb58d97896e173ef12ac9986]
   - conda-forge/linux-64::cffi==1.17.1=py312h06ac9bb_0[md5=a861504bbea4161a9170b85d4d2be840]
   - conda-forge/noarch::h2==4.1.0=pyhd8ed1ab_1[md5=825927dc7b0f287ef8d4d0011bb113b1]
   - conda-forge/noarch::jsonpatch==1.33=pyhd8ed1ab_1[md5=cb60ae9cf02b9fcb8004dec4089e5691]
   - conda-forge/linux-64::libmambapy==1.5.12=py312hbaee817_0[md5=88dd983e44c86cdde2817ecfa7d84d5a]
   - conda-forge/noarch::pip==24.3.1=pyh8b19718_2[md5=04e691b9fadd93a8a9fad87a81d4fd8f]
   - conda-forge/linux-64::ruamel.yaml==0.18.8=py312h66e93f0_0[md5=b77952bccd6b8d5c46e2f54354b4296b]
   - conda-forge/noarch::tqdm==4.67.1=pyhd8ed1ab_1[md5=9efbfdc37242619130ea42b1cc4ed861]
   - conda-forge/linux-64::zstandard==0.23.0=py312hef9b889_1[md5=8b7069e9792ee4e5b4919a7a306d2e67]
   - conda-forge/noarch::conda-package-streaming==0.11.0=pyhd8ed1ab_0[md5=bc9533d8616a97551ed144789bf9c1cd]
   - conda-forge/noarch::urllib3==2.3.0=pyhd8ed1ab_0[md5=32674f8dbfb7b26410ed580dd3c10a29]
   - conda-forge/noarch::conda-package-handling==2.4.0=pyha770c72_1[md5=28b86d110bda4ef40e680d1afa9ddb1d]
   - conda-forge/noarch::requests==2.32.3=pyhd8ed1ab_1[md5=a9b9368f3701a417eac9edbcae7cb737]
   - conda-forge/linux-64::conda==24.11.2=py312h7900ff3_1[md5=2dff8a88fb65b9c99f6c28aad1126c66]
   - conda-forge/noarch::conda-libmamba-solver==24.9.0=pyhd8ed1ab_0[md5=45378d089c5f72c9c0d63d58414c645d]
   - conda-forge/linux-64::mamba==1.5.12=py312h9460a1c_0[md5=59a9360536caad98732fdfdc320e41dc]

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

+ _libgcc_mutex                     0.1  conda_forge         conda-forge         
  + ca-certificates            2024.12.14  hbcca054_0          conda-forge         
  + ld_impl_linux-64                 2.43  h712a8e2_2          conda-forge         
  + pybind11-abi                        4  hd8ed1ab_3          conda-forge         
  + python_abi                       3.12  5_cp312             conda-forge         
  + tzdata                          2024b  hc8b5060_0          conda-forge         
  + libgomp                        14.2.0  h77fa898_1          conda-forge         
  + _openmp_mutex                     4.5  2_gnu               conda-forge         
  + libgcc                         14.2.0  h77fa898_1          conda-forge         
  + c-ares                         1.34.4  hb9d3cd8_0          conda-forge         
  + libexpat                        2.6.4  h5888daf_0          conda-forge         
  + libgcc-ng                      14.2.0  h69a702a_1          conda-forge         
  + liblzma                         5.6.3  hb9d3cd8_1          conda-forge         
  + libstdcxx                      14.2.0  hc0a3c3a_1          conda-forge         
  + libzlib                         1.3.1  hb9d3cd8_2          conda-forge         
  + openssl                         3.4.0  hb9d3cd8_0          conda-forge         
  + reproc                   14.2.5.post0  hb9d3cd8_0          conda-forge         
  + bzip2                           1.0.8  h4bc722e_7          conda-forge         
  + keyutils                        1.6.1  h166bdaf_0          conda-forge         
  + libev                            4.33  hd590300_2          conda-forge         
  + libffi                          3.4.2  h7f98852_5          conda-forge         
  + libiconv                         1.17  hd590300_2          conda-forge         
  + libnsl                          2.0.1  hd590300_0          conda-forge         
  + libsqlite                      3.47.2  hee588c1_0          conda-forge         
  + libssh2                        1.11.1  hf672d98_0          conda-forge         
  + libstdcxx-ng                   14.2.0  h4852527_1          conda-forge         
  + libuuid                        2.38.1  h0b41bf4_0          conda-forge         
  + libxcrypt                      4.4.36  hd590300_1          conda-forge         
  + lz4-c                          1.10.0  h5888daf_1          conda-forge         
  + lzo                              2.10  hd590300_1001       conda-forge         
  + ncurses                           6.5  he02047a_1          conda-forge         
  + reproc-cpp               14.2.5.post0  h5888daf_0          conda-forge         
  + tk                             8.6.13  noxft_h4845f30_101  conda-forge         
  + fmt                            11.0.2  h434a139_0          conda-forge         
  + libedit                  3.1.20191231  he28a2e2_2          conda-forge         
  + libnghttp2                     1.64.0  h161d5f1_0          conda-forge         
  + libsolv                        0.7.30  h3509ff9_0          conda-forge         
  + libxml2                        2.13.5  h0d44e9d_1          conda-forge         
  + readline                          8.2  h8228510_1          conda-forge         
  + yaml-cpp                        0.8.0  h59595ed_0          conda-forge         
  + zstd                            1.5.6  ha6fb4c9_0          conda-forge         
  + krb5                           1.21.3  h659f571_0          conda-forge         
  + libarchive                      3.7.7  h4585015_3          conda-forge         
  + python                         3.12.8  h9e4cc4f_1_cpython  conda-forge         
  + libcurl                        8.11.1  h332b0f4_0          conda-forge         
  + menuinst                        2.2.0  py312h7900ff3_0     conda-forge         
  + archspec                        0.2.3  pyhd8ed1ab_0        conda-forge         
  + boltons                        24.0.0  pyhd8ed1ab_1        conda-forge         
  + brotli-python                   1.1.0  py312h2ec8cdc_2     conda-forge         
  + certifi                    2024.12.14  pyhd8ed1ab_0        conda-forge         
  + charset-normalizer              3.4.1  pyhd8ed1ab_0        conda-forge         
  + colorama                        0.4.6  pyhd8ed1ab_1        conda-forge         
  + distro                          1.9.0  pyhd8ed1ab_1        conda-forge         
  + frozendict                      2.4.6  py312h66e93f0_0     conda-forge         
  + hpack                           4.0.0  pyhd8ed1ab_1        conda-forge         
  + hyperframe                      6.0.1  pyhd8ed1ab_1        conda-forge         
  + idna                             3.10  pyhd8ed1ab_1        conda-forge         
  + jsonpointer                     3.0.0  py312h7900ff3_1     conda-forge         
  + libmamba                       1.5.12  h49b8a8d_0          conda-forge         
  + packaging                        24.2  pyhd8ed1ab_2        conda-forge         
  + platformdirs                    4.3.6  pyhd8ed1ab_1        conda-forge         
  + pluggy                          1.5.0  pyhd8ed1ab_1        conda-forge         
  + pycosat                         0.6.6  py312h66e93f0_2     conda-forge         
  + pycparser                        2.22  pyh29332c3_1        conda-forge         
  + pysocks                         1.7.1  pyha55dd90_7        conda-forge         
  + ruamel.yaml.clib                0.2.8  py312h66e93f0_1     conda-forge         
  + setuptools                     75.6.0  pyhff2d567_1        conda-forge         
  + truststore                     0.10.0  pyhd8ed1ab_0        conda-forge         
  + wheel                          0.45.1  pyhd8ed1ab_1        conda-forge         
  + cffi                           1.17.1  py312h06ac9bb_0     conda-forge         
  + h2                              4.1.0  pyhd8ed1ab_1        conda-forge         
  + jsonpatch                        1.33  pyhd8ed1ab_1        conda-forge         
  + libmambapy                     1.5.12  py312hbaee817_0     conda-forge         
  + pip                            24.3.1  pyh8b19718_2        conda-forge         
  + ruamel.yaml                    0.18.8  py312h66e93f0_0     conda-forge         
  + tqdm                           4.67.1  pyhd8ed1ab_1        conda-forge         
  + zstandard                      0.23.0  py312hef9b889_1     conda-forge         
  + conda-package-streaming        0.11.0  pyhd8ed1ab_0        conda-forge         
  + urllib3                         2.3.0  pyhd8ed1ab_0        conda-forge         
  + conda-package-handling          2.4.0  pyha770c72_1        conda-forge         
  + requests                       2.32.3  pyhd8ed1ab_1        conda-forge         
  + conda                         24.11.2  py312h7900ff3_1     conda-forge         
  + conda-libmamba-solver          24.9.0  pyhd8ed1ab_0        conda-forge         
  + mamba                          1.5.12  py312h9460a1c_0     conda-forge

Summary:

Install: 84 packages

Total download: 0 B

Transaction starting

Transaction finished

To activate this environment, use:

micromamba activate /home/runner/sct_7.2.dev0/python

Or to execute a single command in this environment, use:

micromamba run -p /home/runner/sct_7.2.dev0/python mycommand

installation finished.

Creating conda environment...

Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /home/runner/sct_7.2.dev0/python/envs/venv_sct

added / updated specs:
    - python=3.10

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    bzip2-1.0.8                |       hda65f42_8         254 KB  conda-forge
    ca-certificates-2025.10.5  |       hbd8a1cb_0         152 KB  conda-forge
    ld_impl_linux-64-2.44      |       ha97dd6f_2         730 KB  conda-forge
    libexpat-2.7.1             |       hecca717_0          73 KB  conda-forge
    libffi-3.5.2               |       h9ec8514_0          56 KB  conda-forge
    libgcc-15.2.0              |       h767d61c_7         803 KB  conda-forge
    libgcc-ng-15.2.0           |       h69a702a_7          29 KB  conda-forge
    libgomp-15.2.0             |       h767d61c_7         437 KB  conda-forge
    liblzma-5.8.1              |       hb9d3cd8_2         110 KB  conda-forge
    libnsl-2.0.1               |       hb9d3cd8_1          33 KB  conda-forge
    libsqlite-3.50.4           |       h0c1763c_0         911 KB  conda-forge
    libuuid-2.41.2             |       he9a06e4_0          36 KB  conda-forge
    ncurses-6.5                |       h2d0b736_3         871 KB  conda-forge
    openssl-3.5.4              |       h26f9b46_0         3.0 MB  conda-forge
    pip-25.2                   |     pyh8b19718_0         1.1 MB  conda-forge
    python-3.10.19             |hd994cfb_1_cpython        24.2 MB  conda-forge
    readline-8.2               |       h8c095d6_2         276 KB  conda-forge
    setuptools-80.9.0          |     pyhff2d567_0         731 KB  conda-forge
    tk-8.6.13                  |noxft_hd72426e_102         3.1 MB  conda-forge
    tzdata-2025b               |       h78e105d_0         120 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        36.9 MB

The following NEW packages will be INSTALLED:

_libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu 
  bzip2              conda-forge/linux-64::bzip2-1.0.8-hda65f42_8 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0 
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.44-ha97dd6f_2 
  libexpat           conda-forge/linux-64::libexpat-2.7.1-hecca717_0 
  libffi             conda-forge/linux-64::libffi-3.5.2-h9ec8514_0 
  libgcc             conda-forge/linux-64::libgcc-15.2.0-h767d61c_7 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_7 
  libgomp            conda-forge/linux-64::libgomp-15.2.0-h767d61c_7 
  liblzma            conda-forge/linux-64::liblzma-5.8.1-hb9d3cd8_2 
  libnsl             conda-forge/linux-64::libnsl-2.0.1-hb9d3cd8_1 
  libsqlite          conda-forge/linux-64::libsqlite-3.50.4-h0c1763c_0 
  libuuid            conda-forge/linux-64::libuuid-2.41.2-he9a06e4_0 
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 
  libzlib            conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 
  ncurses            conda-forge/linux-64::ncurses-6.5-h2d0b736_3 
  openssl            conda-forge/linux-64::openssl-3.5.4-h26f9b46_0 
  pip                conda-forge/noarch::pip-25.2-pyh8b19718_0 
  python             conda-forge/linux-64::python-3.10.19-hd994cfb_1_cpython 
  readline           conda-forge/linux-64::readline-8.2-h8c095d6_2 
  setuptools         conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0 
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_hd72426e_102 
  tzdata             conda-forge/noarch::tzdata-2025b-h78e105d_0 
  wheel              conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1

Downloading and Extracting Packages: ...working...
python-3.10.19       | 24.2 MB   |            |   0%

tk-8.6.13            | 3.1 MB    |            |   0%

openssl-3.5.4        | 3.0 MB    |            |   0%

pip-25.2             | 1.1 MB    |            |   0%

libsqlite-3.50.4     | 911 KB    |            |   0%

ncurses-6.5          | 871 KB    |            |   0%

libgcc-15.2.0        | 803 KB    |            |   0%

setuptools-80.9.0    | 731 KB    |            |   0%

ld_impl_linux-64-2.4 | 730 KB    |            |   0%

libgomp-15.2.0       | 437 KB    |            |   0%

readline-8.2         | 276 KB    |            |   0%

bzip2-1.0.8          | 254 KB    |            |   0%

ca-certificates-2025 | 152 KB    |            |   0%

tzdata-2025b         | 120 KB    |            |   0%

liblzma-5.8.1        | 110 KB    |            |   0%

libexpat-2.7.1       | 73 KB     |            |   0%

libffi-3.5.2         | 56 KB     |            |   0%

libuuid-2.41.2       | 36 KB     |            |   0%

libnsl-2.0.1         | 33 KB     |            |   0%

... (more hidden) ...

pip-25.2             | 1.1 MB    | ########## | 100% 
python-3.10.19       | 24.2 MB   | #          |  11%

tk-8.6.13            | 3.1 MB    |            |   1%

openssl-3.5.4        | 3.0 MB    | ######1    |  61%

libsqlite-3.50.4     | 911 KB    | ########## | 100%

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openssl-3.5.4        | 3.0 MB    | ########## | 100%

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ld_impl_linux-64-2.4 | 730 KB    | 2          |   2%

setuptools-80.9.0    | 731 KB    | ########## | 100%

libgomp-15.2.0       | 437 KB    | 3          |   4%

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ld_impl_linux-64-2.4 | 730 KB    | ########## | 100% 
python-3.10.19       | 24.2 MB   | ###6       |  37%

libgomp-15.2.0       | 437 KB    | ########## | 100%

readline-8.2         | 276 KB    | 5          |   6%

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ca-certificates-2025 | 152 KB    | #          |  11%

bzip2-1.0.8          | 254 KB    | 6          |   6%

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tzdata-2025b         | 120 KB    | #3         |  13%

liblzma-5.8.1        | 110 KB    | #4         |  15%

bzip2-1.0.8          | 254 KB    | ########## | 100%

tzdata-2025b         | 120 KB    | ########## | 100%

liblzma-5.8.1        | 110 KB    | ########## | 100%

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python-3.10.19       | 24.2 MB   | ########9  |  89%

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done
Preparing transaction: - \ done
Verifying transaction: / - \ | / - \ | / done
Executing transaction: \ | / - \ | / - \ | / - \ | / - \ | / - \ done
#
# To activate this environment, use
#
#     $ conda activate /home/runner/sct_7.2.dev0/python/envs/venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /home/runner/sct_7.2.dev0/python/envs/venv_sct

added / updated specs:
    - libstdcxx-ng

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    libstdcxx-15.2.0           |       h8f9b012_7         3.7 MB  conda-forge
    libstdcxx-ng-15.2.0        |       h4852527_7          29 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         3.7 MB

The following NEW packages will be INSTALLED:

libstdcxx          conda-forge/linux-64::libstdcxx-15.2.0-h8f9b012_7 
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-15.2.0-h4852527_7

Downloading and Extracting Packages: ...working...
libstdcxx-15.2.0     | 3.7 MB    |            |   0%

libstdcxx-ng-15.2.0  | 29 KB     |            |   0%

libstdcxx-ng-15.2.0  | 29 KB     | ########## | 100%

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libstdcxx-15.2.0     | 3.7 MB    | ########4  |  84% 
libstdcxx-15.2.0     | 3.7 MB    | ########## | 100% 
libstdcxx-15.2.0     | 3.7 MB    | ########## | 100%

done
Preparing transaction: - done
Verifying transaction: | done
Executing transaction: - done
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

# All requested packages already installed.

Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /home/runner/sct_7.2.dev0/python/envs/venv_sct

added / updated specs:
    - xorg-libxinerama

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    libxcb-1.17.0              |       h8a09558_0         387 KB  conda-forge
    pthread-stubs-0.4          |    hb9d3cd8_1002           8 KB  conda-forge
    xorg-libx11-1.8.12         |       h4f16b4b_0         816 KB  conda-forge
    xorg-libxau-1.0.12         |       hb9d3cd8_0          14 KB  conda-forge
    xorg-libxdmcp-1.1.5        |       hb9d3cd8_0          19 KB  conda-forge
    xorg-libxext-1.3.6         |       hb9d3cd8_0          49 KB  conda-forge
    xorg-libxinerama-1.1.5     |       h5888daf_1          14 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         1.3 MB

The following NEW packages will be INSTALLED:

libxcb             conda-forge/linux-64::libxcb-1.17.0-h8a09558_0 
  pthread-stubs      conda-forge/linux-64::pthread-stubs-0.4-hb9d3cd8_1002 
  xorg-libx11        conda-forge/linux-64::xorg-libx11-1.8.12-h4f16b4b_0 
  xorg-libxau        conda-forge/linux-64::xorg-libxau-1.0.12-hb9d3cd8_0 
  xorg-libxdmcp      conda-forge/linux-64::xorg-libxdmcp-1.1.5-hb9d3cd8_0 
  xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.6-hb9d3cd8_0 
  xorg-libxinerama   conda-forge/linux-64::xorg-libxinerama-1.1.5-h5888daf_1

Downloading and Extracting Packages: ...working...
xorg-libx11-1.8.12   | 816 KB    |            |   0%

libxcb-1.17.0        | 387 KB    |            |   0%

xorg-libxext-1.3.6   | 49 KB     |            |   0%

xorg-libxdmcp-1.1.5  | 19 KB     |            |   0%

xorg-libxau-1.0.12   | 14 KB     |            |   0%

xorg-libxinerama-1.1 | 14 KB     |            |   0%

pthread-stubs-0.4    | 8 KB      |            |   0%

xorg-libxau-1.0.12   | 14 KB     | ########## | 100%

xorg-libxext-1.3.6   | 49 KB     | ########## | 100%

libxcb-1.17.0        | 387 KB    | ########## | 100%

xorg-libxdmcp-1.1.5  | 19 KB     | ########## | 100% 
xorg-libx11-1.8.12   | 816 KB    | ########## | 100% 
xorg-libx11-1.8.12   | 816 KB    | ########## | 100%

xorg-libxau-1.0.12   | 14 KB     | ########## | 100%

xorg-libxinerama-1.1 | 14 KB     | ########## | 100%

pthread-stubs-0.4    | 8 KB      | ########## | 100%

xorg-libxext-1.3.6   | 49 KB     | ########## | 100%

xorg-libxdmcp-1.1.5  | 19 KB     | ########## | 100%

xorg-libxinerama-1.1 | 14 KB     | ########## | 100%

pthread-stubs-0.4    | 8 KB      | ########## | 100%

libxcb-1.17.0        | 387 KB    | ########## | 100%

libxcb-1.17.0        | 387 KB    | ########## | 100% 
xorg-libx11-1.8.12   | 816 KB    | ########## | 100%

done
Preparing transaction: - done
Verifying transaction: | / done
Executing transaction: \ done
Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.10/site-packages (25.2)

Installing Python dependencies...

