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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data StatescopeR
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* checking for file ‘StatescopeR/DESCRIPTION’ ... OK
* preparing ‘StatescopeR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘StatescopeR.Rmd’ using rmarkdown
Requirement already satisfied: pip in /var/cache/basilisk/1.24.0/StatescopeR/1.0.0/statescope/lib/python3.11/site-packages (24.0)
Collecting pip
Using cached pip-26.1-py3-none-any.whl.metadata (4.6 kB)
Collecting wheel
Using cached wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
Requirement already satisfied: setuptools in /var/cache/basilisk/1.24.0/StatescopeR/1.0.0/statescope/lib/python3.11/site-packages (79.0.1)
Collecting setuptools
Using cached setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
Collecting packaging>=24.0 (from wheel)
Using cached packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
Using cached pip-26.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.47.0-py3-none-any.whl (32 kB)
Using cached setuptools-82.0.1-py3-none-any.whl (1.0 MB)
Using cached packaging-26.2-py3-none-any.whl (100 kB)
Installing collected packages: setuptools, pip, packaging, wheel
Attempting uninstall: setuptools
Found existing installation: setuptools 79.0.1
Uninstalling setuptools-79.0.1:
Successfully uninstalled setuptools-79.0.1
Attempting uninstall: pip
Found existing installation: pip 24.0
Uninstalling pip-24.0:
Successfully uninstalled pip-24.0
Successfully installed packaging-26.2 pip-26.1 setuptools-82.0.1 wheel-0.47.0
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting deap==1.4.3
Using cached deap-1.4.3-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting cachetools==7.0.5
Using cached cachetools-7.0.5-py3-none-any.whl.metadata (5.6 kB)
Collecting numba==0.62.1
Using cached numba-0.62.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.8 kB)
Collecting pandas==1.5.3
Using cached pandas-1.5.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting joblib==1.5.3
Using cached joblib-1.5.3-py3-none-any.whl.metadata (5.5 kB)
Collecting numpy==1.23.5
Using cached numpy-1.23.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB)
Collecting scipy==1.15.3
Using cached scipy-1.15.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Collecting matplotlib==3.6.3
Using cached matplotlib-3.6.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.8 kB)
Collecting seaborn==0.13.2
Using cached seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
Collecting scikit-learn==1.5.2
Using cached scikit_learn-1.5.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting torch==2.8.0
Using cached torch-2.8.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (30 kB)
Collecting dill==0.3.4
Using cached dill-0.3.4-py2.py3-none-any.whl.metadata (9.6 kB)
Collecting statescope-autogenes==1.0.4.post2
Using cached statescope_autogenes-1.0.4.post2-py3-none-any.whl.metadata (3.0 kB)
Collecting psutil==7.2.2
Using cached psutil-7.2.2-cp36-abi3-manylinux2010_x86_64.manylinux_2_12_x86_64.manylinux_2_28_x86_64.whl.metadata (22 kB)
Collecting array-api-compat!=1.5,>1.4 (from anndata==0.11.4)
Using cached array_api_compat-1.14.0-py3-none-any.whl.metadata (2.5 kB)
Collecting h5py>=3.7 (from anndata==0.11.4)
Using cached h5py-3.16.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.0 kB)
Collecting natsort (from anndata==0.11.4)
Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Requirement already satisfied: packaging>=24.2 in /var/cache/basilisk/1.24.0/StatescopeR/1.0.0/statescope/lib/python3.11/site-packages (from anndata==0.11.4) (26.2)
Collecting llvmlite<0.46,>=0.45.0dev0 (from numba==0.62.1)
Using cached llvmlite-0.45.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (4.9 kB)
Collecting python-dateutil>=2.8.1 (from pandas==1.5.3)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas==1.5.3)
Using cached pytz-2026.1.post1-py2.py3-none-any.whl.metadata (22 kB)
Collecting contourpy>=1.0.1 (from matplotlib==3.6.3)
Using cached contourpy-1.3.3-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (5.5 kB)
Collecting cycler>=0.10 (from matplotlib==3.6.3)
Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib==3.6.3)
Using cached fonttools-4.62.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (117 kB)
Collecting kiwisolver>=1.0.1 (from matplotlib==3.6.3)
Using cached kiwisolver-1.5.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (5.1 kB)
Collecting pillow>=6.2.0 (from matplotlib==3.6.3)
Using cached pillow-12.2.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (8.8 kB)
Collecting pyparsing>=2.2.1 (from matplotlib==3.6.3)
Using cached pyparsing-3.3.2-py3-none-any.whl.metadata (5.8 kB)
Collecting threadpoolctl>=3.1.0 (from scikit-learn==1.5.2)
Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
Collecting filelock (from torch==2.8.0)
Using cached filelock-3.29.0-py3-none-any.whl.metadata (2.0 kB)
Collecting typing-extensions>=4.10.0 (from torch==2.8.0)
Using cached typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
Collecting sympy>=1.13.3 (from torch==2.8.0)
Using cached sympy-1.14.0-py3-none-any.whl.metadata (12 kB)
Collecting networkx (from torch==2.8.0)
Using cached networkx-3.6.1-py3-none-any.whl.metadata (6.8 kB)
Collecting jinja2 (from torch==2.8.0)
Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
Collecting fsspec (from torch==2.8.0)
Using cached fsspec-2026.3.0-py3-none-any.whl.metadata (10 kB)
Collecting nvidia-cuda-nvrtc-cu12==12.8.93 (from torch==2.8.0)
Using cached nvidia_cuda_nvrtc_cu12-12.8.93-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl.metadata (1.7 kB)
Collecting nvidia-cuda-runtime-cu12==12.8.90 (from torch==2.8.0)
Using cached nvidia_cuda_runtime_cu12-12.8.90-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.7 kB)
Collecting nvidia-cuda-cupti-cu12==12.8.90 (from torch==2.8.0)
Using cached nvidia_cuda_cupti_cu12-12.8.90-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.7 kB)
Collecting nvidia-cudnn-cu12==9.10.2.21 (from torch==2.8.0)
Using cached nvidia_cudnn_cu12-9.10.2.21-py3-none-manylinux_2_27_x86_64.whl.metadata (1.8 kB)
Collecting nvidia-cublas-cu12==12.8.4.1 (from torch==2.8.0)
Using cached nvidia_cublas_cu12-12.8.4.1-py3-none-manylinux_2_27_x86_64.whl.metadata (1.7 kB)
Collecting nvidia-cufft-cu12==11.3.3.83 (from torch==2.8.0)
Using cached nvidia_cufft_cu12-11.3.3.83-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.7 kB)
Collecting nvidia-curand-cu12==10.3.9.90 (from torch==2.8.0)
Using cached nvidia_curand_cu12-10.3.9.90-py3-none-manylinux_2_27_x86_64.whl.metadata (1.7 kB)
Collecting nvidia-cusolver-cu12==11.7.3.90 (from torch==2.8.0)
Using cached nvidia_cusolver_cu12-11.7.3.90-py3-none-manylinux_2_27_x86_64.whl.metadata (1.8 kB)
Collecting nvidia-cusparse-cu12==12.5.8.93 (from torch==2.8.0)
Using cached nvidia_cusparse_cu12-12.5.8.93-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.8 kB)
Collecting nvidia-cusparselt-cu12==0.7.1 (from torch==2.8.0)
Using cached nvidia_cusparselt_cu12-0.7.1-py3-none-manylinux2014_x86_64.whl.metadata (7.0 kB)
Collecting nvidia-nccl-cu12==2.27.3 (from torch==2.8.0)
Using cached nvidia_nccl_cu12-2.27.3-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.0 kB)
Collecting nvidia-nvtx-cu12==12.8.90 (from torch==2.8.0)
Using cached nvidia_nvtx_cu12-12.8.90-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.8 kB)
Collecting nvidia-nvjitlink-cu12==12.8.93 (from torch==2.8.0)
Using cached nvidia_nvjitlink_cu12-12.8.93-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl.metadata (1.7 kB)
Collecting nvidia-cufile-cu12==1.13.1.3 (from torch==2.8.0)
Using cached nvidia_cufile_cu12-1.13.1.3-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.7 kB)
Collecting triton==3.4.0 (from torch==2.8.0)
Using cached triton-3.4.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (1.7 kB)
Requirement already satisfied: setuptools>=40.8.0 in /var/cache/basilisk/1.24.0/StatescopeR/1.0.0/statescope/lib/python3.11/site-packages (from triton==3.4.0->torch==2.8.0) (82.0.1)
INFO: pip is looking at multiple versions of contourpy to determine which version is compatible with other requirements. This could take a while.
Collecting contourpy>=1.0.1 (from matplotlib==3.6.3)
Using cached contourpy-1.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.5 kB)
Collecting six>=1.5 (from python-dateutil>=2.8.1->pandas==1.5.3)
Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Collecting mpmath<1.4,>=1.1.0 (from sympy>=1.13.3->torch==2.8.0)
Using cached mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB)
Collecting MarkupSafe>=2.0 (from jinja2->torch==2.8.0)
Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.7 kB)
Using cached anndata-0.11.4-py3-none-any.whl (144 kB)
Using cached deap-1.4.3-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (135 kB)
Using cached cachetools-7.0.5-py3-none-any.whl (13 kB)
Using cached numba-0.62.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.7 MB)
Using cached numpy-1.23.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
Using cached pandas-1.5.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.0 MB)
Using cached joblib-1.5.3-py3-none-any.whl (309 kB)
Using cached scipy-1.15.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (37.7 MB)
Using cached matplotlib-3.6.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.8 MB)
Using cached seaborn-0.13.2-py3-none-any.whl (294 kB)
Using cached scikit_learn-1.5.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.3 MB)
Using cached torch-2.8.0-cp311-cp311-manylinux_2_28_x86_64.whl (888.1 MB)
