Mariano Ruz Jurado
| Snapshot Date: 2026-05-05 13:45 -0400 (Tue, 05 May 2026) |
| git_url: https://git.bioconductor.org/packages/DOtools |
| git_branch: devel |
| git_last_commit: 225bdbb |
| git_last_commit_date: 2026-04-28 09:05:43 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-06 11:34 -0400 (Wed, 06 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4878 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4663 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 616/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DOtools 1.3.0 (landing page) Mariano Ruz Jurado
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
| See other builds for DOtools in R Universe. | ||||||||||||||
|
To the developers/maintainers of the DOtools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DOtools.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: DOtools |
| Version: 1.3.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data DOtools |
| StartedAt: 2026-05-05 02:51:51 -0000 (Tue, 05 May 2026) |
| EndedAt: 2026-05-05 03:00:44 -0000 (Tue, 05 May 2026) |
| EllapsedTime: 533.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data 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
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Collecting cuda-toolkit==13.0.2 (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == "Linux"->torch->scvi-tools==1.3.0)
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Collecting nvidia-cudnn-cu13==9.19.0.56 (from torch->scvi-tools==1.3.0)
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Collecting nvidia-cusparselt-cu13==0.8.0 (from torch->scvi-tools==1.3.0)
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Collecting nvidia-nccl-cu13==2.28.9 (from torch->scvi-tools==1.3.0)
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Collecting nvidia-nvshmem-cu13==3.4.5 (from torch->scvi-tools==1.3.0)
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Collecting triton==3.6.0 (from torch->scvi-tools==1.3.0)
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Collecting nvidia-cublas==13.1.0.3.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == "Linux"->torch->scvi-tools==1.3.0)
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Collecting nvidia-cuda-runtime==13.0.96.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == "Linux"->torch->scvi-tools==1.3.0)
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Collecting nvidia-cufft==12.0.0.61.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == "Linux"->torch->scvi-tools==1.3.0)
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Collecting nvidia-cufile==1.15.1.6.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == "Linux"->torch->scvi-tools==1.3.0)
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Collecting nvidia-cuda-cupti==13.0.85.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == "Linux"->torch->scvi-tools==1.3.0)
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Collecting nvidia-curand==10.4.0.35.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == "Linux"->torch->scvi-tools==1.3.0)
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Collecting nvidia-cusolver==12.0.4.66.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == "Linux"->torch->scvi-tools==1.3.0)
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Collecting nvidia-cusparse==12.6.3.3.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == "Linux"->torch->scvi-tools==1.3.0)
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Collecting nvidia-nvjitlink==13.0.88.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == "Linux"->torch->scvi-tools==1.3.0)
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Collecting nvidia-cuda-nvrtc==13.0.88.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == "Linux"->torch->scvi-tools==1.3.0)
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Collecting nvidia-nvtx==13.0.85.* (from cuda-toolkit[cublas,cudart,cufft,cufile,cupti,curand,cusolver,cusparse,nvjitlink,nvrtc,nvtx]==13.0.2; platform_system == "Linux"->torch->scvi-tools==1.3.0)
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Collecting cuda-pathfinder~=1.1 (from cuda-bindings<14,>=13.0.3->torch->scvi-tools==1.3.0)
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Collecting attrs>=17.3.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2028.0,>=2022.5.0->lightning>=2.0->scvi-tools==1.3.0)
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Collecting frozenlist>=1.1.1 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2028.0,>=2022.5.0->lightning>=2.0->scvi-tools==1.3.0)
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Collecting multidict<7.0,>=4.5 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2028.0,>=2022.5.0->lightning>=2.0->scvi-tools==1.3.0)
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Collecting propcache>=0.2.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2028.0,>=2022.5.0->lightning>=2.0->scvi-tools==1.3.0)
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Collecting yarl<2.0,>=1.17.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2028.0,>=2022.5.0->lightning>=2.0->scvi-tools==1.3.0)
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Collecting idna>=2.0 (from yarl<2.0,>=1.17.0->aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2028.0,>=2022.5.0->lightning>=2.0->scvi-tools==1.3.0)
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INFO: pip is looking at multiple versions of numpyro to determine which version is compatible with other requirements. This could take a while.
