############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data scviR ### ############################################################################## ############################################################################## * checking for file ‘scviR/DESCRIPTION’ ... OK * preparing ‘scviR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘citeseq_tut.Rmd’ using rmarkdown trying URL 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/pbmc_citeseq_5k10k.h5ad.gz' Content type 'application/octet-stream' length 51844928 bytes (49.4 MB) ================================================== downloaded 49.4 MB Channels: - conda-forge Platform: linux-aarch64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/biocbuild/.cache/R/basilisk/1.18.0/scviR/1.6.0/bsklenv added / updated specs: - python=3.10 The following NEW packages will be INSTALLED: _openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h68df207_7 ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.12.14-hcefe29a_0 ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_2 libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5 libgcc conda-forge/linux-aarch64::libgcc-14.2.0-he277a41_1 libgcc-ng conda-forge/linux-aarch64::libgcc-ng-14.2.0-he9431aa_1 libgomp conda-forge/linux-aarch64::libgomp-14.2.0-he277a41_1 liblzma conda-forge/linux-aarch64::liblzma-5.6.3-h86ecc28_1 libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0 libsqlite conda-forge/linux-aarch64::libsqlite-3.48.0-h5eb1b54_1 libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0 libxcrypt conda-forge/linux-aarch64::libxcrypt-4.4.36-h31becfc_1 libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2 ncurses conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3 openssl conda-forge/linux-aarch64::openssl-3.4.0-hd08dc88_1 pip conda-forge/noarch::pip-25.0-pyh8b19718_0 python conda-forge/linux-aarch64::python-3.10.16-h57b00e1_1_cpython readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 setuptools conda-forge/noarch::setuptools-75.8.0-pyhff2d567_0 tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0 tzdata conda-forge/noarch::tzdata-2025a-h78e105d_0 wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - conda-forge Platform: linux-aarch64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.3.0 latest version: 25.1.1 Please update conda by running $ conda update -n base -c conda-forge conda # All requested packages already installed. Channels: - conda-forge Platform: linux-aarch64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.3.0 latest version: 25.1.1 Please update conda by running $ conda update -n base -c conda-forge conda ## Package Plan ## environment location: /home/biocbuild/.cache/R/basilisk/1.18.0/scviR/1.6.0/bsklenv added / updated specs: - numpy=1.24.4 - pandas=1.5.3 - python[version='3.10.*,3.10.*'] The following packages will be downloaded: package | build ---------------------------|----------------- libblas-3.9.0 |28_h1a9f1db_openblas 16 KB conda-forge libcblas-3.9.0 |28_hab92f65_openblas 16 KB conda-forge liblapack-3.9.0 |28_h411afd4_openblas 16 KB conda-forge ------------------------------------------------------------ Total: 49 KB The following NEW packages will be INSTALLED: libblas conda-forge/linux-aarch64::libblas-3.9.0-28_h1a9f1db_openblas libcblas conda-forge/linux-aarch64::libcblas-3.9.0-28_hab92f65_openblas libgfortran conda-forge/linux-aarch64::libgfortran-14.2.0-he9431aa_1 libgfortran5 conda-forge/linux-aarch64::libgfortran5-14.2.0-hb6113d0_1 liblapack conda-forge/linux-aarch64::liblapack-3.9.0-28_h411afd4_openblas libopenblas conda-forge/linux-aarch64::libopenblas-0.3.28-pthreads_h9d3fd7e_1 libstdcxx conda-forge/linux-aarch64::libstdcxx-14.2.0-h3f4de04_1 libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-14.2.0-hf1166c9_1 numpy