##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data scviR
###
##############################################################################
##############################################################################


* 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
Requirement already satisfied: pip in /home/biocbuild/.cache/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages (23.0.1)
Collecting pip
  Using cached pip-25.2-py3-none-any.whl (1.8 MB)
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Requirement already satisfied: setuptools in /home/biocbuild/.cache/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages (65.5.0)
Collecting setuptools
  Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
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 23.0.1
    Uninstalling pip-23.0.1:
      Successfully uninstalled pip-23.0.1
Successfully installed pip-25.2 setuptools-80.9.0 wheel-0.45.1
Collecting pandas==2.2.3
  Using cached pandas-2.2.3-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.whl.metadata (89 kB)
Collecting rope==1.13.0
  Using cached rope-1.13.0-py3-none-any.whl.metadata (6.6 kB)
Collecting scvi-tools==1.3.0
  Using cached scvi_tools-1.3.0-py3-none-any.whl.metadata (19 kB)
Collecting session_info==1.0.1
  Using cached session_info-1.0.1-py3-none-any.whl.metadata (5.1 kB)
Collecting anndata==0.11.4
  Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting chex==0.1.89
  Using cached chex-0.1.89-py3-none-any.whl.metadata (17 kB)
Collecting h5py==3.13.0
  Using cached h5py-3.13.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (2.5 kB)
Collecting jax==0.4.35
  Using cached jax-0.4.35-py3-none-any.whl.metadata (22 kB)
Collecting jaxlib==0.4.35
  Using cached jaxlib-0.4.35-cp310-cp310-manylinux2014_aarch64.whl.metadata (983 bytes)
Collecting joblib==1.4.2
  Using cached joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB)
Collecting lightning==2.5.1.post0
  Using cached lightning-2.5.1.post0-py3-none-any.whl.metadata (39 kB)
Collecting lightning_utilities==0.14.3
  Using cached lightning_utilities-0.14.3-py3-none-any.whl.metadata (5.6 kB)
Collecting llvmlite==0.44.0
  Using cached llvmlite-0.44.0-cp310-cp310-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl.metadata (4.8 kB)
Collecting ml_collections==1.1.0
  Using cached ml_collections-1.1.0-py3-none-any.whl.metadata (22 kB)
Collecting ml_dtypes==0.5.1
  Using cached ml_dtypes-0.5.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (21 kB)
Collecting msgpack==1.1.0
  Using cached msgpack-1.1.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (8.4 kB)
Collecting mudata==0.3.1
  Using cached mudata-0.3.1-py3-none-any.whl.metadata (8.3 kB)
Collecting multipledispatch==0.6.0
  Using cached multipledispatch-0.6.0-py3-none-any.whl.metadata (4.0 kB)
Collecting muon==0.1.7
  Using cached muon-0.1.7-py3-none-any.whl.metadata (7.2 kB)
Collecting natsort==8.4.0
  Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting networkx==3.4.2
  Using cached networkx-3.4.2-py3-none-any.whl.metadata (6.3 kB)
Collecting numba==0.61.2
  Using cached numba-0.61.2-cp310-cp310-manylinux_2_28_aarch64.whl.metadata (2.8 kB)
Collecting numpy==2.2.5
  Using cached numpy-2.2.5-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (63 kB)
Collecting numpyro==0.18.0
  Using cached numpyro-0.18.0-py3-none-any.whl.metadata (37 kB)
Collecting opt_einsum==3.4.0
  Using cached opt_einsum-3.4.0-py3-none-any.whl.metadata (6.3 kB)
Collecting optax==0.2.4
  Using cached optax-0.2.4-py3-none-any.whl.metadata (8.3 kB)
Collecting packaging==24.2
  Using cached packaging-24.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pygments==2.19.1
  Using cached pygments-2.19.1-py3-none-any.whl.metadata (2.5 kB)
Collecting pytz==2025.2
  Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting scipy==1.15.2
  Using cached scipy-1.15.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (61 kB)
Collecting six==1.17.0
  Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Collecting sparse==0.16.0
  Using cached sparse-0.16.0-py2.py3-none-any.whl.metadata (5.3 kB)
Collecting sympy==1.13.1
  Using cached sympy-1.13.1-py3-none-any.whl.metadata (12 kB)
Collecting threadpoolctl==3.6.0
  Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
Collecting toolz==1.0.0
  Using cached toolz-1.0.0-py3-none-any.whl.metadata (5.1 kB)
Collecting torch==2.6.0
  Using cached torch-2.6.0-cp310-cp310-manylinux_2_28_aarch64.whl.metadata (28 kB)
Collecting torchmetrics==1.7.1
  Using cached torchmetrics-1.7.1-py3-none-any.whl.metadata (21 kB)
Collecting tqdm==4.67.1
  Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)
Collecting xarray==2025.4.0
  Using cached xarray-2025.4.0-py3-none-any.whl.metadata (12 kB)
Collecting scikit-misc==0.5.1
  Using cached scikit_misc-0.5.1.tar.gz (298 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'error'
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [10 lines of output]
      + meson setup /home/biocbuild/tmp/pip-install-y_3to20b/scikit-misc_2e373d84dfb24b95ba1fe52f3fd6f215 /home/biocbuild/tmp/pip-install-y_3to20b/scikit-misc_2e373d84dfb24b95ba1fe52f3fd6f215/.mesonpy-r9fhkoaw -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/home/biocbuild/tmp/pip-install-y_3to20b/scikit-misc_2e373d84dfb24b95ba1fe52f3fd6f215/.mesonpy-r9fhkoaw/meson-python-native-file.ini
      The Meson build system
      Version: 1.9.0
      Source dir: /home/biocbuild/tmp/pip-install-y_3to20b/scikit-misc_2e373d84dfb24b95ba1fe52f3fd6f215
      Build dir: /home/biocbuild/tmp/pip-install-y_3to20b/scikit-misc_2e373d84dfb24b95ba1fe52f3fd6f215/.mesonpy-r9fhkoaw
      Build type: native build
      
