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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
--- finished re-building ‘citeseq_tut.Rmd’
--- re-building ‘compch12.Rmd’ using rmarkdown
2025-10-22 18:39:15.493 R[85571:613793238] XType: com.apple.fonts is not accessible.
2025-10-22 18:39:15.493 R[85571:613793238] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘compch12.Rmd’
--- re-building ‘new_citeseq.Rmd’ using rmarkdown
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/DbzU9TanKi-6XAjlMP5To/lib/python3.11/site-packages/numba/cpython/hashing.py:477: UserWarning: FNV hashing is not implemented in Numba. See PEP 456 https://www.python.org/dev/peps/pep-0456/ for rationale over not using FNV. Numba will continue to work, but hashes for built in types will be computed using siphash24. This will permit e.g. dictionaries to continue to behave as expected, however anything relying on the value of the hash opposed to hash as a derived property is likely to not work as expected.
warnings.warn(msg)
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/DbzU9TanKi-6XAjlMP5To/lib/python3.11/site-packages/muon/_core/preproc.py:31: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('scanpy')` instead
if Version(scanpy.__version__) < Version("1.10"):
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/H0Vx98q5SO6BJcNNcH8Oe/lib/python3.11/site-packages/anndata/_core/anndata.py:1794: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
utils.warn_names_duplicates("var")
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/H0Vx98q5SO6BJcNNcH8Oe/lib/python3.11/site-packages/anndata/_core/anndata.py:1794: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
utils.warn_names_duplicates("var")
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/DbzU9TanKi-6XAjlMP5To/lib/python3.11/site-packages/mudata/_core/mudata.py:1598: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
self._update_attr("var", axis=0, join_common=join_common)
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/DbzU9TanKi-6XAjlMP5To/lib/python3.11/site-packages/mudata/_core/mudata.py:947: UserWarning: var_names are not unique. To make them unique, call `.var_names_make_unique`.
warnings.warn(
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/DbzU9TanKi-6XAjlMP5To/lib/python3.11/site-packages/mudata/_core/mudata.py:1461: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
self._update_attr("obs", axis=1, join_common=join_common)
OMP: Info #276: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
OMP: Warning #96: Cannot form a team with 48 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/DbzU9TanKi-6XAjlMP5To/lib/python3.11/site-packages/mudata/_core/mudata.py:1598: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
self._update_attr("var", axis=0, join_common=join_common)
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/DbzU9TanKi-6XAjlMP5To/lib/python3.11/site-packages/mudata/_core/mudata.py:963: UserWarning: Cannot join columns with the same name because var_names are intersecting.
warnings.warn(
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/DbzU9TanKi-6XAjlMP5To/lib/python3.11/site-packages/mudata/_core/mudata.py:1461: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
self._update_attr("obs", axis=1, join_common=join_common)
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/DbzU9TanKi-6XAjlMP5To/lib/python3.11/site-packages/mudata/_core/mudata.py:1598: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
self._update_attr("var", axis=0, join_common=join_common)
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/DbzU9TanKi-6XAjlMP5To/lib/python3.11/site-packages/mudata/_core/mudata.py:1461: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
self._update_attr("obs", axis=1, join_common=join_common)
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.3.4 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
return _run_hook(name, _hook)
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 96, in _run_hook
module = hook()
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 120, in _hook
return _find_and_load(name, import_)
File "/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/Sp6nZCaPHJWykBmoQKpbU/lib/python3.11/site-packages/scvi/__init__.py", line 7, in <module>
from ._settings import settings
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
return _run_hook(name, _hook)
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 96, in _run_hook
module = hook()
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 120, in _hook
return _find_and_load(name, import_)
File "/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/Sp6nZCaPHJWykBmoQKpbU/lib/python3.11/site-packages/scvi/_settings.py", line 8, in <module>
import torch
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
return _run_hook(name, _hook)
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 96, in _run_hook
module = hook()
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 120, in _hook
return _find_and_load(name, import_)
File "/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/Sp6nZCaPHJWykBmoQKpbU/lib/python3.11/site-packages/torch/__init__.py", line 1477, in <module>
from .functional import * # noqa: F403
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
return _run_hook(name, _hook)
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 96, in _run_hook
module = hook()
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 120, in _hook
return _find_and_load(name, import_)
File "/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/Sp6nZCaPHJWykBmoQKpbU/lib/python3.11/site-packages/torch/functional.py", line 9, in <module>
import torch.nn.functional as F
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
return _run_hook(name, _hook)
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 96, in _run_hook
module = hook()
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 120, in _hook
return _find_and_load(name, import_)
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
return _run_hook(name, _hook)
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 96, in _run_hook
module = hook()
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 120, in _hook
return _find_and_load(name, import_)
File "/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/Sp6nZCaPHJWykBmoQKpbU/lib/python3.11/site-packages/torch/nn/__init__.py", line 1, in <module>
from .modules import * # noqa: F403
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
return _run_hook(name, _hook)
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 96, in _run_hook
module = hook()
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 120, in _hook
return _find_and_load(name, import_)
File "/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/Sp6nZCaPHJWykBmoQKpbU/lib/python3.11/site-packages/torch/nn/modules/__init__.py", line 35, in <module>
from .transformer import TransformerEncoder, TransformerDecoder, \
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
return _run_hook(name, _hook)
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 96, in _run_hook
module = hook()
File "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 120, in _hook
return _find_and_load(name, import_)
File "/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/Sp6nZCaPHJWykBmoQKpbU/lib/python3.11/site-packages/torch/nn/modules/transformer.py", line 20, in <module>
device: torch.device = torch.device(torch._C._get_default_device()), # torch.device('cpu'),
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/Sp6nZCaPHJWykBmoQKpbU/lib/python3.11/site-packages/torch/nn/modules/transformer.py:20: UserWarning: Failed to initialize NumPy: _ARRAY_API not found (Triggered internally at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/utils/tensor_numpy.cpp:84.)
device: torch.device = torch.device(torch._C._get_default_device()), # torch.device('cpu'),
[34mINFO [0m Computing empirical prior initialization for protein background.
Quitting from new_citeseq.Rmd:117-120 [what]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_call_impl()`:
! 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.
---
Backtrace:
▆
1. └─scviR()$model$TOTALVI(mdata1)
2. └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'new_citeseq.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 ‘new_citeseq.Rmd’
--- re-building ‘scviR.Rmd’ using rmarkdown
--- finished re-building ‘scviR.Rmd’
SUMMARY: processing the following file failed:
‘new_citeseq.Rmd’
Error: Vignette re-building failed.
Execution halted