conda-forge/linux-aarch64::numpy-1.24.4-py310h7f380f4_0 pandas conda-forge/linux-aarch64::pandas-1.5.3-py310hc3d6b01_1 python-dateutil conda-forge/noarch::python-dateutil-2.9.0.post0-pyhff2d567_1 python_abi conda-forge/linux-aarch64::python_abi-3.10-5_cp310 pytz conda-forge/noarch::pytz-2024.2-pyhd8ed1ab_1 six conda-forge/noarch::six-1.17.0-pyhd8ed1ab_0 Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting anndata==0.10.1 Using cached anndata-0.10.1-py3-none-any.whl.metadata (6.4 kB) Collecting docrep==0.3.2 Using cached docrep-0.3.2.tar.gz (33 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting flax==0.8.1 Using cached flax-0.8.1-py3-none-any.whl.metadata (10 kB) Collecting jax==0.4.23 Using cached jax-0.4.23-py3-none-any.whl.metadata (24 kB) Collecting jaxlib==0.4.23 Using cached jaxlib-0.4.23-cp310-cp310-manylinux2014_aarch64.whl.metadata (2.1 kB) Collecting optax==0.1.9 Using cached optax-0.1.9-py3-none-any.whl.metadata (6.7 kB) Collecting scipy==1.12.0 Using cached scipy-1.12.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (112 kB) Collecting scikit-learn==1.4.0 Using cached scikit_learn-1.4.0-1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (11 kB) Collecting rich==13.7.1 Using cached rich-13.7.1-py3-none-any.whl.metadata (18 kB) Collecting h5py==3.9.0 Using cached h5py-3.9.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (2.5 kB) Collecting torch==1.13.1 Using cached torch-1.13.1-cp310-cp310-manylinux2014_aarch64.whl.metadata (23 kB) Collecting lightning==2.1.4 Using cached lightning-2.1.4-py3-none-any.whl.metadata (57 kB) Collecting torchmetrics==0.11.0 Using cached torchmetrics-0.11.0-py3-none-any.whl.metadata (16 kB) Collecting tqdm==4.66.2 Using cached tqdm-4.66.2-py3-none-any.whl.metadata (57 kB) Collecting ml-collections==0.1.1 Using cached ml_collections-0.1.1.tar.gz (77 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting mudata==0.2.3 Using cached mudata-0.2.3-py3-none-any.whl.metadata (4.7 kB) Collecting scvi-tools==1.1.2 Using cached scvi_tools-1.1.2-py3-none-any.whl.metadata (12 kB) Collecting scanpy==1.9.5 Using cached scanpy-1.9.5-py3-none-any.whl.metadata (5.9 kB) Collecting matplotlib==3.7.3 Using cached matplotlib-3.7.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (5.7 kB) Collecting scikit-misc==0.3.1 Using cached scikit_misc-0.3.1.tar.gz (302 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' Installing backend dependencies: started Installing backend dependencies: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'error' error: subprocess-exited-with-error × Preparing metadata (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [10 lines of output] + meson setup /home/biocbuild/tmp/pip-install-u67vbli4/scikit-misc_706083bed8f04e5cac41aed59e7d24b4 /home/biocbuild/tmp/pip-install-u67vbli4/scikit-misc_706083bed8f04e5cac41aed59e7d24b4/.mesonpy-atbw8p6b -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/home/biocbuild/tmp/pip-install-u67vbli4/scikit-misc_706083bed8f04e5cac41aed59e7d24b4/.mesonpy-atbw8p6b/meson-python-native-file.ini The Meson build system Version: 1.7.0 Source dir: /home/biocbuild/tmp/pip-install-u67vbli4/scikit-misc_706083bed8f04e5cac41aed59e7d24b4 Build dir: /home/biocbuild/tmp/pip-install-u67vbli4/scikit-misc_706083bed8f04e5cac41aed59e7d24b4/.mesonpy-atbw8p6b Build type: native build ../meson.build:5:11: ERROR: Command `/home/biocbuild/tmp/pip-install-u67vbli4/scikit-misc_706083bed8f04e5cac41aed59e7d24b4/skmisc/_build_utils/version_please.py` failed with status 127. A full log can be found at /home/biocbuild/tmp/pip-install-u67vbli4/scikit-misc_706083bed8f04e5cac41aed59e7d24b4/.mesonpy-atbw8p6b/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. Quitting from lines 43-48 [doinit] (citeseq_tut.Rmd) Error: processing vignette 