      ../meson.build:5:11: ERROR: Command `/home/biocbuild/tmp/pip-install-y_3to20b/scikit-misc_2e373d84dfb24b95ba1fe52f3fd6f215/skmisc/_build_utils/version_please.py` failed with status 127.
      
      A full log can be found at /home/biocbuild/tmp/pip-install-y_3to20b/scikit-misc_2e373d84dfb24b95ba1fe52f3fd6f215/.mesonpy-r9fhkoaw/meson-logs/meson-log.txt
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

Quitting from compch12.Rmd:49-53 [getdat2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'pandas==2.2.3'", "'rope==1.13.0'", "'scvi-tools==1.3.0'", "'session_info==1.0.1'", "'anndata==0.11.4'", "'chex==0.1.89'", "'h5py==3.13.0'", "'jax==0.4.35'", "'jaxlib==0.4.35'", "'joblib==1.4.2'", "'lightning==2.5.1.post0'", "'lightning_utilities==0.14.3'", "'llvmlite==0.44.0'", "'ml_collections==1.1.0'", "'ml_dtypes==0.5.1'", "'msgpack==1.1.0'", "'mudata==0.3.1'", "'multipledispatch==0.6.0'", "'muon==0.1.7'", "'natsort==8.4.0'", "'networkx==3.4.2'", "'numba==0.61.2'", "'numpy==2.2.5'", "'numpyro==0.18.0'", "'opt_einsum==3.4.0'", "'optax==0.2.4'", "'packaging==24.2'", "'pygments==2.19.1'", "'pytz==2025.2'", "'scipy==1.15.2'", "'six==1.17.0'", "'sparse==0.16.0'", "'sympy==1.13.1'", "'threadpoolctl==3.6.0'", "'toolz==1.0.0'", "'torch==2.6.0'", "'torchmetrics==1.7.1'", "'tqdm==4.67.1'", "'xarray==2025.4.0'", "'scikit-misc==0.5.1'", "'leidenalg==0.10.2'", "'igraph==0.11.8'"
---
Backtrace:
    ▆
 1. └─scviR::getTotalVI5k10kAdata()
 2.   └─scviR::anndataR()
 3.     └─basilisk::basiliskStart(bsklenv, testload = "anndata")
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           └─reticulate::virtualenv_create(...)
 7.             └─reticulate:::pip_install(python, packages)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'compch12.Rmd' failed with diagnostics:
Error installing package(s): "'pandas==2.2.3'", "'rope==1.13.0'", "'scvi-tools==1.3.0'", "'session_info==1.0.1'", "'anndata==0.11.4'", "'chex==0.1.89'", "'h5py==3.13.0'", "'jax==0.4.35'", "'jaxlib==0.4.35'", "'joblib==1.4.2'", "'lightning==2.5.1.post0'", "'lightning_utilities==0.14.3'", "'llvmlite==0.44.0'", "'ml_collections==1.1.0'", "'ml_dtypes==0.5.1'", "'msgpack==1.1.0'", "'mudata==0.3.1'", "'multipledispatch==0.6.0'", "'muon==0.1.7'", "'natsort==8.4.0'", "'networkx==3.4.2'", "'numba==0.61.2'", "'numpy==2.2.5'", "'numpyro==0.18.0'", "'opt_einsum==3.4.0'", "'optax==0.2.4'", "'packaging==24.2'", "'pygments==2.19.1'", "'pytz==2025.2'", "'scipy==1.15.2'", "'six==1.17.0'", "'sparse==0.16.0'", "'sympy==1.13.1'", "'threadpoolctl==3.6.0'", "'toolz==1.0.0'", "'torch==2.6.0'", "'torchmetrics==1.7.1'", "'tqdm==4.67.1'", "'xarray==2025.4.0'", "'scikit-misc==0.5.1'", "'leidenalg==0.10.2'", "'igraph==0.11.8'"
--- failed re-building ‘compch12.Rmd’