Using requirements.txt (git installation)

Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu
Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment
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Collecting nnunetv2!=2.4.*,<2.6,>2.3.0 (from -r requirements.txt (line 42))
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  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
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Collecting numpy<2 (from -r requirements.txt (line 44))
  Downloading numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
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  Downloading pandas-2.3.3-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB)
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Collecting pyqt5>=5.15.0 (from -r requirements.txt (line 62))
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Collecting pystrum>=0.3 (from -r requirements.txt (line 70))
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Collecting pytest (from -r requirements.txt (line 71))
  Downloading pytest-8.4.2-py3-none-any.whl.metadata (7.7 kB)
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  Downloading scikit_learn-1.7.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (11 kB)
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  Downloading https://download.pytorch.org/whl/cpu/torch-2.2.2%2Bcpu-cp310-cp310-linux_x86_64.whl (186.8 MB)
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  Downloading pyyaml-6.0.3-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB)
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Collecting cython!=0.29.29,>=0.29.24 (from dipy==1.8.0->-r requirements.txt (line 14))
  Downloading cython-3.1.5-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (4.3 kB)
Collecting packaging>=21 (from dipy==1.8.0->-r requirements.txt (line 14))
  Downloading packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
Collecting trx-python>=0.2.9 (from dipy==1.8.0->-r requirements.txt (line 14))
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Collecting dynamic-network-architectures<0.4,>=0.3.1 (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
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Collecting dicom2nifti (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
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Collecting batchgenerators>=0.25 (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading batchgenerators-0.25.1.tar.gz (76 kB)
  Preparing metadata (setup.py): started
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Collecting SimpleITK>=2.2.1 (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading simpleitk-2.5.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.2 kB)
Collecting graphviz (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading graphviz-0.21-py3-none-any.whl.metadata (12 kB)
Collecting tifffile (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading tifffile-2025.5.10-py3-none-any.whl.metadata (31 kB)
Collecting seaborn (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
Collecting imagecodecs (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading imagecodecs-2025.3.30-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (20 kB)
Collecting yacs (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading yacs-0.1.8-py3-none-any.whl.metadata (639 bytes)
Collecting batchgeneratorsv2>=0.2 (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading batchgeneratorsv2-0.3.0.tar.gz (44 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
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Collecting einops (from nnunetv2!=2.4.*,<2.6,>2.3.0->-r requirements.txt (line 42))
  Downloading einops-0.8.1-py3-none-any.whl.metadata (13 kB)
Collecting connected-components-3d (from acvl_utils!=0.2.1->-r requirements.txt (line 7))
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Collecting coloredlogs (from onnxruntime!=1.16.0,<1.22.0,>=1.7.0->-r requirements.txt (line 53))
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Collecting flatbuffers (from onnxruntime!=1.16.0,<1.22.0,>=1.7.0->-r requirements.txt (line 53))
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Collecting protobuf (from onnxruntime!=1.16.0,<1.22.0,>=1.7.0->-r requirements.txt (line 53))
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Collecting sympy (from onnxruntime!=1.16.0,<1.22.0,>=1.7.0->-r requirements.txt (line 53))
  Downloading https://download.pytorch.org/whl/sympy-1.14.0-py3-none-any.whl.metadata (12 kB)
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Collecting typing-extensions>=4.8.0 (from torch<2.3->-r requirements.txt (line 91))
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Building wheels for collected packages: nnunetv2, acvl_utils, dynamic-network-architectures, sqlalchemy, pystrum, batchgenerators, batchgeneratorsv2, docopt
  Building wheel for nnunetv2 (pyproject.toml): started
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  Created wheel for nnunetv2: filename=nnunetv2-2.5.2-py3-none-any.whl size=270734 sha256=0f899771e1c1a82645adfad6fe00151156a168aecea685f6b1ab3a98a8fe8429
  Stored in directory: /home/runner/.cache/pip/wheels/61/b4/d9/5916f251c9378926a472f89e11ebc0dde9d0b7de41826f1c12
  DEPRECATION: Building 'acvl_utils' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'acvl_utils'. Discussion can be found at https://github.com/pypa/pip/issues/6334
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  Created wheel for acvl_utils: filename=acvl_utils-0.2.5-py3-none-any.whl size=27243 sha256=34d494f1757147c5495116a1d508999249d3532cb5ffe4b394ce4669c20140c7
  Stored in directory: /home/runner/.cache/pip/wheels/11/68/32/42aed9ef6a7c3ff868f84b243120481ef8a19d0ddbc2551133
  DEPRECATION: Building 'dynamic-network-architectures' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'dynamic-network-architectures'. Discussion can be found at https://github.com/pypa/pip/issues/6334
  Building wheel for dynamic-network-architectures (setup.py): started
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  Created wheel for dynamic-network-architectures: filename=dynamic_network_architectures-0.3.1-py3-none-any.whl size=30108 sha256=fca1a384d5564e376760e28e100f281cbf48eb147dfc9586f5430e28edb2feaf
  Stored in directory: /home/runner/.cache/pip/wheels/55/1b/13/a6419c8dbf998b9343710355ec3edc5c8e24d9b7b22eec95fb
  DEPRECATION: Building 'sqlalchemy' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'sqlalchemy'. Discussion can be found at https://github.com/pypa/pip/issues/6334
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  Created wheel for sqlalchemy: filename=sqlalchemy-1.3.24-cp310-cp310-linux_x86_64.whl size=1220404 sha256=3d0e64f66ab469d744dac72962aab8821252a0dfef82037ba9ffd75d8f6f3563
  Stored in directory: /home/runner/.cache/pip/wheels/27/51/b3/3481e88d5a5ba95dd4aafedc9316774d941c4ba61cfb93add8
  DEPRECATION: Building 'pystrum' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'pystrum'. Discussion can be found at https://github.com/pypa/pip/issues/6334
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  Created wheel for pystrum: filename=pystrum-0.4-py3-none-any.whl size=19569 sha256=20a30f7c388f30d177f58bb986d82781b4b476c4e41bab6320de3bdc16d30ca3
  Stored in directory: /home/runner/.cache/pip/wheels/aa/08/d0/914025beb5a12a855b8aafd22eeedc547198684a3f4409f66c
  DEPRECATION: Building 'batchgenerators' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'batchgenerators'. Discussion can be found at https://github.com/pypa/pip/issues/6334
  Building wheel for batchgenerators (setup.py): started
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  Created wheel for batchgenerators: filename=batchgenerators-0.25.1-py3-none-any.whl size=93163 sha256=1a287f5c5e2c77501170609bf7238465fabd22f9e8780510d39b71bbfc2c55b7
  Stored in directory: /home/runner/.cache/pip/wheels/be/1b/30/b3f066999ad01855fc903fe7c93c25682333dd5645d5c75434
  Building wheel for batchgeneratorsv2 (pyproject.toml): started
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  Created wheel for batchgeneratorsv2: filename=batchgeneratorsv2-0.3.0-py3-none-any.whl size=65215 sha256=65df84e02f7c82d7c2cd5f181cce535082803d1b383b8cd8c7c4e20b9cf2eab1
  Stored in directory: /home/runner/.cache/pip/wheels/85/91/18/f246cf6cecb275d0e293271390794a0c090621cfc1ab1501c7
  DEPRECATION: Building 'docopt' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'docopt'. Discussion can be found at https://github.com/pypa/pip/issues/6334
  Building wheel for docopt (setup.py): started
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  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13783 sha256=80d5b11012d68e5f292dbc4b9c532c4b04a87bb20968ce582db0a7ea1dece35b
  Stored in directory: /home/runner/.cache/pip/wheels/fc/ab/d4/5da2067ac95b36618c629a5f93f809425700506f72c9732fac
Successfully built nnunetv2 acvl_utils dynamic-network-architectures sqlalchemy pystrum batchgenerators batchgeneratorsv2 docopt
Installing collected packages: xlwt, SimpleITK, pytz, PyQt5-Qt5, py-cpuinfo, mpmath, linecache2, flatbuffers, docopt, dictdiffer, argparse, xlsxwriter, wrapt, urllib3, typing-extensions, traitlets, traceback2, tqdm, tomli, threadpoolctl, tensorboard-data-server, sympy, sqlalchemy, smmap, six, shellingham, setuptools, pyyaml, python-gdcm, PyQt5-sip, pyparsing, pygments, pydicom, psutil, protobuf, portalocker, pluggy, platformdirs, pillow, packaging, orderly-set, numpy, num2words, networkx, ndindex, msgpack, mdurl, MarkupSafe, markdown, lxml, loguru, kiwisolver, joblib, interface-meta, iniconfig, importlib-resources, idna, humanize, humanfriendly, graphviz, future, fsspec, fonttools, filelock, einops, cython, cycler, coverage, click, charset_normalizer, certifi, astor, annotated-types, acres, absl-py, yacs, wquantiles, werkzeug, unittest2, typing-inspection, transforms3d, tifffile, setuptools-scm, sentry-sdk, scipy, requirements-parser, requests, python-dateutil, pyqt5, pydantic-core, onnx, numexpr, nibabel, matplotlib-inline, markdown-it-py, lazy-loader, jinja2, imageio, imagecodecs, h5py, grpcio, gitdb, exceptiongroup, deprecated, deepdiff, csv-diff, contourpy, connected-components-3d, coloredlogs, bidsschematools, trx-python, torch, tensorboard, scikit-learn, scikit-image, rich, pytest, pydantic, pandas, onnxruntime, matplotlib, gryds, gitpython, dicom2nifti, blosc2, bids-validator, wandb, typer, torchvision, seaborn, pytest-cov, pytest_console_scripts, pystrum, nilearn, monai, formulaic, fft-conv-pytorch, dynamic-network-architectures, dipy, batchgenerators, torchio, pybids, neurite, batchgeneratorsv2, acvl_utils, voxelmorph, nnunetv2, ivadomed, totalspineseg
Successfully installed MarkupSafe-3.0.3 PyQt5-Qt5-5.15.2 PyQt5-sip-12.17.1 SimpleITK-2.5.2 absl-py-2.3.1 acres-0.5.0 acvl_utils-0.2.5 annotated-types-0.7.0 argparse-1.4.0 astor-0.8.1 batchgenerators-0.25.1 batchgeneratorsv2-0.3.0 bids-validator-1.14.7.post0 bidsschematools-1.1.0 blosc2-3.10.2 certifi-2025.10.5 charset_normalizer-3.4.4 click-8.3.0 coloredlogs-15.0.1 connected-components-3d-3.26.0 contourpy-1.3.2 coverage-7.11.0 csv-diff-1.2 cycler-0.12.1 cython-3.1.5 deepdiff-8.6.1 deprecated-1.2.18 dicom2nifti-2.6.2 dictdiffer-0.9.0 dipy-1.8.0 docopt-0.6.2 dynamic-network-architectures-0.3.1 einops-0.8.1 exceptiongroup-1.3.0 fft-conv-pytorch-1.2.0 filelock-3.20.0 flatbuffers-25.9.23 fonttools-4.60.1 formulaic-0.3.4 fsspec-2025.9.0 future-1.0.0 gitdb-4.0.12 gitpython-3.1.45 graphviz-0.21 grpcio-1.75.1 gryds-0.0.9 h5py-3.15.1 humanfriendly-10.0 humanize-4.14.0 idna-3.11 imagecodecs-2025.3.30 imageio-2.37.0 importlib-resources-6.5.2 iniconfig-2.3.0 interface-meta-1.3.0 ivadomed-2.9.10 jinja2-3.1.6 joblib-1.5.2 kiwisolver-1.4.9 lazy-loader-0.4 linecache2-1.0.0 loguru-0.7.3 lxml-6.0.2 markdown-3.9 markdown-it-py-4.0.0 matplotlib-3.10.7 matplotlib-inline-0.1.7 mdurl-0.1.2 monai-1.4.0 mpmath-1.3.0 msgpack-1.1.2 ndindex-1.10.0 networkx-3.4.2 neurite-0.2 nibabel-5.3.2 nilearn-0.10.4 nnunetv2-2.5.2 num2words-0.5.14 numexpr-2.14.1 numpy-1.26.4 onnx-1.16.1 onnxruntime-1.21.1 orderly-set-5.5.0 packaging-25.0 pandas-1.5.3 pillow-12.0.0 platformdirs-4.5.0 pluggy-1.6.0 portalocker-3.2.0 protobuf-6.33.0 psutil-7.1.1 py-cpuinfo-9.0.0 pybids-0.15.5 pydantic-2.12.3 pydantic-core-2.41.4 pydicom-3.0.1 pygments-2.19.2 pyparsing-3.2.5 pyqt5-5.15.11 pystrum-0.4 pytest-8.4.2 pytest-cov-7.0.0 pytest_console_scripts-1.4.1 python-dateutil-2.9.0.post0 python-gdcm-3.2.2 pytz-2025.2 pyyaml-6.0.3 requests-2.32.5 requirements-parser-0.13.0 rich-14.2.0 scikit-image-0.25.2 scikit-learn-1.7.2 scipy-1.15.3 seaborn-0.13.2 sentry-sdk-2.42.0 setuptools-80.9.0 setuptools-scm-9.2.2 shellingham-1.5.4 six-1.17.0 smmap-5.0.2 sqlalchemy-1.3.24 sympy-1.14.0 tensorboard-2.20.0 tensorboard-data-server-0.7.2 threadpoolctl-3.6.0 tifffile-2025.5.10 tomli-2.3.0 torch-2.2.2+cpu torchio-0.20.23 torchvision-0.17.2+cpu totalspineseg-20250709 tqdm-4.67.1 traceback2-1.4.0 traitlets-5.14.3 transforms3d-0.4.2 trx-python-0.3 typer-0.19.2 typing-extensions-4.15.0 typing-inspection-0.4.2 unittest2-1.1.0 urllib3-2.5.0 voxelmorph-0.2 wandb-0.22.2 werkzeug-3.1.3 wquantiles-0.6 wrapt-1.17.3 xlsxwriter-3.2.9 xlwt-1.3.0 yacs-0.1.8

