##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/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 /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages (23.0.1)
Collecting pip
  Using cached pip-25.1.1-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 /Users/biocbuild/Library/Caches/org.R-project.R/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-25.1.1 setuptools-80.9.0 wheel-0.45.1
Collecting pandas==2.2.3
  Using cached pandas-2.2.3-cp310-cp310-macosx_10_9_x86_64.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-macosx_10_9_x86_64.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-macosx_10_14_x86_64.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-macosx_10_14_x86_64.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-macosx_10_9_universal2.whl.metadata (21 kB)
Collecting msgpack==1.1.0
  Using cached msgpack-1.1.0-cp310-cp310-macosx_10_9_x86_64.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-macosx_10_14_x86_64.whl.metadata (2.8 kB)
Collecting numpy==2.2.5
  Using cached numpy-2.2.5-cp310-cp310-macosx_10_9_x86_64.whl.metadata (62 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-macosx_10_13_x86_64.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)
ERROR: Ignored the following versions that require a different python version: 0.12.0rc1 Requires-Python >=3.11; 0.12.0rc2 Requires-Python >=3.11; 0.12.0rc3 Requires-Python >=3.11; 0.12.0rc4 Requires-Python >=3.11; 0.36.0 Requires-Python >=3.6,<3.10; 0.37.0 Requires-Python >=3.7,<3.10; 0.52.0 Requires-Python >=3.6,<3.9; 0.52.0rc3 Requires-Python >=3.6,<3.9; 0.53.0 Requires-Python >=3.6,<3.10; 0.53.0rc1.post1 Requires-Python >=3.6,<3.10; 0.53.0rc2 Requires-Python >=3.6,<3.10; 0.53.0rc3 Requires-Python >=3.6,<3.10; 0.53.1 Requires-Python >=3.6,<3.10; 0.54.0 Requires-Python >=3.7,<3.10; 0.54.0rc2 Requires-Python >=3.7,<3.10; 0.54.0rc3 Requires-Python >=3.7,<3.10; 0.54.1 Requires-Python >=3.7,<3.10; 1.16.0 Requires-Python >=3.11; 1.16.0rc1 Requires-Python >=3.11; 1.16.0rc2 Requires-Python >=3.11; 1.6.2 Requires-Python >=3.7,<3.10; 1.6.3 Requires-Python >=3.7,<3.10; 1.7.0 Requires-Python >=3.7,<3.10; 1.7.1 Requires-Python >=3.7,<3.10; 2.3.0 Requires-Python >=3.11; 2.3.0rc1 Requires-Python >=3.11; 2.3.1 Requires-Python >=3.11; 3.5 Requires-Python >=3.11; 3.5rc0 Requires-Python >=3.11
ERROR: Could not find a version that satisfies the requirement torch==2.6.0 (from versions: 1.11.0, 1.12.0, 1.12.1, 1.13.0, 1.13.1, 2.0.0, 2.0.1, 2.1.0, 2.1.1, 2.1.2, 2.2.0, 2.2.1, 2.2.2)
ERROR: No matching distribution found for torch==2.6.0

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 /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages (23.0.1)
Collecting pip
  Using cached pip-25.1.1-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 /Users/biocbuild/Library/Caches/org.R-project.R/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-25.1.1 setuptools-80.9.0 wheel-0.45.1
Collecting pandas==2.2.3
  Using cached pandas-2.2.3-cp310-cp310-macosx_10_9_x86_64.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-macosx_10_9_x86_64.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-macosx_10_14_x86_64.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-macosx_10_14_x86_64.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-macosx_10_9_universal2.whl.metadata (21 kB)
Collecting msgpack==1.1.0
  Using cached msgpack-1.1.0-cp310-cp310-macosx_10_9_x86_64.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-macosx_10_14_x86_64.whl.metadata (2.8 kB)
Collecting numpy==2.2.5
  Using cached numpy-2.2.5-cp310-cp310-macosx_10_9_x86_64.whl.metadata (62 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-macosx_10_13_x86_64.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)
ERROR: Ignored the following versions that require a different python version: 0.12.0rc1 Requires-Python >=3.11; 0.12.0rc2 Requires-Python >=3.11; 0.12.0rc3 Requires-Python >=3.11; 0.12.0rc4 Requires-Python >=3.11; 0.36.0 Requires-Python >=3.6,<3.10; 0.37.0 Requires-Python >=3.7,<3.10; 0.52.0 Requires-Python >=3.6,<3.9; 0.52.0rc3 Requires-Python >=3.6,<3.9; 0.53.0 Requires-Python >=3.6,<3.10; 0.53.0rc1.post1 Requires-Python >=3.6,<3.10; 0.53.0rc2 Requires-Python >=3.6,<3.10; 0.53.0rc3 Requires-Python >=3.6,<3.10; 0.53.1 Requires-Python >=3.6,<3.10; 0.54.0 Requires-Python >=3.7,<3.10; 0.54.0rc2 Requires-Python >=3.7,<3.10; 0.54.0rc3 Requires-Python >=3.7,<3.10; 0.54.1 Requires-Python >=3.7,<3.10; 1.16.0 Requires-Python >=3.11; 1.16.0rc1 Requires-Python >=3.11; 1.16.0rc2 Requires-Python >=3.11; 1.6.2 Requires-Python >=3.7,<3.10; 1.6.3 Requires-Python >=3.7,<3.10; 1.7.0 Requires-Python >=3.7,<3.10; 1.7.1 Requires-Python >=3.7,<3.10; 2.3.0 Requires-Python >=3.11; 2.3.0rc1 Requires-Python >=3.11; 2.3.1 Requires-Python >=3.11; 3.5 Requires-Python >=3.11; 3.5rc0 Requires-Python >=3.11
ERROR: Could not find a version that satisfies the requirement torch==2.6.0 (from versions: 1.11.0, 1.12.0, 1.12.1, 1.13.0, 1.13.1, 2.0.0, 2.0.1, 2.1.0, 2.1.1, 2.1.2, 2.2.0, 2.2.1, 2.2.2)
ERROR: No matching distribution found for torch==2.6.0

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