--- re-building ‘new_citeseq.Rmd’ using rmarkdown
Requirement already satisfied: pip in /home/biocbuild/.cache/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages (23.0.1)
Collecting pip
  Using cached pip-25.2-py3-none-any.whl (1.8 MB)
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Requirement already satisfied: setuptools in /home/biocbuild/.cache/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages (65.5.0)
Collecting setuptools
  Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
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 23.0.1
    Uninstalling pip-23.0.1:
      Successfully uninstalled pip-23.0.1
Successfully installed pip-25.2 setuptools-80.9.0 wheel-0.45.1
Collecting pandas==2.2.3
  Using cached pandas-2.2.3-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.whl.metadata (89 kB)
Collecting rope==1.13.0
  Using cached rope-1.13.0-py3-none-any.whl.metadata (6.6 kB)
Collecting scvi-tools==1.3.0
  Using cached scvi_tools-1.3.0-py3-none-any.whl.metadata (19 kB)
Collecting session_info==1.0.1
  Using cached session_info-1.0.1-py3-none-any.whl.metadata (5.1 kB)
Collecting anndata==0.11.4
  Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting chex==0.1.89
  Using cached chex-0.1.89-py3-none-any.whl.metadata (17 kB)
Collecting h5py==3.13.0
  Using cached h5py-3.13.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (2.5 kB)
Collecting jax==0.4.35
  Using cached jax-0.4.35-py3-none-any.whl.metadata (22 kB)
Collecting jaxlib==0.4.35
  Using cached jaxlib-0.4.35-cp310-cp310-manylinux2014_aarch64.whl.metadata (983 bytes)
Collecting joblib==1.4.2
  Using cached joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB)
Collecting lightning==2.5.1.post0
  Using cached lightning-2.5.1.post0-py3-none-any.whl.metadata (39 kB)
Collecting lightning_utilities==0.14.3
  Using cached lightning_utilities-0.14.3-py3-none-any.whl.metadata (5.6 kB)
Collecting llvmlite==0.44.0
  Using cached llvmlite-0.44.0-cp310-cp310-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl.metadata (4.8 kB)
Collecting ml_collections==1.1.0
  Using cached ml_collections-1.1.0-py3-none-any.whl.metadata (22 kB)
Collecting ml_dtypes==0.5.1
  Using cached ml_dtypes-0.5.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (21 kB)
Collecting msgpack==1.1.0
  Using cached msgpack-1.1.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (8.4 kB)
Collecting mudata==0.3.1
  Using cached mudata-0.3.1-py3-none-any.whl.metadata (8.3 kB)
Collecting multipledispatch==0.6.0
  Using cached multipledispatch-0.6.0-py3-none-any.whl.metadata (4.0 kB)
Collecting muon==0.1.7
  Using cached muon-0.1.7-py3-none-any.whl.metadata (7.2 kB)
Collecting natsort==8.4.0
  Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting networkx==3.4.2
  Using cached networkx-3.4.2-py3-none-any.whl.metadata (6.3 kB)