Installing spinalcordtoolbox...

Obtaining file:///home/runner/sct_7.2.dev0
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Checking if build backend supports build_editable: started
  Checking if build backend supports build_editable: finished with status 'done'
  Getting requirements to build editable: started
  Getting requirements to build editable: finished with status 'done'
  Preparing editable metadata (pyproject.toml): started
  Preparing editable metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: spinalcordtoolbox
  Building editable for spinalcordtoolbox (pyproject.toml): started
  Building editable for spinalcordtoolbox (pyproject.toml): finished with status 'done'
  Created wheel for spinalcordtoolbox: filename=spinalcordtoolbox-7.2.dev0-0.editable-py3-none-any.whl size=9857 sha256=12cd1cafc61c7a9a2a2cdf17b753e9dff188a37fb41ef83498e656458a7d08ee
  Stored in directory: /tmp/pip-ephem-wheel-cache-8x_luzj5/wheels/29/26/62/cf9910ce78d28f5231ab6a31eafe946f8ca65cb20b62bea290
Successfully built spinalcordtoolbox
Installing collected packages: spinalcordtoolbox
Successfully installed spinalcordtoolbox-7.2.dev0

Creating launchers for Python scripts...

Installing binaries...

sct_download_data -d binaries_linux -k

--
Spinal Cord Toolbox (7.2.dev0)

sct_download_data -d binaries_linux -k
--

Trying URL: https://github.com/spinalcordtoolbox/spinalcordtoolbox-binaries/releases/download/r20221109/spinalcordtoolbox-binaries_linux.tar.gz
Downloading: spinalcordtoolbox-binaries_linux.tar.gz
Creating temporary folder (/tmp/sct_2025-10-20_11-05-11_install-data_na9d631e)
Unzip data to: /tmp/sct_2025-10-20_11-05-11_install-data_na9d631e
Copying data to: /home/runner/sct_7.2.dev0/bin
Removing temporary folders...
Done!

Total runtime; 2.572 seconds.

All requirements installed!

Installing data...

mkdir -p /home/runner/sct_7.2.dev0/data

sct_download_data -d default -k

--
Spinal Cord Toolbox (7.2.dev0)

sct_download_data -d default -k
--

Trying URL: https://github.com/spinalcordtoolbox/PAM50/releases/download/r20250730/PAM50-r20250730.zip
Downloading: PAM50-r20250730.zip
Creating temporary folder (/tmp/sct_2025-10-20_11-05-14_install-data_c8gs39ju)
Unzip data to: /tmp/sct_2025-10-20_11-05-14_install-data_c8gs39ju
Copying data to: /home/runner/sct_7.2.dev0/data/PAM50
Removing temporary folders...
Trying URL: https://github.com/spinalcordtoolbox/deepseg_gm_models/releases/download/r20180205/20220325_deepseg_gm_models_onnx.zip
Downloading: 20220325_deepseg_gm_models_onnx.zip
Creating temporary folder (/tmp/sct_2025-10-20_11-05-14_install-data_q_xbc2rr)
Unzip data to: /tmp/sct_2025-10-20_11-05-14_install-data_q_xbc2rr
Copying data to: /home/runner/sct_7.2.dev0/data/deepseg_gm_models
Removing temporary folders...
Trying URL: https://github.com/spinalcordtoolbox/deepseg_sc_models/releases/download/r20180610/20220325_deepseg_sc_models_onnx.zip
Downloading: 20220325_deepseg_sc_models_onnx.zip
Creating temporary folder (/tmp/sct_2025-10-20_11-05-14_install-data_vo4q18ox)
Unzip data to: /tmp/sct_2025-10-20_11-05-14_install-data_vo4q18ox
Copying data to: /home/runner/sct_7.2.dev0/data/deepseg_sc_models
Removing temporary folders...
Trying URL: https://github.com/spinalcordtoolbox/deepseg_lesion_models/releases/download/r20180613/20220325_deepseg_lesion_models_onnx.zip
Downloading: 20220325_deepseg_lesion_models_onnx.zip
Creating temporary folder (/tmp/sct_2025-10-20_11-05-15_install-data_u2xoo84_)
Unzip data to: /tmp/sct_2025-10-20_11-05-15_install-data_u2xoo84_
Copying data to: /home/runner/sct_7.2.dev0/data/deepseg_lesion_models
Removing temporary folders...
Trying URL: https://github.com/ivadomed/multimodal-registration/releases/download/r20220512/models.zip
Downloading: models.zip
Creating temporary folder (/tmp/sct_2025-10-20_11-05-16_install-data_9hz5ogru)
Unzip data to: /tmp/sct_2025-10-20_11-05-16_install-data_9hz5ogru
Copying data to: /home/runner/sct_7.2.dev0/data/deepreg_models
Removing temporary folders...
Trying URL: https://github.com/spinalcordtoolbox/PAM50-normalized-metrics/archive/refs/tags/r20250321.zip
Downloading: PAM50-normalized-metrics-r20250321.zip
Creating temporary folder (/tmp/sct_2025-10-20_11-05-19_install-data_hzi_raq9)
Unzip data to: /tmp/sct_2025-10-20_11-05-19_install-data_hzi_raq9
Copying data to: /home/runner/sct_7.2.dev0/data/PAM50_normalized_metrics
Removing temporary folders...
Done!

Total runtime; 6.184 seconds.

WARNING: no checks will be run (installation will not be validated)

Installation finished successfully!

変更されたテキスト

ファイルを開く

*******************************
* Welcome to SCT installation *
*******************************

Checking OS type and version...

Linux imaging-gpu-05 5.15.0-153-generic #163-Ubuntu SMP Thu Aug 7 16:37:18 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux

Checking requirements...

OK!

SCT version ......... 7.2.dev0
Installation type ... in-place
Operating system .... linux (unknown)
Shell config ........ /home/lchauvin/.bashrc

Checking permissions on required file /home/lchauvin/.bashrc:
  - File exists: True
  - File ownership: True
  - Read permissions: True
  - Write permissions: True

WARNING: Directory already exists. Files will be overwritten.

