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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data scviR
###
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* 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
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /private/var/cache/basilisk/1.17.0/scviR/1.5.0/bsklenv
added / updated specs:
- python=3.10
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
ca-certificates conda-forge/osx-64::ca-certificates-2024.2.2-h8857fd0_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libsqlite conda-forge/osx-64::libsqlite-3.45.3-h92b6c6a_0
libzlib conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5
ncurses conda-forge/osx-64::ncurses-6.4.20240210-h73e2aa4_0
openssl conda-forge/osx-64::openssl-3.3.0-hd75f5a5_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.10.14-h00d2728_0_cpython
readline conda-forge/osx-64::readline-8.2-h9e318b2_1
setuptools conda-forge/noarch::setuptools-69.5.1-pyhd8ed1ab_0
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.4.0
Please update conda by running
$ conda update -n base -c defaults conda
# All requested packages already installed.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.4.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /private/var/cache/basilisk/1.17.0/scviR/1.5.0/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
---------------------------|-----------------
pandas-1.5.3 | py310hecf8f37_1 10.9 MB conda-forge
------------------------------------------------------------
Total: 10.9 MB
The following NEW packages will be INSTALLED:
libblas conda-forge/osx-64::libblas-3.9.0-22_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-22_osx64_openblas
libcxx conda-forge/osx-64::libcxx-16.0.6-hd57cbcb_0
libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
liblapack conda-forge/osx-64::liblapack-3.9.0-22_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.27-openmp_hfef2a42_0
llvm-openmp conda-forge/osx-64::llvm-openmp-18.1.3-hb6ac08f_0
numpy conda-forge/osx-64::numpy-1.24.4-py310h7451ae0_0
pandas conda-forge/osx-64::pandas-1.5.3-py310hecf8f37_1
python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0
python_abi conda-forge/osx-64::python_abi-3.10-4_cp310
pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
Downloading and Extracting Packages
pandas-1.5.3 | 10.9 MB | | 0%
pandas-1.5.3 | 10.9 MB | | 0%
pandas-1.5.3 | 10.9 MB | ###9 | 40%
pandas-1.5.3 | 10.9 MB | #######3 | 74%
pandas-1.5.3 | 10.9 MB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting anndata==0.10.1
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Requirement already satisfied: six in /private/var/cache/basilisk/1.17.0/scviR/1.5.0/bsklenv/lib/python3.10/site-packages (from docrep==0.3.2) (1.16.0)
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Collecting ml-dtypes>=0.2.0 (from jax==0.4.23)
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Collecting pygments<3.0.0,>=2.13.0 (from rich==13.7.1)
Using cached pygments-2.17.2-py3-none-any.whl.metadata (2.6 kB)
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Collecting lightning-utilities<2.0,>=0.8.0 (from lightning==2.1.4)
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Collecting pytorch-lightning (from lightning==2.1.4)
Downloading pytorch_lightning-2.2.4-py3-none-any.whl.metadata (21 kB)
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Collecting numpyro>=0.12.1 (from scvi-tools==1.1.2)
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Collecting pyro-ppl>=1.6.0 (from scvi-tools==1.1.2)
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Collecting pyro-api>=0.1.1 (from pyro-ppl>=1.6.0->scvi-tools==1.1.2)
Using cached pyro_api-0.1.2-py3-none-any.whl.metadata (2.5 kB)
INFO: pip is looking at multiple versions of pyro-ppl to determine which version is compatible with other requirements. This could take a while.
