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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 DOtools
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* checking for file ‘DOtools/DESCRIPTION’ ... OK
* preparing ‘DOtools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DOtools.Rmd’ using rmarkdown
Requirement already satisfied: pip in /var/cache/basilisk/1.22.0/DOtools/1.0.1/DOtools_env/lib/python3.11/site-packages (24.0)
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Installing collected packages: setuptools, pip, packaging, wheel
Attempting uninstall: setuptools
Found existing installation: setuptools 79.0.1
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Installing collected packages: texttable, pytz, pyro-api, nvidia-cusparselt-cu12, multipledispatch, mpmath, zipp, wrapt, urllib3, tzdata, typing-extensions, triton, tqdm, toolz, threadpoolctl, tensorboard-data-server, sympy, six, simplejson, session-info2, PyYAML, pyparsing, pygments, protobuf, propcache, pillow, opt-einsum, nvidia-nvtx-cu12, nvidia-nvshmem-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, nest_asyncio, natsort, multidict, msgpack, mdurl, markupsafe, markdown, llvmlite, legacy-api-wrap, kiwisolver, joblib, importlib_resources, igraph, idna, humanize, google-crc32c, fsspec, frozenlist, fonttools, filelock, etils, et-xmlfile, cycler, cuda-pathfinder, click, charset_normalizer, certifi, attrs, array-api-compat, aiohappyeyeballs, absl-py, yarl, werkzeug, treescope, scipy, scikit-misc, requests, python-dateutil, pydot, patsy, openpyxl, nvidia-cusparse-cu12, nvidia-cufft-cu12, nvidia-cudnn-cu12, numcodecs, numba, ml-dtypes, ml-collections, markdown-it-py, lightning-utilities, leidenalg, jinja2, h5py, grpcio, donfig, docrep, deprecated, cuda-bindings, contourpy, aiosignal, zarr, tensorstore, tensorboard, sparse, scikit-learn, rich, pandas, nvidia-cusolver-cu12, matplotlib, jaxlib, aiohttp, xarray, torch, statsmodels, seaborn, pynndescent, jax, anndata, umap-learn, torchmetrics, scanpro, pyro-ppl, orbax-checkpoint, numpyro, mudata, chex, scanpy, pytorch-lightning, optax, scib, lightning, flax, celltypist, scvi-tools
Successfully installed PyYAML-6.0.3 absl-py-2.4.0 aiohappyeyeballs-2.6.1 aiohttp-3.13.3 aiosignal-1.4.0 anndata-0.12.10 array-api-compat-1.13.0 attrs-25.4.0 celltypist-1.6.3 certifi-2026.1.4 charset_normalizer-3.4.4 chex-0.1.90 click-8.3.1 contourpy-1.3.3 cuda-bindings-12.9.4 cuda-pathfinder-1.3.3 cycler-0.12.1 deprecated-1.3.1 docrep-0.3.2 donfig-0.8.1.post1 et-xmlfile-2.0.0 etils-1.13.0 filelock-3.20.3 flax-0.10.4 fonttools-4.61.1 frozenlist-1.8.0 fsspec-2026.2.0 google-crc32c-1.8.0 grpcio-1.78.0 h5py-3.15.1 humanize-4.15.0 idna-3.11 igraph-1.0.0 importlib_resources-6.5.2 jax-0.4.35 jaxlib-0.4.35 jinja2-3.1.6 joblib-1.5.3 kiwisolver-1.4.9 legacy-api-wrap-1.5 leidenalg-0.11.0 lightning-2.6.1 lightning-utilities-0.15.2 llvmlite-0.46.0 markdown-3.10.2 markdown-it-py-4.0.0 markupsafe-3.0.3 matplotlib-3.10.8 mdurl-0.1.2 ml-collections-1.1.0 ml-dtypes-0.5.4 mpmath-1.3.0 msgpack-1.1.2 mudata-0.3.3 multidict-6.7.1 multipledispatch-1.0.0 natsort-8.4.0 nest_asyncio-1.6.0 networkx-3.6.1 numba-0.63.1 numcodecs-0.16.5 numpy-1.26.4 numpyro-0.19.0 nvidia-cublas-cu12-12.8.4.1 nvidia-cuda-cupti-cu12-12.8.90 nvidia-cuda-nvrtc-cu12-12.8.93 nvidia-cuda-runtime-cu12-12.8.90 nvidia-cudnn-cu12-9.10.2.21 nvidia-cufft-cu12-11.3.3.83 nvidia-cufile-cu12-1.13.1.3 nvidia-curand-cu12-10.3.9.90 nvidia-cusolver-cu12-11.7.3.90 nvidia-cusparse-cu12-12.5.8.93 nvidia-cusparselt-cu12-0.7.1 nvidia-nccl-cu12-2.27.5 nvidia-nvjitlink-cu12-12.8.93 nvidia-nvshmem-cu12-3.4.5 nvidia-nvtx-cu12-12.8.90 openpyxl-3.1.5 opt-einsum-3.4.0 optax-0.2.5 orbax-checkpoint-0.11.5 pandas-2.3.3 patsy-1.0.2 pillow-12.1.0 