SCT will be installed here: [/scratch/02/lchauvin/workspace/projects/spinalcordtoolbox]

Skipping copy of source files (source and destination folders are the same)

Downloading Miniforge...

wget -nv -O /tmp/tmp.fRYleHJK6d/miniforge.sh https://github.com/conda-forge/miniforge/releases/download/24.11.2-1/Miniforge3-Linux-x86_64.sh

Installing Miniforge...

bash /tmp/tmp.fRYleHJK6d/miniforge.sh -p /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python -b -f

PREFIX=/scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python
Unpacking payload ...
Extracting _libgcc_mutex-0.1-conda_forge.tar.bz2
Extracting ca-certificates-2024.12.14-hbcca054_0.conda
Extracting ld_impl_linux-64-2.43-h712a8e2_2.conda
Extracting pybind11-abi-4-hd8ed1ab_3.tar.bz2
Extracting python_abi-3.12-5_cp312.conda
Extracting tzdata-2024b-hc8b5060_0.conda
Extracting libgomp-14.2.0-h77fa898_1.conda
Extracting _openmp_mutex-4.5-2_gnu.tar.bz2
Extracting libgcc-14.2.0-h77fa898_1.conda
Extracting c-ares-1.34.4-hb9d3cd8_0.conda
Extracting libexpat-2.6.4-h5888daf_0.conda
Extracting libgcc-ng-14.2.0-h69a702a_1.conda
Extracting liblzma-5.6.3-hb9d3cd8_1.conda
Extracting libstdcxx-14.2.0-hc0a3c3a_1.conda
Extracting libzlib-1.3.1-hb9d3cd8_2.conda
Extracting openssl-3.4.0-hb9d3cd8_0.conda
Extracting reproc-14.2.5.post0-hb9d3cd8_0.conda
Extracting bzip2-1.0.8-h4bc722e_7.conda
Extracting keyutils-1.6.1-h166bdaf_0.tar.bz2
Extracting libev-4.33-hd590300_2.conda
Extracting libffi-3.4.2-h7f98852_5.tar.bz2
Extracting libiconv-1.17-hd590300_2.conda
Extracting libnsl-2.0.1-hd590300_0.conda
Extracting libsqlite-3.47.2-hee588c1_0.conda
Extracting libssh2-1.11.1-hf672d98_0.conda
Extracting libstdcxx-ng-14.2.0-h4852527_1.conda
Extracting libuuid-2.38.1-h0b41bf4_0.conda
Extracting libxcrypt-4.4.36-hd590300_1.conda
Extracting lz4-c-1.10.0-h5888daf_1.conda
Extracting lzo-2.10-hd590300_1001.conda
Extracting ncurses-6.5-he02047a_1.conda
Extracting reproc-cpp-14.2.5.post0-h5888daf_0.conda
Extracting tk-8.6.13-noxft_h4845f30_101.conda
Extracting fmt-11.0.2-h434a139_0.conda
Extracting libedit-3.1.20191231-he28a2e2_2.tar.bz2
Extracting libnghttp2-1.64.0-h161d5f1_0.conda
Extracting libsolv-0.7.30-h3509ff9_0.conda
Extracting libxml2-2.13.5-h0d44e9d_1.conda
Extracting readline-8.2-h8228510_1.conda
Extracting yaml-cpp-0.8.0-h59595ed_0.conda
Extracting zstd-1.5.6-ha6fb4c9_0.conda
Extracting krb5-1.21.3-h659f571_0.conda
Extracting libarchive-3.7.7-h4585015_3.conda
Extracting python-3.12.8-h9e4cc4f_1_cpython.conda
Extracting libcurl-8.11.1-h332b0f4_0.conda
Extracting menuinst-2.2.0-py312h7900ff3_0.conda
Extracting archspec-0.2.3-pyhd8ed1ab_0.conda
Extracting boltons-24.0.0-pyhd8ed1ab_1.conda
Extracting brotli-python-1.1.0-py312h2ec8cdc_2.conda
Extracting certifi-2024.12.14-pyhd8ed1ab_0.conda
Extracting charset-normalizer-3.4.1-pyhd8ed1ab_0.conda
Extracting colorama-0.4.6-pyhd8ed1ab_1.conda
Extracting distro-1.9.0-pyhd8ed1ab_1.conda
Extracting frozendict-2.4.6-py312h66e93f0_0.conda
Extracting hpack-4.0.0-pyhd8ed1ab_1.conda
Extracting hyperframe-6.0.1-pyhd8ed1ab_1.conda
Extracting idna-3.10-pyhd8ed1ab_1.conda
Extracting jsonpointer-3.0.0-py312h7900ff3_1.conda
Extracting libmamba-1.5.12-h49b8a8d_0.conda
Extracting packaging-24.2-pyhd8ed1ab_2.conda
Extracting platformdirs-4.3.6-pyhd8ed1ab_1.conda
Extracting pluggy-1.5.0-pyhd8ed1ab_1.conda
Extracting pycosat-0.6.6-py312h66e93f0_2.conda
Extracting pycparser-2.22-pyh29332c3_1.conda
Extracting pysocks-1.7.1-pyha55dd90_7.conda
Extracting ruamel.yaml.clib-0.2.8-py312h66e93f0_1.conda
Extracting setuptools-75.6.0-pyhff2d567_1.conda
Extracting truststore-0.10.0-pyhd8ed1ab_0.conda
Extracting wheel-0.45.1-pyhd8ed1ab_1.conda
Extracting cffi-1.17.1-py312h06ac9bb_0.conda
Extracting h2-4.1.0-pyhd8ed1ab_1.conda
Extracting jsonpatch-1.33-pyhd8ed1ab_1.conda
Extracting libmambapy-1.5.12-py312hbaee817_0.conda
Extracting pip-24.3.1-pyh8b19718_2.conda
Extracting ruamel.yaml-0.18.8-py312h66e93f0_0.conda
Extracting tqdm-4.67.1-pyhd8ed1ab_1.conda
Extracting zstandard-0.23.0-py312hef9b889_1.conda
Extracting conda-package-streaming-0.11.0-pyhd8ed1ab_0.conda
Extracting urllib3-2.3.0-pyhd8ed1ab_0.conda
Extracting conda-package-handling-2.4.0-pyha770c72_1.conda
Extracting requests-2.32.3-pyhd8ed1ab_1.conda
Extracting conda-24.11.2-py312h7900ff3_1.conda
Extracting conda-libmamba-solver-24.9.0-pyhd8ed1ab_0.conda
Extracting mamba-1.5.12-py312h9460a1c_0.conda

Installing base environment...

Transaction

Prefix: /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python

Updating specs:

Summary:

Install: 84 packages

Total download: 0 B

Transaction starting

Transaction finished

To activate this environment, use:

micromamba activate /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python

Or to execute a single command in this environment, use:

micromamba run -p /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python mycommand

installation finished.

Creating conda environment...

Channels:
 - defaults
 - conda-forge
 - nodefaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct

added / updated specs:
    - python=3.10

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |             main           3 KB
    _openmp_mutex-5.1          |            1_gnu          21 KB
    bzip2-1.0.8                |       h5eee18b_6         262 KB
    ca-certificates-2025.9.9   |       h06a4308_0         127 KB
    expat-2.7.1                |       h6a678d5_0         182 KB
    ld_impl_linux-64-2.44      |       h153f514_2         672 KB
    libffi-3.4.4               |       h6a678d5_1         141 KB
    libgcc-ng-11.2.0           |       h1234567_1         5.3 MB
    libgomp-11.2.0             |       h1234567_1         474 KB
    libstdcxx-ng-11.2.0        |       h1234567_1         4.7 MB
    libuuid-1.41.5             |       h5eee18b_0          27 KB
    libxcb-1.17.0              |       h9b100fa_0         430 KB
    libzlib-1.3.1              |       hb25bd0a_0          59 KB
    ncurses-6.5                |       h7934f7d_0         1.1 MB
    openssl-3.0.18             |       hd6dcaed_0         4.5 MB
    pip-25.2                   |     pyhc872135_0         1.2 MB
    pthread-stubs-0.3          |       h0ce48e5_1           5 KB
    python-3.10.18             |       h1a3bd86_0        26.5 MB
    readline-8.3               |       hc2a1206_0         471 KB
    setuptools-80.9.0          |  py310h06a4308_0         1.4 MB
    sqlite-3.50.2              |       hb25bd0a_1         1.1 MB
    tk-8.6.15                  |       h54e0aa7_0         3.4 MB
    tzdata-2025b               |       h04d1e81_0         116 KB
    wheel-0.45.1               |  py310h06a4308_0         115 KB
    xorg-libx11-1.8.12         |       h9b100fa_1         895 KB
    xorg-libxau-1.0.12         |       h9b100fa_0          13 KB
    xorg-libxdmcp-1.1.5        |       h9b100fa_0          19 KB
    xorg-xorgproto-2024.1      |       h5eee18b_1         580 KB
    xz-5.6.4                   |       h5eee18b_1         567 KB
    zlib-1.3.1                 |       hb25bd0a_0          96 KB
    ------------------------------------------------------------
                                           Total:        54.5 MB

The following NEW packages will be INSTALLED:

_libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main 
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu 
  bzip2              pkgs/main/linux-64::bzip2-1.0.8-h5eee18b_6 
  ca-certificates    pkgs/main/linux-64::ca-certificates-2025.9.9-h06a4308_0 
  expat              pkgs/main/linux-64::expat-2.7.1-h6a678d5_0 
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.44-h153f514_2 
  libffi             pkgs/main/linux-64::libffi-3.4.4-h6a678d5_1 
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1 
  libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1 
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1 
  libuuid            pkgs/main/linux-64::libuuid-1.41.5-h5eee18b_0 
  libxcb             pkgs/main/linux-64::libxcb-1.17.0-h9b100fa_0 
  libzlib            pkgs/main/linux-64::libzlib-1.3.1-hb25bd0a_0 
  ncurses            pkgs/main/linux-64::ncurses-6.5-h7934f7d_0 
  openssl            pkgs/main/linux-64::openssl-3.0.18-hd6dcaed_0 
  pip                pkgs/main/noarch::pip-25.2-pyhc872135_0 
  pthread-stubs      pkgs/main/linux-64::pthread-stubs-0.3-h0ce48e5_1 
  python             pkgs/main/linux-64::python-3.10.18-h1a3bd86_0 
  readline           pkgs/main/linux-64::readline-8.3-hc2a1206_0 
  setuptools         pkgs/main/linux-64::setuptools-80.9.0-py310h06a4308_0 
  sqlite             pkgs/main/linux-64::sqlite-3.50.2-hb25bd0a_1 
  tk                 pkgs/main/linux-64::tk-8.6.15-h54e0aa7_0 
  tzdata             pkgs/main/noarch::tzdata-2025b-h04d1e81_0 
  wheel              pkgs/main/linux-64::wheel-0.45.1-py310h06a4308_0 
  xorg-libx11        pkgs/main/linux-64::xorg-libx11-1.8.12-h9b100fa_1 
  xorg-libxau        pkgs/main/linux-64::xorg-libxau-1.0.12-h9b100fa_0 
  xorg-libxdmcp      pkgs/main/linux-64::xorg-libxdmcp-1.1.5-h9b100fa_0 
  xorg-xorgproto     pkgs/main/linux-64::xorg-xorgproto-2024.1-h5eee18b_1 
  xz                 pkgs/main/linux-64::xz-5.6.4-h5eee18b_1 
  zlib               pkgs/main/linux-64::zlib-1.3.1-hb25bd0a_0