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Collecting threadpoolctl>=3.2.0 (from scikit-learn>=0.21.2->scvi-tools==1.3.0)
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Collecting mpmath<1.4,>=1.1.0 (from sympy>=1.13.3->torch->scvi-tools==1.3.0)
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Collecting grpcio>=1.48.2 (from tensorboard>=2.0->scvi-tools==1.3.0)
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Collecting markdown>=2.6.8 (from tensorboard>=2.0->scvi-tools==1.3.0)
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Collecting protobuf!=4.24.0,>=3.19.6 (from tensorboard>=2.0->scvi-tools==1.3.0)
Using cached protobuf-7.34.1-cp310-abi3-manylinux2014_aarch64.whl.metadata (595 bytes)
Collecting tensorboard-data-server<0.8.0,>=0.7.0 (from tensorboard>=2.0->scvi-tools==1.3.0)
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Collecting werkzeug>=1.0.1 (from tensorboard>=2.0->scvi-tools==1.3.0)
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Collecting markupsafe>=2.1.1 (from werkzeug>=1.0.1->tensorboard>=2.0->scvi-tools==1.3.0)
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Collecting donfig>=0.8 (from zarr!=3.0.*,>=2.18.7->anndata>=0.11->scvi-tools==1.3.0)
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Collecting google-crc32c>=1.5 (from zarr!=3.0.*,>=2.18.7->anndata>=0.11->scvi-tools==1.3.0)
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Collecting numcodecs>=0.14 (from zarr!=3.0.*,>=2.18.7->anndata>=0.11->scvi-tools==1.3.0)
Using cached numcodecs-0.16.5-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl.metadata (3.4 kB)
INFO: pip is looking at multiple versions of zarr to determine which version is compatible with other requirements. This could take a while.
Collecting zarr!=3.0.*,>=2.18.7 (from anndata>=0.11->scvi-tools==1.3.0)
Using cached zarr-3.1.5-py3-none-any.whl.metadata (10 kB)
Collecting wrapt<3,>=1.10 (from deprecated->scib==1.1.7)
Using cached wrapt-2.1.2-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl.metadata (7.4 kB)
INFO: pip is looking at multiple versions of flax to determine which version is compatible with other requirements. This could take a while.
Collecting flax (from scvi-tools==1.3.0)
Using cached flax-0.12.6-py3-none-any.whl.metadata (11 kB)
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Using cached flax-0.12.0-py3-none-any.whl.metadata (11 kB)
INFO: pip is still looking at multiple versions of flax to determine which version is compatible with other requirements. This could take a while.
Using cached flax-0.11.2-py3-none-any.whl.metadata (11 kB)
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Using cached flax-0.10.7-py3-none-any.whl.metadata (11 kB)
Using cached flax-0.10.6-py3-none-any.whl.metadata (11 kB)
INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. See https://pip.pypa.io/warnings/backtracking for guidance. If you want to abort this run, press Ctrl + C.
Using cached flax-0.10.5-py3-none-any.whl.metadata (11 kB)
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Collecting msgpack (from flax->scvi-tools==1.3.0)
Using cached msgpack-1.1.2-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl.metadata (8.1 kB)
Collecting orbax-checkpoint (from flax->scvi-tools==1.3.0)
Downloading orbax_checkpoint-0.11.37-py3-none-any.whl.metadata (2.8 kB)
Collecting tensorstore (from flax->scvi-tools==1.3.0)
Using cached tensorstore-0.1.82-cp311-cp311-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl.metadata (3.3 kB)
Collecting treescope>=0.1.7 (from flax->scvi-tools==1.3.0)
Using cached treescope-0.1.10-py3-none-any.whl.metadata (6.6 kB)
INFO: pip is looking at multiple versions of optax to determine which version is compatible with other requirements. This could take a while.