propcache-0.4.1 protobuf-6.33.5 pydot-4.0.1 pygments-2.19.2 pynndescent-0.6.0 pyparsing-3.3.2 pyro-api-0.1.2 pyro-ppl-1.9.1 python-dateutil-2.9.0.post0 pytorch-lightning-2.6.1 pytz-2025.2 requests-2.32.5 rich-14.3.2 scanpro-0.3.2 scanpy-1.11.5 scib-1.1.7 scikit-learn-1.8.0 scikit-misc-0.5.2 scipy-1.15.3 scvi-tools-1.3.0 seaborn-0.13.2 session-info2-0.4 simplejson-3.20.2 six-1.17.0 sparse-0.17.0 statsmodels-0.14.6 sympy-1.14.0 tensorboard-2.20.0 tensorboard-data-server-0.7.2 tensorstore-0.1.81 texttable-1.7.0 threadpoolctl-3.6.0 toolz-1.1.0 torch-2.10.0 torchmetrics-1.8.2 tqdm-4.67.3 treescope-0.1.10 triton-3.6.0 typing-extensions-4.15.0 tzdata-2025.3 umap-learn-0.5.11 urllib3-2.6.3 werkzeug-3.1.5 wrapt-2.1.1 xarray-2026.1.0 yarl-1.22.0 zarr-3.1.5 zipp-3.23.0
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⚙️ Configuration:
🛠️ indata: /tmp/RtmpXhcu2H/filecc4e5174a624/ad.h5ad
🛠️ model: Healthy_COVID19_PBMC.pkl
🛠️ transpose-input: False
🛠️ gene-file: None
🛠️ cell-file: None
🛠️ mode: best_match
🛠️ p-thres: 0.5
🛠️ majority-voting: True
🛠️ outdir: /tmp/RtmpXhcu2H/filecc4e5174a624
🛠️ prefix:
🛠️ xlsx: False
🛠️ plot-results: False
🛠️ quiet: False
🛠️ over-clustering: leiden0.3
🛠️ min-prop: 0.0
📁 Input file is '/tmp/RtmpXhcu2H/filecc4e5174a624/ad.h5ad'
⏳ Loading data
⚠️ Warning: invalid expression matrix, expect ALL genes and log1p normalized expression to 10000 counts per cell. The prediction result may not be accurate
🔬 Input data has 2807 cells and 800 genes
🔗 Matching reference genes in the model
🧬 609 features used for prediction
⚖️ Scaling input data
🖋️ Predicting labels
✅ Prediction done!
🗳️ Majority voting the predictions
✅ Majority voting done!
[INFO] Your data doesn't have replicates! Artificial replicates will be simulated to run scanpro.
[INFO] Simulation may take some minutes...
[INFO] Generating 3 replicates and running 100 simulations...
[INFO] Finished 100 simulations in 4.0 seconds
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d88' "Y8 d88 88b 888 888 888 88. .8 888 88b 888 d88( "8 888
888 888ooo888 888 888 888 88..8 888 888 888 `"Y88b. 888
888 .o8 888 .o 888 888 888 . `888' 888 888 888 o. )88b 888 .
Y8bod8P `Y8bod8P' o888o o888o "888" .8' 888bod8P' o888o 8""888P' "888"
.o..P' 888
`Y8P' o888o @Teichmann lab
⚙️ Configuration:
🛠️ indata: /tmp/RtmpXhcu2H/filecc4e5577777da/ad.h5ad
🛠️ model: Healthy_COVID19_PBMC.pkl
🛠️ transpose-input: False
🛠️ gene-file: None
🛠️ cell-file: None
🛠️ mode: best_match
🛠️ p-thres: 0.5
🛠️ majority-voting: True
🛠️ outdir: /tmp/RtmpXhcu2H/filecc4e5577777da
🛠️ prefix:
🛠️ xlsx: False
🛠️ plot-results: False
🛠️ quiet: False
🛠️ over-clustering: annotation_recluster
🛠️ min-prop: 0.0
📁 Input file is '/tmp/RtmpXhcu2H/filecc4e5577777da/ad.h5ad'
⏳ Loading data
⚠️ Warning: invalid expression matrix, expect ALL genes and log1p normalized expression to 10000 counts per cell. The prediction result may not be accurate
🔬 Input data has 1799 cells and 800 genes
🔗 Matching reference genes in the model
🧬 609 features used for prediction
⚖️ Scaling input data
🖋️ Predicting labels
✅ Prediction done!
🗳️ Majority voting the predictions
✅ Majority voting done!
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!!! Assuming GO Terms are preprocessed (Only Significant terms included)
Quitting from DOtools.Rmd:648-660 [Bar]
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<error/rlang_error>
Error in `DO.BarplotWilcox()`:
! could not find function "DO.BarplotWilcox"
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'DOtools.Rmd' failed with diagnostics:
could not find function "DO.BarplotWilcox"
--- failed re-building ‘DOtools.Rmd’
SUMMARY: processing the following file failed:
‘DOtools.Rmd’
Error: Vignette re-building failed.
Execution halted