Using cached dill-0.3.4-py2.py3-none-any.whl (86 kB)
Using cached statescope_autogenes-1.0.4.post2-py3-none-any.whl (14 kB)
Using cached psutil-7.2.2-cp36-abi3-manylinux2010_x86_64.manylinux_2_12_x86_64.manylinux_2_28_x86_64.whl (155 kB)
Using cached nvidia_cublas_cu12-12.8.4.1-py3-none-manylinux_2_27_x86_64.whl (594.3 MB)
Using cached nvidia_cuda_cupti_cu12-12.8.90-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (10.2 MB)
Using cached nvidia_cuda_nvrtc_cu12-12.8.93-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl (88.0 MB)
Using cached nvidia_cuda_runtime_cu12-12.8.90-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (954 kB)
Using cached nvidia_cudnn_cu12-9.10.2.21-py3-none-manylinux_2_27_x86_64.whl (706.8 MB)
Using cached nvidia_cufft_cu12-11.3.3.83-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (193.1 MB)
Using cached nvidia_cufile_cu12-1.13.1.3-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (1.2 MB)
Using cached nvidia_curand_cu12-10.3.9.90-py3-none-manylinux_2_27_x86_64.whl (63.6 MB)
Using cached nvidia_cusolver_cu12-11.7.3.90-py3-none-manylinux_2_27_x86_64.whl (267.5 MB)
Using cached nvidia_cusparse_cu12-12.5.8.93-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (288.2 MB)
Using cached nvidia_cusparselt_cu12-0.7.1-py3-none-manylinux2014_x86_64.whl (287.2 MB)
Using cached nvidia_nccl_cu12-2.27.3-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (322.4 MB)
Using cached nvidia_nvjitlink_cu12-12.8.93-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl (39.3 MB)
Using cached nvidia_nvtx_cu12-12.8.90-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (89 kB)
Using cached triton-3.4.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (155.5 MB)
Using cached llvmlite-0.45.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (56.3 MB)
Using cached array_api_compat-1.14.0-py3-none-any.whl (60 kB)
Using cached contourpy-1.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (326 kB)
Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB)
Using cached fonttools-4.62.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (5.1 MB)
Using cached h5py-3.16.0-cp311-cp311-manylinux_2_28_x86_64.whl (5.0 MB)
Using cached kiwisolver-1.5.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (1.4 MB)
Using cached pillow-12.2.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (7.1 MB)
Using cached pyparsing-3.3.2-py3-none-any.whl (122 kB)
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Using cached pytz-2026.1.post1-py2.py3-none-any.whl (510 kB)
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Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
Using cached natsort-8.4.0-py3-none-any.whl (38 kB)
Using cached networkx-3.6.1-py3-none-any.whl (2.1 MB)
Installing collected packages: pytz, nvidia-cusparselt-cu12, mpmath, typing-extensions, triton, threadpoolctl, sympy, six, pyparsing, psutil, pillow, nvidia-nvtx-cu12, nvidia-nvjitlink-cu12, nvidia-nccl-cu12, nvidia-curand-cu12, nvidia-cufile-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, numpy, networkx, natsort, MarkupSafe, llvmlite, kiwisolver, joblib, fsspec, fonttools, filelock, dill, cycler, cachetools, array-api-compat, scipy, python-dateutil, nvidia-cusparse-cu12, nvidia-cufft-cu12, nvidia-cudnn-cu12, numba, jinja2, h5py, deap, contourpy, scikit-learn, pandas, nvidia-cusolver-cu12, matplotlib, torch, seaborn, anndata, statescope-autogenes
ERROR: Could not install packages due to an OSError: [Errno 28] No space left on device
Quitting from StatescopeR.Rmd:106-135 [Prepare StatescopeR input]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'anndata==0.11.4'", "'deap==1.4.3'", "'cachetools==7.0.5'", "'numba==0.62.1'", "'pandas==1.5.3'", "'joblib==1.5.3'", "'numpy==1.23.5'", "'scipy==1.15.3'", "'matplotlib==3.6.3'", "'seaborn==0.13.2'", "'scikit-learn==1.5.2'", "'torch==2.8.0'", "'dill==0.3.4'", "'statescope-autogenes==1.0.4.post2'", "'psutil==7.2.2'"
---
Backtrace:
▆
1. └─StatescopeR::select_genes(scRNAseq, 30L, 50L, labels = scRNAseq$`cell type`)
2. └─basilisk::basiliskStart(statescope)
3. └─basilisk::obtainEnvironmentPath(env)
4. └─basilisk::setupBasiliskEnv(...)
5. └─reticulate::virtualenv_create(...)
6. └─reticulate:::pip_install(python, packages)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'StatescopeR.Rmd' failed with diagnostics:
Error installing package(s): "'anndata==0.11.4'", "'deap==1.4.3'", "'cachetools==7.0.5'", "'numba==0.62.1'", "'pandas==1.5.3'", "'joblib==1.5.3'", "'numpy==1.23.5'", "'scipy==1.15.3'", "'matplotlib==3.6.3'", "'seaborn==0.13.2'", "'scikit-learn==1.5.2'", "'torch==2.8.0'", "'dill==0.3.4'", "'statescope-autogenes==1.0.4.post2'", "'psutil==7.2.2'"
--- failed re-building ‘StatescopeR.Rmd’
SUMMARY: processing the following file failed:
‘StatescopeR.Rmd’
Error: Vignette re-building failed.
Execution halted