Collecting optax (from scvi-tools==1.3.0)
Using cached optax-0.2.7-py3-none-any.whl.metadata (7.9 kB)
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Collecting chex>=0.1.87 (from optax->scvi-tools==1.3.0)
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INFO: pip is looking at multiple versions of chex to determine which version is compatible with other requirements. This could take a while.
Collecting chex>=0.1.87 (from optax->scvi-tools==1.3.0)
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Collecting toolz>=0.9.0 (from chex>=0.1.87->optax->scvi-tools==1.3.0)
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Collecting etils[epath,epy] (from orbax-checkpoint->flax->scvi-tools==1.3.0)
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INFO: pip is looking at multiple versions of orbax-checkpoint to determine which version is compatible with other requirements. This could take a while.
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Installing collected packages: texttable, pytz, pyro-api, nvidia-cusparselt-cu13, multipledispatch, mpmath, cuda-toolkit, zipp, wrapt, urllib3, tzdata, typing-extensions, triton, tqdm, toolz, threadpoolctl, tensorboard-data-server, sympy, six, simplejson, setuptools, session-info2, PyYAML, pyparsing, pygments, protobuf, propcache, pillow, opt-einsum, nvidia-nvtx, nvidia-nvshmem-cu13, nvidia-nvjitlink, nvidia-nccl-cu13, nvidia-curand, nvidia-cufile, nvidia-cuda-runtime, nvidia-cuda-nvrtc, nvidia-cuda-cupti, nvidia-cublas, numpy, networkx, nest_asyncio, natsort, multidict, msgpack, mdurl, markupsafe, markdown, llvmlite, legacy-api-wrap, kiwisolver, joblib, 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, scverse-misc, scipy, scikit-misc, requests, python-dateutil, pydot, patsy, openpyxl, nvidia-cusparse, nvidia-cufft, nvidia-cudnn-cu13, 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, matplotlib, jaxlib, aiohttp, xarray, statsmodels, seaborn, pynndescent, jax, anndata, umap-learn, torch, scanpro, orbax-checkpoint, numpyro, mudata, chex, torchmetrics, scanpy, pyro-ppl, optax, scib, pytorch-lightning, flax, celltypist, lightning, scvi-tools
Attempting uninstall: setuptools
Found existing installation: setuptools 82.0.1
Uninstalling setuptools-82.0.1:
Successfully uninstalled setuptools-82.0.1
Successfully installed PyYAML-6.0.3 absl-py-2.4.0 aiohappyeyeballs-2.6.1 aiohttp-3.13.5 aiosignal-1.4.0 anndata-0.12.11 array-api-compat-1.14.0 attrs-26.1.0 celltypist-1.6.3 certifi-2026.4.22 charset_normalizer-3.4.7 chex-0.1.90 click-8.3.3 contourpy-1.3.3 cuda-bindings-13.2.0 cuda-pathfinder-1.5.4 cuda-toolkit-13.0.2 cycler-0.12.1 deprecated-1.3.1 docrep-0.3.2 donfig-0.8.1.post1 et-xmlfile-2.0.0 etils-1.14.0 filelock-3.29.0 flax-0.10.4 fonttools-4.62.1 frozenlist-1.8.0 fsspec-2026.4.0 google-crc32c-1.8.0 grpcio-1.80.0 h5py-3.16.0 humanize-4.15.0 idna-3.13 igraph-1.0.0 jax-0.4.35 jaxlib-0.4.35 jinja2-3.1.6 joblib-1.5.3 kiwisolver-1.5.0 legacy-api-wrap-1.5 leidenalg-0.11.0 lightning-2.6.1 lightning-utilities-0.15.3 llvmlite-0.47.0 markdown-3.10.2 markdown-it-py-4.0.0 markupsafe-3.0.3 matplotlib-3.10.9 mdurl-0.1.2 ml-collections-1.1.0 ml-dtypes-0.5.4 mpmath-1.3.0 msgpack-1.1.2 mudata-0.3.7 multidict-6.7.1 