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This page was generated on 2025-08-18 11:44 -0400 (Mon, 18 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4566
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1948/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scviR 1.8.0  (landing page)
Vincent Carey
Snapshot Date: 2025-08-14 13:40 -0400 (Thu, 14 Aug 2025)
git_url: https://git.bioconductor.org/packages/scviR
git_branch: RELEASE_3_21
git_last_commit: a4f406f
git_last_commit_date: 2025-04-15 13:10:58 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


BUILD results for scviR on merida1

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: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data scviR
StartedAt: 2025-08-14 22:25:15 -0400 (Thu, 14 Aug 2025)
EndedAt: 2025-08-14 22:28:58 -0400 (Thu, 14 Aug 2025)
EllapsedTime: 223.0 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
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/scviR/1.8.0/bsklenv/lib/python3.10/site-packages/anndata/__init__.py:51: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024.
  warnings.warn(
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/reticulate/python/rpytools/loader.py:120: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  return _find_and_load(name, import_)
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/scviR/1.8.0/bsklenv/lib/python3.10/site-packages/anndata/__init__.py:51: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024.
  warnings.warn(

Quitting from citeseq_tut.Rmd:56-58 [dogetv]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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::getCiteseqTutvae()
 2.   └─scvi$model$`_totalvi`$TOTALVI$load(vaedir, adata)
 3.     └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'citeseq_tut.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 ‘citeseq_tut.Rmd’

--- re-building ‘compch12.Rmd’ using rmarkdown
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/scviR/1.8.0/bsklenv/lib/python3.10/site-packages/anndata/__init__.py:51: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024.
  warnings.warn(
2025-08-14 22:28:14.166 R[59874:318927533] XType: com.apple.fonts is not accessible.
2025-08-14 22:28:14.166 R[59874:318927533] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘compch12.Rmd’

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

SUMMARY: processing the following file failed:
  ‘citeseq_tut.Rmd’

Error: Vignette re-building failed.
Execution halted