Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-18 11:44 -0400 (Mon, 18 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R 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 1948/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scviR 1.8.0 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | 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. |
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 |
############################################################################## ############################################################################## ### ### 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