multipledispatch-1.0.0 natsort-8.4.0 nest_asyncio-1.6.0 networkx-3.6.1 numba-0.65.1 numcodecs-0.16.5 numpy-1.26.4 numpyro-0.19.0 nvidia-cublas-13.1.0.3 nvidia-cuda-cupti-13.0.85 nvidia-cuda-nvrtc-13.0.88 nvidia-cuda-runtime-13.0.96 nvidia-cudnn-cu13-9.19.0.56 nvidia-cufft-12.0.0.61 nvidia-cufile-1.15.1.6 nvidia-curand-10.4.0.35 nvidia-cusolver-12.0.4.66 nvidia-cusparse-12.6.3.3 nvidia-cusparselt-cu13-0.8.0 nvidia-nccl-cu13-2.28.9 nvidia-nvjitlink-13.0.88 nvidia-nvshmem-cu13-3.4.5 nvidia-nvtx-13.0.85 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-12.2.0 propcache-0.4.1 protobuf-7.34.1 pydot-4.0.1 pygments-2.20.0 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-2026.2 requests-2.33.1 rich-15.0.0 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 scverse-misc-0.0.3 scvi-tools-1.3.0 seaborn-0.13.2 session-info2-0.4.1 setuptools-81.0.0 simplejson-4.1.1 six-1.17.0 sparse-0.18.0 statsmodels-0.14.6 sympy-1.14.0 tensorboard-2.20.0 tensorboard-data-server-0.7.2 tensorstore-0.1.82 texttable-1.7.0 threadpoolctl-3.6.0 toolz-1.1.0 torch-2.11.0 torchmetrics-1.9.0 tqdm-4.67.3 treescope-0.1.10 triton-3.6.0 typing-extensions-4.15.0 tzdata-2026.2 umap-learn-0.5.12 urllib3-2.6.3 werkzeug-3.1.8 wrapt-2.1.2 xarray-2026.4.0 yarl-1.23.0 zarr-3.1.5 zipp-3.23.1
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⚙️ Configuration:
🛠️ indata: /home/biocbuild/tmp/Rtmp3MZ35G/file28ae05863e3af/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: /home/biocbuild/tmp/Rtmp3MZ35G/file28ae05863e3af
🛠️ prefix:
🛠️ xlsx: False
🛠️ plot-results: False
🛠️ quiet: False
🛠️ over-clustering: leiden0.3
🛠️ min-prop: 0.0
📁 Input file is '/home/biocbuild/tmp/Rtmp3MZ35G/file28ae05863e3af/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 5.77 seconds
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.ooooo. .ooooo. 888 888 .o888oo oooo ooo oo.ooooo. oooo .oooo.o .o888oo
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: /home/biocbuild/tmp/Rtmp3MZ35G/file28ae0531bae584/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: /home/biocbuild/tmp/Rtmp3MZ35G/file28ae0531bae584
🛠️ prefix:
🛠️ xlsx: False
🛠️ plot-results: False
🛠️ quiet: False
🛠️ over-clustering: annotation_recluster
🛠️ min-prop: 0.0
📁 Input file is '/home/biocbuild/tmp/Rtmp3MZ35G/file28ae0531bae584/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 1802 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:699-715 [Box]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `ValidateCellGroups()`:
! The following cell names provided to cells.1 are not present:
---
Backtrace:
▆
1. └─DOtools::DO.BoxPlot(...)
2. ├─DOtools:::.suppressAllWarnings(...)
3. │ └─base::withCallingHandlers(...)
4. ├─Seurat::FindMarkers(...)
5. └─Seurat:::FindMarkers.Seurat(...)
6. ├─Seurat::FindMarkers(...)
7. └─Seurat:::FindMarkers.Assay(...)
8. ├─Seurat::FindMarkers(...)
9. └─Seurat:::FindMarkers.default(...)
10. └─Seurat:::ValidateCellGroups(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'DOtools.Rmd' failed with diagnostics:
The following cell names provided to cells.1 are not present:
--- failed re-building ‘DOtools.Rmd’
SUMMARY: processing the following file failed:
‘DOtools.Rmd’
Error: Vignette re-building failed.
Execution halted