non-interactive mode  ******************************* * 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 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.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: - 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 /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%  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) ... ... (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%  sqlite-3.50.2 | 1.1 MB | ########## | 100%  openssl-3.0.18 | 4.5 MB | ########## | 100%  xorg-libx11-1.8.12 | 895 KB | ########## | 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%  ld_impl_linux-64-2.4 | 672 KB | ########## | 100%  xz-5.6.4 | 567 KB | ########## | 100%  xz-5.6.4 | 567 KB | ########## | 100%  libgomp-11.2.0 | 474 KB | ########## | 100%  libgomp-11.2.0 | 474 KB | ########## | 100%  xorg-xorgproto-2024. | 580 KB | ########## | 100%  xorg-xorgproto-2024. | 580 KB | ########## | 100%  expat-2.7.1 | 182 KB | ########## | 100%  expat-2.7.1 | 182 KB | ########## | 100%  libxcb-1.17.0 | 430 KB | ########## | 100%  libxcb-1.17.0 | 430 KB | ########## | 100%  bzip2-1.0.8 | 262 KB | ########## | 100%  bzip2-1.0.8 | 262 KB | ########## | 100%  readline-8.3 | 471 KB | ########## | 100%  readline-8.3 | 471 KB | ########## | 100%  libffi-3.4.4 | 141 KB | ########## | 100%  libffi-3.4.4 | 141 KB | ########## | 100%  ... (more hidden) ... ... (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%  libgomp-15.2.0 | 437 KB | ########## | 100%  openssl-3.5.4 | 3.0 MB | ########## | 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%  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%  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%  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%  curl-8.14.1 | 176 KB | ########## | 100%  zstd-1.5.7 | 554 KB | ########## | 100%  zstd-1.5.7 | 554 KB | ########## | 100%  libssh2-1.11.1 | 298 KB | ########## | 100%  libssh2-1.11.1 | 298 KB | ########## | 100%  libffi-3.5.2 | 56 KB | ########## | 100%  libffi-3.5.2 | 56 KB | ########## | 100%  patch-2.8 | 114 KB | ########## | 100%  patch-2.8 | 114 KB | ########## | 100%  libedit-3.1.20250104 | 132 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%  xorg-libxinerama-1.1 | 14 KB | ########## | 100%  xorg-libxinerama-1.1 | 14 KB | ########## | 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: - 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%  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%  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 :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) :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