Downloading and Extracting Packages: ...working...
python-3.10.18       | 26.5 MB   |            |   0%

libgcc-ng-11.2.0     | 5.3 MB    |            |   0%

libstdcxx-ng-11.2.0  | 4.7 MB    |            |   0%

openssl-3.0.18       | 4.5 MB    |            |   0%

tk-8.6.15            | 3.4 MB    |            |   0%

setuptools-80.9.0    | 1.4 MB    |            |   0%

pip-25.2             | 1.2 MB    |            |   0%

sqlite-3.50.2        | 1.1 MB    |            |   0%

ncurses-6.5          | 1.1 MB    |            |   0%

xorg-libx11-1.8.12   | 895 KB    |            |   0%

ld_impl_linux-64-2.4 | 672 KB    |            |   0%

xorg-xorgproto-2024. | 580 KB    |            |   0%

xz-5.6.4             | 567 KB    |            |   0%

libgomp-11.2.0       | 474 KB    |            |   0%

readline-8.3         | 471 KB    |            |   0%

libxcb-1.17.0        | 430 KB    |            |   0%

bzip2-1.0.8          | 262 KB    |            |   0%

expat-2.7.1          | 182 KB    |            |   0%

libffi-3.4.4         | 141 KB    |            |   0%

... (more hidden) ...
python-3.10.18       | 26.5 MB   |            |   0%

libgcc-ng-11.2.0     | 5.3 MB    |            |   0%

libstdcxx-ng-11.2.0  | 4.7 MB    |            |   0%

tk-8.6.15            | 3.4 MB    |            |   0%

openssl-3.0.18       | 4.5 MB    |            |   0% 
python-3.10.18       | 26.5 MB   | 4          |   5%

libstdcxx-ng-11.2.0  | 4.7 MB    | #          |  11%

libgcc-ng-11.2.0     | 5.3 MB    | ##1        |  21%

tk-8.6.15            | 3.4 MB    | #1         |  12%

openssl-3.0.18       | 4.5 MB    | 5          |   5% 
python-3.10.18       | 26.5 MB   | #8         |  19%

tk-8.6.15            | 3.4 MB    | ####7      |  47%

libgcc-ng-11.2.0     | 5.3 MB    | ########## | 100%

openssl-3.0.18       | 4.5 MB    | ##8        |  28%

libstdcxx-ng-11.2.0  | 4.7 MB    | ########## | 100%

libstdcxx-ng-11.2.0  | 4.7 MB    | ########## | 100% 
python-3.10.18       | 26.5 MB   | ###6       |  36%

tk-8.6.15            | 3.4 MB    | #########3 |  93%

pip-25.2             | 1.2 MB    | 1          |   1%

openssl-3.0.18       | 4.5 MB    | #####      |  50%

setuptools-80.9.0    | 1.4 MB    | 1          |   1% 
python-3.10.18       | 26.5 MB   | #####      |  51%

pip-25.2             | 1.2 MB    | ########## | 100%

tk-8.6.15            | 3.4 MB    | ########## | 100%

openssl-3.0.18       | 4.5 MB    | #########3 |  93%

setuptools-80.9.0    | 1.4 MB    | ########## | 100%

setuptools-80.9.0    | 1.4 MB    | ########## | 100% 
python-3.10.18       | 26.5 MB   | ######6    |  66%

sqlite-3.50.2        | 1.1 MB    | 1          |   1%

xorg-libx11-1.8.12   | 895 KB    | 1          |   2%

openssl-3.0.18       | 4.5 MB    | ########## | 100%

ncurses-6.5          | 1.1 MB    | 1          |   1%

sqlite-3.50.2        | 1.1 MB    | ########## | 100% 
python-3.10.18       | 26.5 MB   | ########   |  81%

xorg-libx11-1.8.12   | 895 KB    | ########## | 100%

ncurses-6.5          | 1.1 MB    | ########## | 100%

ld_impl_linux-64-2.4 | 672 KB    | 2          |   2%

xz-5.6.4             | 567 KB    | 2          |   3%

xorg-xorgproto-2024. | 580 KB    | 2          |   3% 
python-3.10.18       | 26.5 MB   | #########8 |  98%

ld_impl_linux-64-2.4 | 672 KB    | ########## | 100%

libstdcxx-ng-11.2.0  | 4.7 MB    | ########## | 100%

xz-5.6.4             | 567 KB    | ########## | 100%

libgomp-11.2.0       | 474 KB    | 3          |   3%

xorg-xorgproto-2024. | 580 KB    | ########## | 100%

libgomp-11.2.0       | 474 KB    | ########## | 100%

libxcb-1.17.0        | 430 KB    | 3          |   4%

libgcc-ng-11.2.0     | 5.3 MB    | ########## | 100%

readline-8.3         | 471 KB    | 3          |   3%

expat-2.7.1          | 182 KB    | 8          |   9%

bzip2-1.0.8          | 262 KB    | 6          |   6%

libxcb-1.17.0        | 430 KB    | ########## | 100%

expat-2.7.1          | 182 KB    | ########## | 100%

bzip2-1.0.8          | 262 KB    | ########## | 100%

readline-8.3         | 471 KB    | ########## | 100%

libffi-3.4.4         | 141 KB    | #1         |  11%

libffi-3.4.4         | 141 KB    | ########## | 100%

... (more hidden) ...

pip-25.2             | 1.2 MB    | ########## | 100%

pip-25.2             | 1.2 MB    | ########## | 100% 
python-3.10.18       | 26.5 MB   | ########## | 100%

tk-8.6.15            | 3.4 MB    | ########## | 100%

sqlite-3.50.2        | 1.1 MB    | ########## | 100%

openssl-3.0.18       | 4.5 MB    | ########## | 100%

xorg-libx11-1.8.12   | 895 KB    | ########## | 100%

setuptools-80.9.0    | 1.4 MB    | ########## | 100%

ld_impl_linux-64-2.4 | 672 KB    | ########## | 100%

xz-5.6.4             | 567 KB    | ########## | 100%

libgomp-11.2.0       | 474 KB    | ########## | 100%

xorg-xorgproto-2024. | 580 KB    | ########## | 100%

expat-2.7.1          | 182 KB    | ########## | 100%

libxcb-1.17.0        | 430 KB    | ########## | 100%

bzip2-1.0.8          | 262 KB    | ########## | 100%

readline-8.3         | 471 KB    | ########## | 100%

libffi-3.4.4         | 141 KB    | ########## | 100%

... (more hidden) ...

ncurses-6.5          | 1.1 MB    | ########## | 100%

ncurses-6.5          | 1.1 MB    | ########## | 100% 
python-3.10.18       | 26.5 MB   | ########## | 100%

done
Preparing transaction: - \ done
Verifying transaction: / - \ | / - \ | / - \ | done
Executing transaction: - \ | / - \ | / - \ | / - done
#
# To activate this environment, use
#
#     $ conda activate /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Channels:
 - conda-forge
 - defaults
 - nodefaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct

added / updated specs:
    - libstdcxx-ng

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    ca-certificates-2025.10.5  |       hbd8a1cb_0         152 KB  conda-forge
    libgcc-15.2.0              |       h767d61c_7         803 KB  conda-forge
    libgcc-ng-15.2.0           |       h69a702a_7          29 KB  conda-forge
    libgomp-15.2.0             |       h767d61c_7         437 KB  conda-forge
    libstdcxx-15.2.0           |       h8f9b012_7         3.7 MB  conda-forge
    libstdcxx-ng-15.2.0        |       h4852527_7          29 KB  conda-forge
    openssl-3.5.4              |       h26f9b46_0         3.0 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         8.1 MB

The following NEW packages will be INSTALLED:

libgcc             conda-forge/linux-64::libgcc-15.2.0-h767d61c_7 
  libstdcxx          conda-forge/linux-64::libstdcxx-15.2.0-h8f9b012_7

The following packages will be UPDATED:

ca-certificates    pkgs/main/linux-64::ca-certificates-2~ --> conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0 
  libgcc-ng          pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-15.2.0-h69a702a_7 
  libgomp              pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-15.2.0-h767d61c_7 
  libstdcxx-ng       pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-15.2.0-h4852527_7 
  openssl              pkgs/main::openssl-3.0.18-hd6dcaed_0 --> conda-forge::openssl-3.5.4-h26f9b46_0

Downloading and Extracting Packages: ...working...
libstdcxx-15.2.0     | 3.7 MB    |            |   0%

openssl-3.5.4        | 3.0 MB    |            |   0%

libgcc-15.2.0        | 803 KB    |            |   0%

libgomp-15.2.0       | 437 KB    |            |   0%

ca-certificates-2025 | 152 KB    |            |   0%

libstdcxx-ng-15.2.0  | 29 KB     |            |   0%

libgcc-ng-15.2.0     | 29 KB     |            |   0%

libgomp-15.2.0       | 437 KB    | 3          |   4%

libgcc-15.2.0        | 803 KB    | 1          |   2%

openssl-3.5.4        | 3.0 MB    |            |   1%

ca-certificates-2025 | 152 KB    | #          |  11% 
libstdcxx-15.2.0     | 3.7 MB    |            |   0%

ca-certificates-2025 | 152 KB    | ########## | 100%

libgomp-15.2.0       | 437 KB    | ########## | 100%

libgcc-15.2.0        | 803 KB    | ########## | 100%

ca-certificates-2025 | 152 KB    | ########## | 100%

openssl-3.5.4        | 3.0 MB    | #####8     |  59%

libgcc-ng-15.2.0     | 29 KB     | #####5     |  56%

libgcc-ng-15.2.0     | 29 KB     | ########## | 100%

libstdcxx-ng-15.2.0  | 29 KB     | #####5     |  56%

libstdcxx-ng-15.2.0  | 29 KB     | ########## | 100% 
libstdcxx-15.2.0     | 3.7 MB    | ####1      |  42%