'citeseq_tut.Rmd' failed with diagnostics: failed to install additional packages via pip --- failed re-building ‘citeseq_tut.Rmd’ --- re-building ‘compch12.Rmd’ using rmarkdown trying URL 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/ch12sce.rda' Content type 'application/octet-stream' length 58079368 bytes (55.4 MB) ================================================== downloaded 55.4 MB trying URL 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/full_5k10k_totalVI.h5ad' Content type 'application/octet-stream' length 1216903940 bytes (1160.5 MB) ================================================== downloaded 1160.5 MB Channels: - conda-forge Platform: linux-aarch64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/biocbuild/.cache/R/basilisk/1.18.0/scviR/1.6.0/bsklenv added / updated specs: - python=3.10 The following NEW packages will be INSTALLED: _openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h68df207_7 ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.12.14-hcefe29a_0 ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_2 libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5 libgcc conda-forge/linux-aarch64::libgcc-14.2.0-he277a41_1 libgcc-ng conda-forge/linux-aarch64::libgcc-ng-14.2.0-he9431aa_1 libgomp conda-forge/linux-aarch64::libgomp-14.2.0-he277a41_1 liblzma conda-forge/linux-aarch64::liblzma-5.6.3-h86ecc28_1 libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0 libsqlite conda-forge/linux-aarch64::libsqlite-3.48.0-h5eb1b54_1 libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0 libxcrypt conda-forge/linux-aarch64::libxcrypt-4.4.36-h31becfc_1 libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2 ncurses conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3 openssl conda-forge/linux-aarch64::openssl-3.4.0-hd08dc88_1 pip conda-forge/noarch::pip-25.0-pyh8b19718_0 python conda-forge/linux-aarch64::python-3.10.16-h57b00e1_1_cpython readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 setuptools conda-forge/noarch::setuptools-75.8.0-pyhff2d567_0 tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0 tzdata conda-forge/noarch::tzdata-2025a-h78e105d_0 wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - conda-forge Platform: linux-aarch64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.3.0 latest version: 25.1.1 Please update conda by running $ conda update -n base -c conda-forge conda # All requested packages already installed. Channels: - conda-forge Platform: linux-aarch64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.3.0 latest version: 25.1.1 Please update conda by running $ conda update -n base -c conda-forge conda ## Package Plan ## environment location: /home/biocbuild/.cache/R/basilisk/1.18.0/scviR/1.6.0/bsklenv added / updated specs: - numpy=1.24.4 - pandas=1.5.3 - python[version='3.10.*,3.10.*'] The following NEW packages will be INSTALLED: libblas conda-forge/linux-aarch64::libblas-3.9.0-28_h1a9f1db_openblas libcblas conda-forge/linux-aarch64::libcblas-3.9.0-28_hab92f65_openblas libgfortran conda-forge/linux-aarch64::libgfortran-14.2.0-he9431aa_1 libgfortran5 conda-forge/linux-aarch64::libgfortran5-14.2.0-hb6113d0_1 liblapack conda-forge/linux-aarch64::liblapack-3.9.0-28_h411afd4_openblas libopenblas conda-forge/linux-aarch64::libopenblas-0.3.28-pthreads_h9d3fd7e_1 libstdcxx conda-forge/linux-aarch64::libstdcxx-14.2.0-h3f4de04_1 libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-14.2.0-hf1166c9_1 numpy conda-forge/linux-aarch64::numpy-1.24.4-py310h7f380f4_0 pandas conda-forge/linux-aarch64::pandas-1.5.3-py310hc3d6b01_1 python-dateutil conda-forge/noarch::python-dateutil-2.9.0.post0-pyhff2d567_1 python_abi conda-forge/linux-aarch64::python_abi-3.10-5_cp310 pytz conda-forge/noarch::pytz-2024.2-pyhd8ed1ab_1 six