Multiple platform build/check report for BioC 3.21 - BUILD results for scviR on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4777
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4458
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*

BUILD results for scviR on lconway

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.

raw results

Summary

Package: scviR

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data scviR

StartedAt: 2025-03-19 18:41:45 -0400 (Wed, 19 Mar 2025)

EndedAt: 2025-03-19 18:49:15 -0400 (Wed, 19 Mar 2025)

EllapsedTime: 449.6 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### 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
trying URL 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/pbmc_citeseq_5k10k.h5ad.gz'
Content type 'application/octet-stream' length 51844928 bytes (49.4 MB)
==================================================
downloaded 49.4 MB

Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/scviR/1.7.0/bsklenv/lib/python3.10/site-packages (23.0.1)
Collecting pip
  Using cached pip-25.0.1-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/1.19.2/scviR/1.7.0/bsklenv/lib/python3.10/site-packages (65.5.0)
Collecting setuptools
  Using cached setuptools-77.0.1-py3-none-any.whl (1.3 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-25.0.1 setuptools-77.0.1 wheel-0.45.1
ERROR: Could not find a version that satisfies the requirement python==3.10 (from versions: none)
ERROR: No matching distribution found for python==3.10

Quitting from citeseq_tut.Rmd:42-48 [doinit]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'python==3.10'", "'numpy==1.24.4'", "'pandas==1.5.3'", "'anndata==0.10.1'", "'docrep==0.3.2'", "'flax==0.8.1'", "'jax==0.4.23'", "'jaxlib==0.4.23'", "'optax==0.1.9'", "'scipy==1.12.0'", "'scikit-learn==1.4.0'", "'rich==13.7.1'", "'h5py==3.9.0'", "'torch==1.13.1'", "'lightning==2.1.4'", "'torchmetrics==0.11.0'", "'tqdm==4.66.2'", "'ml-collections==0.1.1'", "'mudata==0.2.3'", "'scvi-tools==1.1.2'", "'scanpy==1.9.5'", "'matplotlib==3.7.3'", "'scikit-misc==0.3.1'"
---
Backtrace:
    ▆
 1. └─scviR::getCiteseq5k10kPbmcs()
 2.   └─scviR::anndataR()
 3.     └─basilisk::basiliskStart(bsklenv)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           └─reticulate::virtualenv_install(...)
 7.             └─reticulate:::pip_install(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'citeseq_tut.Rmd' failed with diagnostics:
Error installing package(s): "'python==3.10'", "'numpy==1.24.4'", "'pandas==1.5.3'", "'anndata==0.10.1'", "'docrep==0.3.2'", "'flax==0.8.1'", "'jax==0.4.23'", "'jaxlib==0.4.23'", "'optax==0.1.9'", "'scipy==1.12.0'", "'scikit-learn==1.4.0'", "'rich==13.7.1'", "'h5py==3.9.0'", "'torch==1.13.1'", "'lightning==2.1.4'", "'torchmetrics==0.11.0'", "'tqdm==4.66.2'", "'ml-collections==0.1.1'", "'mudata==0.2.3'", "'scvi-tools==1.1.2'", "'scanpy==1.9.5'", "'matplotlib==3.7.3'", "'scikit-misc==0.3.1'"
--- failed re-building ‘citeseq_tut.Rmd’

--- re-building ‘compch12.Rmd’ using rmarkdown
trying URL 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/ch12sce.rda'
Content type 'application/octet-stream' length 58079368 bytes (55.4 MB)
==================================================
downloaded 55.4 MB

trying URL 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/full_5k10k_totalVI.h5ad'
Content type 'application/octet-stream' length 1216903940 bytes (1160.5 MB)
==================================================
downloaded 1160.5 MB

Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/scviR/1.7.0/bsklenv/lib/python3.10/site-packages (23.0.1)
Collecting pip
  Using cached pip-25.0.1-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/1.19.2/scviR/1.7.0/bsklenv/lib/python3.10/site-packages (65.5.0)
Collecting setuptools
  Using cached setuptools-77.0.1-py3-none-any.whl (1.3 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-25.0.1 setuptools-77.0.1 wheel-0.45.1
ERROR: Could not find a version that satisfies the requirement python==3.10 (from versions: none)
ERROR: No matching distribution found for python==3.10

Quitting from compch12.Rmd:49-53 [getdat2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'python==3.10'", "'numpy==1.24.4'", "'pandas==1.5.3'", "'anndata==0.10.1'", "'docrep==0.3.2'", "'flax==0.8.1'", "'jax==0.4.23'", "'jaxlib==0.4.23'", "'optax==0.1.9'", "'scipy==1.12.0'", "'scikit-learn==1.4.0'", "'rich==13.7.1'", "'h5py==3.9.0'", "'torch==1.13.1'", "'lightning==2.1.4'", "'torchmetrics==0.11.0'", "'tqdm==4.66.2'", "'ml-collections==0.1.1'", "'mudata==0.2.3'", "'scvi-tools==1.1.2'", "'scanpy==1.9.5'", "'matplotlib==3.7.3'", "'scikit-misc==0.3.1'"
---
Backtrace:
    ▆
 1. └─scviR::getTotalVI5k10kAdata()
 2.   └─scviR::anndataR()
 3.     └─basilisk::basiliskStart(bsklenv)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           └─reticulate::virtualenv_install(...)
 7.             └─reticulate:::pip_install(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'compch12.Rmd' failed with diagnostics:
Error installing package(s): "'python==3.10'", "'numpy==1.24.4'", "'pandas==1.5.3'", "'anndata==0.10.1'", "'docrep==0.3.2'", "'flax==0.8.1'", "'jax==0.4.23'", "'jaxlib==0.4.23'", "'optax==0.1.9'", "'scipy==1.12.0'", "'scikit-learn==1.4.0'", "'rich==13.7.1'", "'h5py==3.9.0'", "'torch==1.13.1'", "'lightning==2.1.4'", "'torchmetrics==0.11.0'", "'tqdm==4.66.2'", "'ml-collections==0.1.1'", "'mudata==0.2.3'", "'scvi-tools==1.1.2'", "'scanpy==1.9.5'", "'matplotlib==3.7.3'", "'scikit-misc==0.3.1'"
--- failed re-building ‘compch12.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted