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R CMD BUILD
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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
Calculating gene variances
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Calculating feature variances of standardized and clipped values
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Calculating gene variances
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Calculating feature variances of standardized and clipped values
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Using method 'umap'
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Requirement already satisfied: pip in /var/cache/basilisk/1.21.5/DOtools/0.99.3/DOtools_env/lib/python3.11/site-packages (24.0)
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Requirement already satisfied: setuptools in /var/cache/basilisk/1.21.5/DOtools/0.99.3/DOtools_env/lib/python3.11/site-packages (65.5.0)
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Installing collected packages: wheel, setuptools, pip
Attempting uninstall: setuptools
Found existing installation: setuptools 65.5.0
Uninstalling setuptools-65.5.0:
Successfully uninstalled setuptools-65.5.0
Attempting uninstall: pip
Found existing installation: pip 24.0
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Installing collected packages: texttable, pytz, pyro-api, nvidia-cusparselt-cu12, multipledispatch, mpmath, zipp, urllib3, tzdata, typing-extensions, triton, tqdm, toolz, threadpoolctl, tensorboard-data-server, sympy, six, simplejson, session-info2, PyYAML, pyparsing, pygments, protobuf, propcache, pillow, packaging, opt-einsum, 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, nest_asyncio, natsort, multidict, msgpack, mdurl, MarkupSafe, markdown, llvmlite, legacy-api-wrap, kiwisolver, joblib, importlib_resources, igraph, idna, humanize, grpcio, fsspec, frozenlist, fonttools, filelock, etils, et-xmlfile, cycler, crc32c, click, charset_normalizer, certifi, attrs, array-api-compat, aiohappyeyeballs, absl-py, yarl, werkzeug, treescope, scipy, requests, python-dateutil, 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, donfig, docrep, contourpy, aiosignal, tensorstore, tensorboard, sparse, scikit-learn, rich, pandas, nvidia-cusolver-cu12, matplotlib, jaxlib, aiohttp, zarr, xarray, torch, statsmodels, seaborn, pynndescent, jax, umap-learn, torchmetrics, scanpro, pyro-ppl, orbax-checkpoint, numpyro, chex, anndata, scanpy, pytorch-lightning, optax, mudata, lightning, flax, celltypist, scvi-tools
Successfully installed MarkupSafe-3.0.2 PyYAML-6.0.2 absl-py-2.3.1 aiohappyeyeballs-2.6.1 aiohttp-3.12.15 aiosignal-1.4.0 anndata-0.12.1 array-api-compat-1.12.0 attrs-25.3.0 celltypist-1.6.3 certifi-2025.8.3 charset_normalizer-3.4.2 chex-0.1.90 click-8.2.1 contourpy-1.3.3 crc32c-2.7.1 cycler-0.12.1 docrep-0.3.2 donfig-0.8.1.post1 et-xmlfile-2.0.0 etils-1.13.0 filelock-3.18.0 flax-0.10.4 fonttools-4.59.0 frozenlist-1.7.0 fsspec-2025.7.0 grpcio-1.74.0 h5py-3.14.0 humanize-4.12.3 idna-3.10 igraph-0.11.9 importlib_resources-6.5.2 jax-0.4.35 jaxlib-0.4.35 jinja2-3.1.6 joblib-1.5.1 kiwisolver-1.4.8 legacy-api-wrap-1.4.1 leidenalg-0.10.2 lightning-2.5.2 lightning-utilities-0.15.1 llvmlite-0.44.0 markdown-3.8.2 markdown-it-py-3.0.0 matplotlib-3.10.5 mdurl-0.1.2 ml-collections-1.1.0 ml-dtypes-0.5.3 mpmath-1.3.0 msgpack-1.1.1 mudata-0.3.2 multidict-6.6.3 multipledispatch-1.0.0 natsort-8.4.0 nest_asyncio-1.6.0 networkx-3.5 numba-0.61.2 numcodecs-0.16.1 numpy-1.26.4 numpyro-0.19.0 nvidia-cublas-cu12-12.6.4.1 nvidia-cuda-cupti-cu12-12.6.80 nvidia-cuda-nvrtc-cu12-12.6.77 nvidia-cuda-runtime-cu12-12.6.77 nvidia-cudnn-cu12-9.5.1.17 nvidia-cufft-cu12-11.3.0.4 nvidia-cufile-cu12-1.11.1.6 nvidia-curand-cu12-10.3.7.77 nvidia-cusolver-cu12-11.7.1.2 nvidia-cusparse-cu12-12.5.4.2 nvidia-cusparselt-cu12-0.6.3 nvidia-nccl-cu12-2.26.2 nvidia-nvjitlink-cu12-12.6.85 nvidia-nvtx-cu12-12.6.77 openpyxl-3.1.5 opt-einsum-3.4.0 optax-0.2.5 orbax-checkpoint-0.11.5 packaging-25.0 pandas-2.3.1 patsy-1.0.1 pillow-11.3.0 propcache-0.3.2 protobuf-6.31.1 pygments-2.19.2 pynndescent-0.5.13 pyparsing-3.2.3 pyro-api-0.1.2 pyro-ppl-1.9.1 python-dateutil-2.9.0.post0 pytorch-lightning-2.5.2 pytz-2025.2 requests-2.32.4 rich-14.1.0 scanpro-0.3.2 scanpy-1.11.4 scikit-learn-1.7.1 scipy-1.15.3 scvi-tools-1.3.0 seaborn-0.13.2 session-info2-0.2 simplejson-3.20.1 six-1.17.0 sparse-0.17.0 statsmodels-0.14.5 sympy-1.14.0 tensorboard-2.20.0 tensorboard-data-server-0.7.2 tensorstore-0.1.76 texttable-1.7.0 threadpoolctl-3.6.0 toolz-1.0.0 torch-2.7.1 torchmetrics-1.8.0 tqdm-4.67.1 treescope-0.1.9 triton-3.3.1 typing-extensions-4.14.1 tzdata-2025.2 umap-learn-0.5.9.post2 urllib3-2.5.0 werkzeug-3.1.3 xarray-2025.7.1 yarl-1.20.1 zarr-3.1.1 zipp-3.23.0
📜 Retrieving model list from server https://celltypist.cog.sanger.ac.uk/models/models.json
📚 Total models in list: 54
📂 Storing models in /home/pkgbuild/.celltypist/data/models
💾 Downloading model [1/54]: Immune_All_Low.pkl
💾 Downloading model [2/54]: Immune_All_High.pkl
💾 Downloading model [3/54]: Adult_COVID19_PBMC.pkl
💾 Downloading model [4/54]: Adult_CynomolgusMacaque_Hippocampus.pkl
💾 Downloading model [5/54]: Adult_Human_MTG.pkl
💾 Downloading model [6/54]: Adult_Human_PancreaticIslet.pkl
💾 Downloading model [7/54]: Adult_Human_PrefrontalCortex.pkl
💾 Downloading model [8/54]: Adult_Human_Skin.pkl
💾 Downloading model [9/54]: Adult_Human_Vascular.pkl
💾 Downloading model [10/54]: Adult_Mouse_Gut.pkl
💾 Downloading model [11/54]: Adult_Mouse_OlfactoryBulb.pkl
💾 Downloading model [12/54]: Adult_Pig_Hippocampus.pkl
💾 Downloading model [13/54]: Adult_RhesusMacaque_Hippocampus.pkl
💾 Downloading model [14/54]: Autopsy_COVID19_Lung.pkl
💾 Downloading model [15/54]: COVID19_HumanChallenge_Blood.pkl
💾 Downloading model [16/54]: COVID19_Immune_Landscape.pkl
💾 Downloading model [17/54]: Cells_Adult_Breast.pkl
💾 Downloading model [18/54]: Cells_Fetal_Lung.pkl
💾 Downloading model [19/54]: Cells_Human_Tonsil.pkl
💾 Downloading model [20/54]: Cells_Intestinal_Tract.pkl
💾 Downloading model [21/54]: Cells_Lung_Airway.pkl
💾 Downloading model [22/54]: Developing_Human_Brain.pkl
💾 Downloading model [23/54]: Developing_Human_Gonads.pkl
💾 Downloading model [24/54]: Developing_Human_Hippocampus.pkl
💾 Downloading model [25/54]: Developing_Human_Organs.pkl
💾 Downloading model [26/54]: Developing_Human_Thymus.pkl
💾 Downloading model [27/54]: Developing_Mouse_Brain.pkl
💾 Downloading model [28/54]: Developing_Mouse_Hippocampus.pkl
💾 Downloading model [29/54]: Fetal_Human_AdrenalGlands.pkl
💾 Downloading model [30/54]: Fetal_Human_Pancreas.pkl
💾 Downloading model [31/54]: Fetal_Human_Pituitary.pkl
💾 Downloading model [32/54]: Fetal_Human_Retina.pkl
💾 Downloading model [33/54]: Fetal_Human_Skin.pkl
💾 Downloading model [34/54]: Healthy_Adult_Heart.pkl
💾 Downloading model [35/54]: Healthy_COVID19_PBMC.pkl
💾 Downloading model [36/54]: Healthy_Human_Liver.pkl
💾 Downloading model [37/54]: Healthy_Mouse_Liver.pkl
💾 Downloading model [38/54]: Human_AdultAged_Hippocampus.pkl
💾 Downloading model [39/54]: Human_Colorectal_Cancer.pkl
💾 Downloading model [40/54]: Human_Developmental_Retina.pkl
💾 Downloading model [41/54]: Human_Embryonic_YolkSac.pkl
💾 Downloading model [42/54]: Human_Endometrium_Atlas.pkl
💾 Downloading model [43/54]: Human_IPF_Lung.pkl
💾 Downloading model [44/54]: Human_Longitudinal_Hippocampus.pkl
💾 Downloading model [45/54]: Human_Lung_Atlas.pkl
💾 Downloading model [46/54]: Human_PF_Lung.pkl
💾 Downloading model [47/54]: Human_Placenta_Decidua.pkl
💾 Downloading model [48/54]: Lethal_COVID19_Lung.pkl
💾 Downloading model [49/54]: Mouse_Dentate_Gyrus.pkl
💾 Downloading model [50/54]: Mouse_Isocortex_Hippocampus.pkl
💾 Downloading model [51/54]: Mouse_Postnatal_DentateGyrus.pkl
💾 Downloading model [52/54]: Mouse_Whole_Brain.pkl
💾 Downloading model [53/54]: Nuclei_Lung_Airway.pkl
💾 Downloading model [54/54]: Pan_Fetal_Human.pkl
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⚙️ Configuration:
🛠️ indata: /tmp/RtmpKyg18h/file35d42b31330064/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/RtmpKyg18h/file35d42b31330064
🛠️ prefix:
🛠️ xlsx: False
🛠️ plot-results: False
🛠️ quiet: False
🛠️ over-clustering: seurat_clusters
🛠️ min-prop: 0.0
📁 Input file is '/tmp/RtmpKyg18h/file35d42b31330064/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 3.71 seconds
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⚙️ Configuration:
🛠️ indata: /tmp/RtmpKyg18h/file35d42b25351f9f/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/RtmpKyg18h/file35d42b25351f9f
🛠️ prefix:
🛠️ xlsx: False
🛠️ plot-results: False
🛠️ quiet: False
🛠️ over-clustering: annotation_recluster
🛠️ min-prop: 0.0
📁 Input file is '/tmp/RtmpKyg18h/file35d42b25351f9f/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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Quitting from DOtools.Rmd:345-360 [GO analysis2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `scan()`:
! line 9 did not have 2 elements
---
Backtrace:
▆
1. └─DOtools::DO.enrichR(...)
2. └─enrichR::enrichr(genes = df_down[[gene_column]], databases = go_catgs)
3. └─base::lapply(...)
4. └─enrichR (local) FUN(X[[i]], ...)
5. └─utils::read.table(...)
6. └─base::scan(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'DOtools.Rmd' failed with diagnostics:
line 9 did not have 2 elements
--- failed re-building ‘DOtools.Rmd’
--- re-building ‘adfct.Rmd’ using rmarkdown
[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 3.93 seconds
--- finished re-building ‘adfct.Rmd’
--- re-building ‘cb.Rmd’ using rmarkdown
--- finished re-building ‘cb.Rmd’
SUMMARY: processing the following file failed:
‘DOtools.Rmd’
Error: Vignette re-building failed.
Execution halted