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Collecting yarl<2.0,>=1.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2025.0,>=2022.5.0->lightning==2.1.4)
Using cached yarl-1.9.4-cp310-cp310-macosx_10_9_x86_64.whl.metadata (31 kB)
Collecting async-timeout<5.0,>=4.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2025.0,>=2022.5.0->lightning==2.1.4)
Using cached async_timeout-4.0.3-py3-none-any.whl.metadata (4.2 kB)
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Using cached importlib_resources-6.4.0-py3-none-any.whl.metadata (3.9 kB)
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Using cached zipp-3.18.1-py3-none-any.whl.metadata (3.5 kB)
Collecting idna>=2.0 (from yarl<2.0,>=1.0->aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]<2025.0,>=2022.5.0->lightning==2.1.4)
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Installing collected packages: pyro-api, multipledispatch, array-api-compat, zipp, typing-extensions, tqdm, toolz, threadpoolctl, stdlib-list, scipy, scikit-misc, PyYAML, pyparsing, pygments, protobuf, pillow, patsy, packaging, opt-einsum, networkx, nest_asyncio, natsort, multidict, msgpack, ml-dtypes, mdurl, llvmlite, kiwisolver, joblib, importlib_resources, idna, h5py, fsspec, frozenlist, fonttools, exceptiongroup, etils, docrep, cycler, contourpy, contextlib2, attrs, async-timeout, absl-py, yarl, torch, tensorstore, session-info, scikit-learn, numba, ml-collections, matplotlib, markdown-it-py, lightning-utilities, jaxlib, jax, aiosignal, torchmetrics, statsmodels, seaborn, rich, pyro-ppl, pynndescent, numpyro, chex, anndata, aiohttp, umap-learn, orbax-checkpoint, optax, mudata, scanpy, pytorch-lightning, flax, lightning, scvi-tools
Successfully installed PyYAML-6.0.1 absl-py-2.1.0 aiohttp-3.9.5 aiosignal-1.3.1 anndata-0.10.1 array-api-compat-1.6 async-timeout-4.0.3 attrs-23.2.0 chex-0.1.86 contextlib2-21.6.0 contourpy-1.2.1 cycler-0.12.1 docrep-0.3.2 etils-1.7.0 exceptiongroup-1.2.1 flax-0.8.1 fonttools-4.51.0 frozenlist-1.4.1 fsspec-2024.3.1 h5py-3.9.0 idna-3.7 importlib_resources-6.4.0 jax-0.4.23 jaxlib-0.4.23 joblib-1.4.0 kiwisolver-1.4.5 lightning-2.1.4 lightning-utilities-0.11.2 llvmlite-0.42.0 markdown-it-py-3.0.0 matplotlib-3.7.3 mdurl-0.1.2 ml-collections-0.1.1 ml-dtypes-0.4.0 msgpack-1.0.8 mudata-0.2.3 multidict-6.0.5 multipledispatch-1.0.0 natsort-8.4.0 nest_asyncio-1.6.0 networkx-3.3 numba-0.59.1 numpyro-0.14.0 opt-einsum-3.3.0 optax-0.1.9 orbax-checkpoint-0.5.10 packaging-24.0 patsy-0.5.6 pillow-10.3.0 protobuf-5.26.1 pygments-2.17.2 pynndescent-0.5.12 pyparsing-3.1.2 pyro-api-0.1.2 pyro-ppl-1.8.6 pytorch-lightning-2.2.4 rich-13.7.1 scanpy-1.9.5 scikit-learn-1.4.0 scikit-misc-0.3.1 scipy-1.12.0 scvi-tools-1.1.2 seaborn-0.13.2 session-info-1.0.0 statsmodels-0.14.2 stdlib-list-0.10.0 tensorstore-0.1.58 threadpoolctl-3.5.0 toolz-0.12.1 torch-1.13.1 torchmetrics-0.11.0 tqdm-4.66.2 typing-extensions-4.11.0 umap-learn-0.5.6 yarl-1.9.4 zipp-3.18.1
/private/var/cache/basilisk/1.17.0/scviR/1.5.0/bsklenv/lib/python3.10/site-packages/anndata/__init__.py:51: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024.
warnings.warn(
/private/var/cache/basilisk/1.17.0/scviR/1.5.0/bsklenv/lib/python3.10/site-packages/anndata/__init__.py:51: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024.
warnings.warn(
Quitting from lines at lines 57-58 [dogetv] (citeseq_tut.Rmd)
Error: processing vignette 'citeseq_tut.Rmd' failed with diagnostics:
RuntimeWarning:
Found Intel OpenMP ('libiomp') and LLVM OpenMP ('libomp') loaded at
the same time. Both libraries are known to be incompatible and this
can cause random crashes or deadlocks on Linux when loaded in the
same Python program.
Using threadpoolctl may cause crashes or deadlocks. For more
information and possible workarounds, please see
https://github.com/joblib/threadpoolctl/blob/master/multiple_openmp.md
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘citeseq_tut.Rmd’
--- re-building ‘compch12.Rmd’ using rmarkdown
/private/var/cache/basilisk/1.17.0/scviR/1.5.0/bsklenv/lib/python3.10/site-packages/anndata/__init__.py:51: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024.
warnings.warn(
2024-05-01 22:42:19.239 R[62161:395364754] XType: com.apple.fonts is not accessible.
2024-05-01 22:42:19.239 R[62161:395364754] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘compch12.Rmd’
--- re-building ‘scviR.Rmd’ using rmarkdown
--- finished re-building ‘scviR.Rmd’
SUMMARY: processing the following file failed:
‘citeseq_tut.Rmd’
Error: Vignette re-building failed.
Execution halted
