Vincent Carey
| Snapshot Date: 2025-08-13 13:45 -0400 (Wed, 13 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/scviR |
| git_branch: devel |
| git_last_commit: 5dd474c |
| git_last_commit_date: 2025-05-12 05:55:48 -0400 (Mon, 12 May 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-14 12:12 -0400 (Thu, 14 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 1929/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scviR 1.9.11 (landing page) Vincent Carey
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the scviR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scviR.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: scviR |
| Version: 1.9.11 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data scviR |
| StartedAt: 2025-08-12 02:42:52 -0000 (Tue, 12 Aug 2025) |
| EndedAt: 2025-08-12 02:44:35 -0000 (Tue, 12 Aug 2025) |
| EllapsedTime: 103.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### 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-dkif1x_b/scikit-misc_4558ab14aa1e4e6bb917aefdeafe225e /home/biocbuild/tmp/pip-install-dkif1x_b/scikit-misc_4558ab14aa1e4e6bb917aefdeafe225e/.mesonpy-i0rziube -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/home/biocbuild/tmp/pip-install-dkif1x_b/scikit-misc_4558ab14aa1e4e6bb917aefdeafe225e/.mesonpy-i0rziube/meson-python-native-file.ini
The Meson build system
Version: 1.8.3
Source dir: /home/biocbuild/tmp/pip-install-dkif1x_b/scikit-misc_4558ab14aa1e4e6bb917aefdeafe225e
Build dir: /home/biocbuild/tmp/pip-install-dkif1x_b/scikit-misc_4558ab14aa1e4e6bb917aefdeafe225e/.mesonpy-i0rziube
Build type: native build
../meson.build:5:11: ERROR: Command `/home/biocbuild/tmp/pip-install-dkif1x_b/scikit-misc_4558ab14aa1e4e6bb917aefdeafe225e/skmisc/_build_utils/version_please.py` failed with status 127.
A full log can be found at /home/biocbuild/tmp/pip-install-dkif1x_b/scikit-misc_4558ab14aa1e4e6bb917aefdeafe225e/.mesonpy-i0rziube/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-vcmgfv9n/scikit-misc_6d1aa1d61b964c288afe049a9a972b54 /home/biocbuild/tmp/pip-install-vcmgfv9n/scikit-misc_6d1aa1d61b964c288afe049a9a972b54/.mesonpy-9gsl93xc -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/home/biocbuild/tmp/pip-install-vcmgfv9n/scikit-misc_6d1aa1d61b964c288afe049a9a972b54/.mesonpy-9gsl93xc/meson-python-native-file.ini
The Meson build system
Version: 1.8.3
Source dir: /home/biocbuild/tmp/pip-install-vcmgfv9n/scikit-misc_6d1aa1d61b964c288afe049a9a972b54
Build dir: /home/biocbuild/tmp/pip-install-vcmgfv9n/scikit-misc_6d1aa1d61b964c288afe049a9a972b54/.mesonpy-9gsl93xc
Build type: native build
../meson.build:5:11: ERROR: Command `/home/biocbuild/tmp/pip-install-vcmgfv9n/scikit-misc_6d1aa1d61b964c288afe049a9a972b54/skmisc/_build_utils/version_please.py` failed with status 127.
A full log can be found at /home/biocbuild/tmp/pip-install-vcmgfv9n/scikit-misc_6d1aa1d61b964c288afe049a9a972b54/.mesonpy-9gsl93xc/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