libgomp-15.2.0       | 437 KB    | ########## | 100%

openssl-3.5.4        | 3.0 MB    | ########## | 100%

libgcc-ng-15.2.0     | 29 KB     | ########## | 100%

libgcc-ng-15.2.0     | 29 KB     | ########## | 100% 
libstdcxx-15.2.0     | 3.7 MB    | ########2  |  83%

libgcc-15.2.0        | 803 KB    | ########## | 100%

libstdcxx-ng-15.2.0  | 29 KB     | ########## | 100%

libgcc-15.2.0        | 803 KB    | ########## | 100%

libstdcxx-ng-15.2.0  | 29 KB     | ########## | 100% 
libstdcxx-15.2.0     | 3.7 MB    | ########## | 100%

openssl-3.5.4        | 3.0 MB    | ########## | 100% 
libstdcxx-15.2.0     | 3.7 MB    | ########## | 100%

done
Preparing transaction: - done
Verifying transaction: | / done
Executing transaction: \ done
Channels:
 - conda-forge
 - defaults
 - nodefaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct

added / updated specs:
    - libffi

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    c-ares-1.34.5              |       hb9d3cd8_0         202 KB  conda-forge
    curl-8.14.1                |       h332b0f4_0         176 KB  conda-forge
    graalpy-23.0.0             | 0_graalvm_native       326.8 MB  conda-forge
    keyutils-1.6.3             |       hb9d3cd8_0         131 KB  conda-forge
    libcurl-8.14.1             |       h332b0f4_0         439 KB  conda-forge
    libedit-3.1.20250104       | pl5321h7949ede_0         132 KB  conda-forge
    libffi-3.5.2               |       h9ec8514_0          56 KB  conda-forge
    libnghttp2-1.67.0          |       had1ee68_0         651 KB  conda-forge
    libssh2-1.11.1             |       hcf80075_0         298 KB  conda-forge
    patch-2.8                  |    hb03c661_1002         114 KB  conda-forge
    python-3.10.8              |0_native230_graalpy          88 KB  conda-forge
    python_abi-3.10            |8_graalpy230_310_native           7 KB  conda-forge
    zstd-1.5.7                 |       hb8e6e7a_2         554 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       329.6 MB

The following NEW packages will be INSTALLED:

c-ares             conda-forge/linux-64::c-ares-1.34.5-hb9d3cd8_0 
  curl               conda-forge/linux-64::curl-8.14.1-h332b0f4_0 
  graalpy            conda-forge/linux-64::graalpy-23.0.0-0_graalvm_native 
  keyutils           conda-forge/linux-64::keyutils-1.6.3-hb9d3cd8_0 
  krb5               conda-forge/linux-64::krb5-1.21.3-h659f571_0 
  libcurl            conda-forge/linux-64::libcurl-8.14.1-h332b0f4_0 
  libedit            conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0 
  libev              conda-forge/linux-64::libev-4.33-hd590300_2 
  libnghttp2         conda-forge/linux-64::libnghttp2-1.67.0-had1ee68_0 
  libssh2            conda-forge/linux-64::libssh2-1.11.1-hcf80075_0 
  patch              conda-forge/linux-64::patch-2.8-hb03c661_1002 
  python_abi         conda-forge/noarch::python_abi-3.10-8_graalpy230_310_native 
  zstd               conda-forge/linux-64::zstd-1.5.7-hb8e6e7a_2

The following packages will be UPDATED:

libffi                 pkgs/main::libffi-3.4.4-h6a678d5_1 --> conda-forge::libffi-3.5.2-h9ec8514_0

The following packages will be SUPERSEDED by a higher-priority channel:

python               pkgs/main::python-3.10.18-h1a3bd86_0 --> conda-forge::python-3.10.8-0_native230_graalpy

Downloading and Extracting Packages: ...working...
graalpy-23.0.0       | 326.8 MB  |            |   0%

libnghttp2-1.67.0    | 651 KB    |            |   0%

zstd-1.5.7           | 554 KB    |            |   0%

libcurl-8.14.1       | 439 KB    |            |   0%

libssh2-1.11.1       | 298 KB    |            |   0%

c-ares-1.34.5        | 202 KB    |            |   0%

curl-8.14.1          | 176 KB    |            |   0%

libedit-3.1.20250104 | 132 KB    |            |   0%

keyutils-1.6.3       | 131 KB    |            |   0%

patch-2.8            | 114 KB    |            |   0%

python-3.10.8        | 88 KB     |            |   0%

libffi-3.5.2         | 56 KB     |            |   0%

python_abi-3.10      | 7 KB      |            |   0%

libcurl-8.14.1       | 439 KB    | 3          |   4%

libnghttp2-1.67.0    | 651 KB    | 2          |   2%

libssh2-1.11.1       | 298 KB    | 5          |   5%

libcurl-8.14.1       | 439 KB    | ########## | 100%

libnghttp2-1.67.0    | 651 KB    | ########## | 100%

libcurl-8.14.1       | 439 KB    | ########## | 100%

zstd-1.5.7           | 554 KB    | 2          |   3%

libssh2-1.11.1       | 298 KB    | ########## | 100%

c-ares-1.34.5        | 202 KB    | 7          |   8%

libnghttp2-1.67.0    | 651 KB    | ########## | 100%

c-ares-1.34.5        | 202 KB    | ########## | 100%

keyutils-1.6.3       | 131 KB    | #2         |  12%

keyutils-1.6.3       | 131 KB    | ########## | 100%

curl-8.14.1          | 176 KB    | 9          |   9%

zstd-1.5.7           | 554 KB    | ########## | 100%

curl-8.14.1          | 176 KB    | ########## | 100%

patch-2.8            | 114 KB    | #3         |  14%

libffi-3.5.2         | 56 KB     | ##8        |  28%

libffi-3.5.2         | 56 KB     | ########## | 100%

patch-2.8            | 114 KB    | ########## | 100% 
graalpy-23.0.0       | 326.8 MB  |            |   0%

libedit-3.1.20250104 | 132 KB    | #2         |  12%

keyutils-1.6.3       | 131 KB    | ########## | 100%

libedit-3.1.20250104 | 132 KB    | ########## | 100%

python-3.10.8        | 88 KB     | #8         |  18%

python-3.10.8        | 88 KB     | ########## | 100%

python_abi-3.10      | 7 KB      | ########## | 100%

c-ares-1.34.5        | 202 KB    | ########## | 100%

c-ares-1.34.5        | 202 KB    | ########## | 100% 
graalpy-23.0.0       | 326.8 MB  |            |   1%

curl-8.14.1          | 176 KB    | ########## | 100%

zstd-1.5.7           | 554 KB    | ########## | 100%

libssh2-1.11.1       | 298 KB    | ########## | 100%

libffi-3.5.2         | 56 KB     | ########## | 100%

patch-2.8            | 114 KB    | ########## | 100%

libedit-3.1.20250104 | 132 KB    | ########## | 100%

python_abi-3.10      | 7 KB      | ########## | 100%

python-3.10.8        | 88 KB     | ########## | 100%

python-3.10.8        | 88 KB     | ########## | 100% 
graalpy-23.0.0       | 326.8 MB  | 1          |   1% 
graalpy-23.0.0       | 326.8 MB  | 2          |   2% 
graalpy-23.0.0       | 326.8 MB  | 3          |   3% 
graalpy-23.0.0       | 326.8 MB  | 4          |   4% 
graalpy-23.0.0       | 326.8 MB  | 5          |   5% 
graalpy-23.0.0       | 326.8 MB  | 6          |   6% 
graalpy-23.0.0       | 326.8 MB  | 6          |   7% 
graalpy-23.0.0       | 326.8 MB  | 7          |   8% 
graalpy-23.0.0       | 326.8 MB  | 8          |   8% 
graalpy-23.0.0       | 326.8 MB  | 9          |   9% 
graalpy-23.0.0       | 326.8 MB  | 9          |  10% 
graalpy-23.0.0       | 326.8 MB  | #          |  10% 
graalpy-23.0.0       | 326.8 MB  | #1         |  12% 
graalpy-23.0.0       | 326.8 MB  | #3         |  14% 
graalpy-23.0.0       | 326.8 MB  | #5         |  15% 
graalpy-23.0.0       | 326.8 MB  | #6         |  17% 
graalpy-23.0.0       | 326.8 MB  | #8         |  19% 
graalpy-23.0.0       | 326.8 MB  | ##         |  20% 
graalpy-23.0.0       | 326.8 MB  | ##1        |  22% 
graalpy-23.0.0       | 326.8 MB  | ##4        |  24% 
graalpy-23.0.0       | 326.8 MB  | ##5        |  26% 
graalpy-23.0.0       | 326.8 MB  | ##8        |  28% 
graalpy-23.0.0       | 326.8 MB  | ###        |  30% 
graalpy-23.0.0       | 326.8 MB  | ###2       |  32% 
graalpy-23.0.0       | 326.8 MB  | ###4       |  34% 
graalpy-23.0.0       | 326.8 MB  | ###6       |  36% 
graalpy-23.0.0       | 326.8 MB  | ###8       |  38% 
graalpy-23.0.0       | 326.8 MB  | ####       |  41% 
graalpy-23.0.0       | 326.8 MB  | ####2      |  43% 
graalpy-23.0.0       | 326.8 MB  | ####4      |  45% 
graalpy-23.0.0       | 326.8 MB  | ####6      |  47% 
graalpy-23.0.0       | 326.8 MB  | ####8      |  49% 
graalpy-23.0.0       | 326.8 MB  | #####      |  51% 
graalpy-23.0.0       | 326.8 MB  | #####2     |  53% 
graalpy-23.0.0       | 326.8 MB  | #####4     |  55% 
graalpy-23.0.0       | 326.8 MB  | #####7     |  57% 
graalpy-23.0.0       | 326.8 MB  | #####9     |  60% 
graalpy-23.0.0       | 326.8 MB  | ######1    |  62% 
graalpy-23.0.0       | 326.8 MB  | ######3    |  64% 
graalpy-23.0.0       | 326.8 MB  | ######5    |  66% 
graalpy-23.0.0       | 326.8 MB  | ######7    |  68% 
graalpy-23.0.0       | 326.8 MB  | ######9    |  69% 
graalpy-23.0.0       | 326.8 MB  | #######1   |  72% 
graalpy-23.0.0       | 326.8 MB  | #######3   |  74% 
graalpy-23.0.0       | 326.8 MB  | #######6   |  77% 
graalpy-23.0.0       | 326.8 MB  | #######9   |  79% 
graalpy-23.0.0       | 326.8 MB  | ########1  |  82% 
graalpy-23.0.0       | 326.8 MB  | ########4  |  85% 
graalpy-23.0.0       | 326.8 MB  | ########7  |  88% 
graalpy-23.0.0       | 326.8 MB  | #########  |  90% 
graalpy-23.0.0       | 326.8 MB  | #########2 |  93% 
graalpy-23.0.0       | 326.8 MB  | #########5 |  95% 
graalpy-23.0.0       | 326.8 MB  | #########8 |  98% 
graalpy-23.0.0       | 326.8 MB  | ########## | 100% 
graalpy-23.0.0       | 326.8 MB  | ########## | 100%

done
Preparing transaction: - \ done
Verifying transaction: / - \ | done
Executing transaction: - \ | / done
Channels:
 - conda-forge
 - defaults
 - nodefaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct

added / updated specs:
    - xorg-libxinerama

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    xorg-libxext-1.3.6         |       hb9d3cd8_0          49 KB  conda-forge
    xorg-libxinerama-1.1.5     |       h5888daf_1          14 KB  conda-forge
    ------------------------------------------------------------
                                           Total:          62 KB