Collecting numba==0.61.2
  Using cached numba-0.61.2-cp310-cp310-manylinux_2_28_aarch64.whl.metadata (2.8 kB)
Collecting numpy==2.2.5
  Using cached numpy-2.2.5-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (63 kB)
Collecting numpyro==0.18.0
  Using cached numpyro-0.18.0-py3-none-any.whl.metadata (37 kB)
Collecting opt_einsum==3.4.0
  Using cached opt_einsum-3.4.0-py3-none-any.whl.metadata (6.3 kB)
Collecting optax==0.2.4
  Using cached optax-0.2.4-py3-none-any.whl.metadata (8.3 kB)
Collecting packaging==24.2
  Using cached packaging-24.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pygments==2.19.1
  Using cached pygments-2.19.1-py3-none-any.whl.metadata (2.5 kB)
Collecting pytz==2025.2
  Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting scipy==1.15.2
  Using cached scipy-1.15.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (61 kB)
Collecting six==1.17.0
  Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Collecting sparse==0.16.0
  Using cached sparse-0.16.0-py2.py3-none-any.whl.metadata (5.3 kB)
Collecting sympy==1.13.1
  Using cached sympy-1.13.1-py3-none-any.whl.metadata (12 kB)
Collecting threadpoolctl==3.6.0
  Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
Collecting toolz==1.0.0
  Using cached toolz-1.0.0-py3-none-any.whl.metadata (5.1 kB)
Collecting torch==2.6.0
  Using cached torch-2.6.0-cp310-cp310-manylinux_2_28_aarch64.whl.metadata (28 kB)
Collecting torchmetrics==1.7.1
  Using cached torchmetrics-1.7.1-py3-none-any.whl.metadata (21 kB)
Collecting tqdm==4.67.1
  Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)
Collecting xarray==2025.4.0
  Using cached xarray-2025.4.0-py3-none-any.whl.metadata (12 kB)
Collecting scikit-misc==0.5.1
  Using cached scikit_misc-0.5.1.tar.gz (298 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'error'
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [10 lines of output]
      + meson setup /home/biocbuild/tmp/pip-install-000n0zgb/scikit-misc_57989659f696487d9a28bb342d0f782d /home/biocbuild/tmp/pip-install-000n0zgb/scikit-misc_57989659f696487d9a28bb342d0f782d/.mesonpy-cs8dh_gz -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/home/biocbuild/tmp/pip-install-000n0zgb/scikit-misc_57989659f696487d9a28bb342d0f782d/.mesonpy-cs8dh_gz/meson-python-native-file.ini
      The Meson build system
      Version: 1.9.0
      Source dir: /home/biocbuild/tmp/pip-install-000n0zgb/scikit-misc_57989659f696487d9a28bb342d0f782d
      Build dir: /home/biocbuild/tmp/pip-install-000n0zgb/scikit-misc_57989659f696487d9a28bb342d0f782d/.mesonpy-cs8dh_gz
      Build type: native build
      
      ../meson.build:5:11: ERROR: Command `/home/biocbuild/tmp/pip-install-000n0zgb/scikit-misc_57989659f696487d9a28bb342d0f782d/skmisc/_build_utils/version_please.py` failed with status 127.
      
      A full log can be found at /home/biocbuild/tmp/pip-install-000n0zgb/scikit-misc_57989659f696487d9a28bb342d0f782d/.mesonpy-cs8dh_gz/meson-logs/meson-log.txt
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

Quitting from new_citeseq.Rmd:41-48 [doe44]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'pandas==2.2.3'", "'rope==1.13.0'", "'scvi-tools==1.3.0'", "'session_info==1.0.1'", "'anndata==0.11.4'", "'chex==0.1.89'", "'h5py==3.13.0'", "'jax==0.4.35'", "'jaxlib==0.4.35'", "'joblib==1.4.2'", "'lightning==2.5.1.post0'", "'lightning_utilities==0.14.3'", "'llvmlite==0.44.0'", "'ml_collections==1.1.0'", "'ml_dtypes==0.5.1'", "'msgpack==1.1.0'", "'mudata==0.3.1'", "'multipledispatch==0.6.0'", "'muon==0.1.7'", "'natsort==8.4.0'", "'networkx==3.4.2'", "'numba==0.61.2'", "'numpy==2.2.5'", "'numpyro==0.18.0'", "'opt_einsum==3.4.0'", "'optax==0.2.4'", "'packaging==24.2'", "'pygments==2.19.1'", "'pytz==2025.2'", "'scipy==1.15.2'", "'six==1.17.0'", "'sparse==0.16.0'", "'sympy==1.13.1'", "'threadpoolctl==3.6.0'", "'toolz==1.0.0'", "'torch==2.6.0'", "'torchmetrics==1.7.1'", "'tqdm==4.67.1'", "'xarray==2025.4.0'", "'scikit-misc==0.5.1'", "'leidenalg==0.10.2'", "'igraph==0.11.8'"
---
Backtrace:
    ▆
 1. └─scviR::muonR()
 2.   └─basilisk::basiliskStart(bsklenv, testload = "anndata")
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         └─reticulate::virtualenv_create(...)
 6.           └─reticulate:::pip_install(python, packages)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'new_citeseq.Rmd' failed with diagnostics:
Error installing package(s): "'pandas==2.2.3'", "'rope==1.13.0'", "'scvi-tools==1.3.0'", "'session_info==1.0.1'", "'anndata==0.11.4'", "'chex==0.1.89'", "'h5py==3.13.0'", "'jax==0.4.35'", "'jaxlib==0.4.35'", "'joblib==1.4.2'", "'lightning==2.5.1.post0'", "'lightning_utilities==0.14.3'", "'llvmlite==0.44.0'", "'ml_collections==1.1.0'", "'ml_dtypes==0.5.1'", "'msgpack==1.1.0'", "'mudata==0.3.1'", "'multipledispatch==0.6.0'", "'muon==0.1.7'", "'natsort==8.4.0'", "'networkx==3.4.2'", "'numba==0.61.2'", "'numpy==2.2.5'", "'numpyro==0.18.0'", "'opt_einsum==3.4.0'", "'optax==0.2.4'", "'packaging==24.2'", "'pygments==2.19.1'", "'pytz==2025.2'", "'scipy==1.15.2'", "'six==1.17.0'", "'sparse==0.16.0'", "'sympy==1.13.1'", "'threadpoolctl==3.6.0'", "'toolz==1.0.0'", "'torch==2.6.0'", "'torchmetrics==1.7.1'", "'tqdm==4.67.1'", "'xarray==2025.4.0'", "'scikit-misc==0.5.1'", "'leidenalg==0.10.2'", "'igraph==0.11.8'"
--- failed re-building ‘new_citeseq.Rmd’

--- re-building ‘scviR.Rmd’ using rmarkdown
--- finished re-building ‘scviR.Rmd’

SUMMARY: processing the following files failed:
  ‘compch12.Rmd’ ‘new_citeseq.Rmd’

Error: Vignette re-building failed.
Execution halted