conda-forge/noarch::six-1.17.0-pyhd8ed1ab_0 Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting anndata==0.10.1 Using cached anndata-0.10.1-py3-none-any.whl.metadata (6.4 kB) Collecting docrep==0.3.2 Using cached docrep-0.3.2.tar.gz (33 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting flax==0.8.1 Using cached flax-0.8.1-py3-none-any.whl.metadata (10 kB) Collecting jax==0.4.23 Using cached jax-0.4.23-py3-none-any.whl.metadata (24 kB) Collecting jaxlib==0.4.23 Using cached jaxlib-0.4.23-cp310-cp310-manylinux2014_aarch64.whl.metadata (2.1 kB) Collecting optax==0.1.9 Using cached optax-0.1.9-py3-none-any.whl.metadata (6.7 kB) Collecting scipy==1.12.0 Using cached scipy-1.12.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (112 kB) Collecting scikit-learn==1.4.0 Using cached scikit_learn-1.4.0-1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (11 kB) Collecting rich==13.7.1 Using cached rich-13.7.1-py3-none-any.whl.metadata (18 kB) Collecting h5py==3.9.0 Using cached h5py-3.9.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (2.5 kB) Collecting torch==1.13.1 Using cached torch-1.13.1-cp310-cp310-manylinux2014_aarch64.whl.metadata (23 kB) Collecting lightning==2.1.4 Using cached lightning-2.1.4-py3-none-any.whl.metadata (57 kB) Collecting torchmetrics==0.11.0 Using cached torchmetrics-0.11.0-py3-none-any.whl.metadata (16 kB) Collecting tqdm==4.66.2 Using cached tqdm-4.66.2-py3-none-any.whl.metadata (57 kB) Collecting ml-collections==0.1.1 Using cached ml_collections-0.1.1.tar.gz (77 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting mudata==0.2.3 Using cached mudata-0.2.3-py3-none-any.whl.metadata (4.7 kB) Collecting scvi-tools==1.1.2 Using cached scvi_tools-1.1.2-py3-none-any.whl.metadata (12 kB) Collecting scanpy==1.9.5 Using cached scanpy-1.9.5-py3-none-any.whl.metadata (5.9 kB) Collecting matplotlib==3.7.3 Using cached matplotlib-3.7.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (5.7 kB) Collecting scikit-misc==0.3.1 Using cached scikit_misc-0.3.1.tar.gz (302 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' Installing backend dependencies: started Installing backend dependencies: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'error' error: subprocess-exited-with-error × Preparing metadata (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [10 lines of output] + meson setup /home/biocbuild/tmp/pip-install-ppzv3vd4/scikit-misc_ce4374bff6da4544b67e9fbffcd6f8eb /home/biocbuild/tmp/pip-install-ppzv3vd4/scikit-misc_ce4374bff6da4544b67e9fbffcd6f8eb/.mesonpy-bkg_xo4x -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/home/biocbuild/tmp/pip-install-ppzv3vd4/scikit-misc_ce4374bff6da4544b67e9fbffcd6f8eb/.mesonpy-bkg_xo4x/meson-python-native-file.ini The Meson build system Version: 1.7.0 Source dir: /home/biocbuild/tmp/pip-install-ppzv3vd4/scikit-misc_ce4374bff6da4544b67e9fbffcd6f8eb Build dir: /home/biocbuild/tmp/pip-install-ppzv3vd4/scikit-misc_ce4374bff6da4544b67e9fbffcd6f8eb/.mesonpy-bkg_xo4x Build type: native build ../meson.build:5:11: ERROR: Command `/home/biocbuild/tmp/pip-install-ppzv3vd4/scikit-misc_ce4374bff6da4544b67e9fbffcd6f8eb/skmisc/_build_utils/version_please.py` failed with status 127. A full log can be found at /home/biocbuild/tmp/pip-install-ppzv3vd4/scikit-misc_ce4374bff6da4544b67e9fbffcd6f8eb/.mesonpy-bkg_xo4x/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. Quitting from lines 50-53 [getdat2] (compch12.Rmd) Error: processing vignette 'compch12.Rmd' failed with diagnostics: failed to install additional packages via pip --- failed re-building ‘compch12.Rmd’ --- re-building ‘scviR.Rmd’ using rmarkdown --- finished re-building ‘scviR.Rmd’ SUMMARY: processing the following files failed: ‘citeseq_tut.Rmd’ ‘compch12.Rmd’ Error: Vignette re-building failed. Execution halted