The following NEW packages will be INSTALLED:

xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.6-hb9d3cd8_0 
  xorg-libxinerama   conda-forge/linux-64::xorg-libxinerama-1.1.5-h5888daf_1

Downloading and Extracting Packages: ...working...
xorg-libxext-1.3.6   | 49 KB     |            |   0%

xorg-libxinerama-1.1 | 14 KB     |            |   0% 
xorg-libxext-1.3.6   | 49 KB     | ###2       |  33% 
xorg-libxext-1.3.6   | 49 KB     | ########## | 100% 
xorg-libxext-1.3.6   | 49 KB     | ########## | 100%

xorg-libxinerama-1.1 | 14 KB     | ########## | 100%

==> WARNING: A newer version of conda exists. <==
    current version: 24.11.2
    latest version: 25.9.1

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct

added / updated specs:
    - git

The following packages will be downloaded:

package                    |            build
    ---------------------------|-----------------
    git-2.51.0                 | pl5321h8305f47_1        10.7 MB  conda-forge
    libexpat-2.7.1             |       hecca717_0          73 KB  conda-forge
    libiconv-1.18              |       h3b78370_2         772 KB  conda-forge
    pcre2-10.46                |       h1321c63_0         1.2 MB  conda-forge
    perl-5.32.1                | 7_hd590300_perl5        12.7 MB  conda-forge
    ------------------------------------------------------------
                                           Total:        25.4 MB

The following NEW packages will be INSTALLED:

git                conda-forge/linux-64::git-2.51.0-pl5321h8305f47_1 
  libexpat           conda-forge/linux-64::libexpat-2.7.1-hecca717_0 
  libiconv           conda-forge/linux-64::libiconv-1.18-h3b78370_2 
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 
  pcre2              conda-forge/linux-64::pcre2-10.46-h1321c63_0 
  perl               conda-forge/linux-64::perl-5.32.1-7_hd590300_perl5

Downloading and Extracting Packages: ...working...
perl-5.32.1          | 12.7 MB   |            |   0%

git-2.51.0           | 10.7 MB   |            |   0%

pcre2-10.46          | 1.2 MB    |            |   0%

libiconv-1.18        | 772 KB    |            |   0%

libexpat-2.7.1       | 73 KB     |            |   0%

libexpat-2.7.1       | 73 KB     | ##1        |  22%

libexpat-2.7.1       | 73 KB     | ########## | 100%

pcre2-10.46          | 1.2 MB    | 1          |   1%

libexpat-2.7.1       | 73 KB     | ########## | 100% 
perl-5.32.1          | 12.7 MB   |            |   0%

libiconv-1.18        | 772 KB    | 2          |   2%

git-2.51.0           | 10.7 MB   |            |   0%

pcre2-10.46          | 1.2 MB    | ########## | 100%

pcre2-10.46          | 1.2 MB    | ########## | 100% 
perl-5.32.1          | 12.7 MB   | #7         |  18%

libiconv-1.18        | 772 KB    | ########## | 100%

git-2.51.0           | 10.7 MB   | #3         |  13% 
perl-5.32.1          | 12.7 MB   | ######5    |  65%

libiconv-1.18        | 772 KB    | ########## | 100%

git-2.51.0           | 10.7 MB   | ####9      |  50% 
perl-5.32.1          | 12.7 MB   | ########## | 100% 
perl-5.32.1          | 12.7 MB   | ########## | 100%

pcre2-10.46          | 1.2 MB    | ########## | 100%

git-2.51.0           | 10.7 MB   | ########## | 100%

git-2.51.0           | 10.7 MB   | ########## | 100% 
perl-5.32.1          | 12.7 MB   | ########## | 100%

done
Preparing transaction: - done
Verifying transaction: | / - \ | / - \ done
Executing transaction: / - \ done
<frozen graalpy.pip_hook>:48: RuntimeWarning: You are using an untested version of pip. GraalPy provides patches and workarounds for a number of packages when used with compatible pip versions. We recommend to stick with the pip version that ships with this version of GraalPy.
WARNING: Disabling truststore because platform isn't supported
Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.10/site-packages (25.2)

Installing Python dependencies...

Using requirements.txt (git installation)

<frozen graalpy.pip_hook>:48: RuntimeWarning: You are using an untested version of pip. GraalPy provides patches and workarounds for a number of packages when used with compatible pip versions. We recommend to stick with the pip version that ships with this version of GraalPy.
WARNING: Disabling truststore because platform isn't supported
Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu
Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment
Collecting certifi
  Using cached certifi-2025.10.5-py3-none-any.whl.metadata (2.5 kB)
Collecting acvl_utils!=0.2.1 (from -r requirements.txt (line 7))
  Using cached acvl_utils-0.2.5.tar.gz (29 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting blosc2<3.9.0 (from -r requirements.txt (line 10))
  Using cached blosc2-3.8.0.tar.gz (3.8 MB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting dipy==1.8.0 (from -r requirements.txt (line 12))
  Using cached dipy-1.8.0.tar.gz (6.5 MB)
  Installing build dependencies: started
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): still running...
  Preparing metadata (pyproject.toml): finished with status 'error'
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [53 lines of output]
      + meson setup /tmp/pip-install-gn9aomip/dipy_e68bd84e8a5f4aafb5171c94b41f5756 /tmp/pip-install-gn9aomip/dipy_e68bd84e8a5f4aafb5171c94b41f5756/.mesonpy-187uu8c7 -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/tmp/pip-install-gn9aomip/dipy_e68bd84e8a5f4aafb5171c94b41f5756/.mesonpy-187uu8c7/meson-python-native-file.ini
      The Meson build system
      Version: 1.9.1
      Source dir: /tmp/pip-install-gn9aomip/dipy_e68bd84e8a5f4aafb5171c94b41f5756
      Build dir: /tmp/pip-install-gn9aomip/dipy_e68bd84e8a5f4aafb5171c94b41f5756/.mesonpy-187uu8c7
      Build type: native build
      Project name: dipy
      Project version: 1.8.0
      C compiler for the host machine: cc (gcc 11.4.0 "cc (Ubuntu 11.4.0-1ubuntu1~22.04.2) 11.4.0")
      C linker for the host machine: cc ld.bfd 2.38
      C++ compiler for the host machine: c++ (gcc 11.4.0 "c++ (Ubuntu 11.4.0-1ubuntu1~22.04.2) 11.4.0")
      C++ linker for the host machine: c++ ld.bfd 2.38
      Cython compiler for the host machine: cython (cython 3.1.4)
      Host machine cpu family: x86_64
      Host machine cpu: x86_64
      Program python found: YES (/scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct/bin/python3.10)
      Run-time dependency python found: YES 3.10
      Program cython found: YES (/tmp/pip-build-env-iti1pbxp/overlay/bin/cython)
      Library m found: YES
      Compiler for C supports arguments -Wno-maybe-uninitialized: YES
      Compiler for C supports arguments -Wno-discarded-qualifiers: YES
      Compiler for C supports arguments -Wno-empty-body: YES
      Compiler for C supports arguments -Wno-implicit-function-declaration: YES
      Compiler for C supports arguments -Wno-parentheses: YES
      Compiler for C supports arguments -Wno-switch: YES
      Compiler for C supports arguments -Wno-unused-label: YES
      Compiler for C supports arguments -Wno-unused-variable: YES
      Compiler for C++ supports arguments -Wno-cpp: YES
      Compiler for C++ supports arguments -Wno-deprecated-declarations: YES
      Compiler for C++ supports arguments -Wno-class-memaccess: YES
      Compiler for C++ supports arguments -Wno-format-truncation: YES
      Compiler for C++ supports arguments -Wno-format-extra-args: YES
      Compiler for C++ supports arguments -Wno-format: YES
      Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES
      Compiler for C++ supports arguments -Wno-sign-compare: YES
      Compiler for C++ supports arguments -Wno-switch: YES
      Compiler for C++ supports arguments -Wno-terminate: YES
      Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES
      Compiler for C++ supports arguments -Wno-unused-function: YES
      Compiler for C++ supports arguments -Wno-unused-local-typedefs: YES
      Compiler for C++ supports arguments -Wno-unused-variable: YES
      Compiler for C++ supports arguments -Wno-int-in-bool-context: YES
      
      ../dipy/meson.build:106:17: ERROR: Command `/scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/python/envs/venv_sct/bin/python3.10 -c '
      import numpy as np
      try:
        incdir = os.path.relpath(np.get_include())
      except Exception:
        incdir = np.get_include()
      print(incdir)
        '` failed with status -6.
      
      A full log can be found at /tmp/pip-install-gn9aomip/dipy_e68bd84e8a5f4aafb5171c94b41f5756/.mesonpy-187uu8c7/meson-logs/meson-log.txt
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

Failed running pip install: 1

Installation failed!

Please find the file "/scratch/02/lchauvin/workspace/projects/spinalcordtoolbox/install_sct_log.txt",
then upload it as a .txt attachment in a new topic on SCT's forum:
--> https://forum.spinalcordmri.org/c/sct