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GPU-enabled build/check report for BioC 3.23
Report updated every 6 hours

This page was generated on 2026-04-30 13:45 -0400 (Thu, 30 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
biocgpuLinux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-02-04 r89376) -- "Unsuffered Consequences" 276
kakapo1Linux (Ubuntu 24.04.3 LTS)x86_644.6.0 beta (2026-04-12 r89874) -- "Because it was There" 291
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 3/3HostnameOS / ArchINSTALLBUILDCHECK
scviR 1.12.0  (landing page)
Vincent Carey
Snapshot Date: 2026-04-30 10:00 -0400 (Thu, 30 Apr 2026)
git_url: https://git.bioconductor.org/packages/scviR
git_branch: RELEASE_3_23
git_last_commit: 574204b
git_last_commit_date: 2026-04-28 09:00:13 -0400 (Tue, 28 Apr 2026)
biocgpuLinux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
kakapo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped

BUILD results for scviR on biocgpu

To the developers/maintainers of the scviR package:
- 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: 1.12.0
Command: /home/biocbuild/bbs-3.23-bioc-gpu/R/bin/R CMD build --keep-empty-dirs --no-resave-data scviR
StartedAt: 2026-04-30 10:58:17 -0400 (Thu, 30 Apr 2026)
EndedAt: 2026-04-30 11:00:02 -0400 (Thu, 30 Apr 2026)
EllapsedTime: 105.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc-gpu/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 (it is needed 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
The magick package is required to crop "/tmp/RtmpQXZGNY/Rbuild42cf79e92670/scviR/vignettes/compch12_files/figure-html/lkkey-1.png" but not available.
The magick package is required to crop "/tmp/RtmpQXZGNY/Rbuild42cf79e92670/scviR/vignettes/compch12_files/figure-html/lkadt-1.png" but not available.
The magick package is required to crop "/tmp/RtmpQXZGNY/Rbuild42cf79e92670/scviR/vignettes/compch12_files/figure-html/dosubcl-1.png" but not available.
The magick package is required to crop "/tmp/RtmpQXZGNY/Rbuild42cf79e92670/scviR/vignettes/compch12_files/figure-html/lkgra-1.png" but not available.
The magick package is required to crop "/tmp/RtmpQXZGNY/Rbuild42cf79e92670/scviR/vignettes/compch12_files/figure-html/lktotumap-1.png" but not available.
The magick package is required to crop "/tmp/RtmpQXZGNY/Rbuild42cf79e92670/scviR/vignettes/compch12_files/figure-html/domattot-1.png" but not available.
The magick package is required to crop "/tmp/RtmpQXZGNY/Rbuild42cf79e92670/scviR/vignettes/compch12_files/figure-html/lkconc-1.png" but not available.
The magick package is required to crop "/tmp/RtmpQXZGNY/Rbuild42cf79e92670/scviR/vignettes/compch12_files/figure-html/lksubsss-1.png" but not available.
The magick package is required to crop "/tmp/RtmpQXZGNY/Rbuild42cf79e92670/scviR/vignettes/compch12_files/figure-html/lkgradvi-1.png" but not available.
--- finished re-building ‘compch12.Rmd’

--- re-building ‘new_citeseq.Rmd’ using rmarkdown
/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/CKhqANXmjfjFhYnlEj3Xc/lib/python3.12/site-packages/muon/_core/preproc.py:31: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('scanpy')` instead
  if Version(scanpy.__version__) < Version("1.10"):
/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/A8zkXzLjevrhg_9MKDMVj/lib/python3.12/site-packages/anndata/_core/anndata.py:1880: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
  utils.warn_names_duplicates("var")
/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/A8zkXzLjevrhg_9MKDMVj/lib/python3.12/site-packages/anndata/_core/anndata.py:1880: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
  utils.warn_names_duplicates("var")
/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/CKhqANXmjfjFhYnlEj3Xc/lib/python3.12/site-packages/mudata/_core/mudata.py:1416: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
  self._update_attr("var", axis=0, join_common=join_common)
/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/CKhqANXmjfjFhYnlEj3Xc/lib/python3.12/site-packages/mudata/_core/mudata.py:565: UserWarning: var_names are not unique. To make them unique, call `.var_names_make_unique`.
  self._update_attr_legacy(attr, axis, join_common, **kwargs)
/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/CKhqANXmjfjFhYnlEj3Xc/lib/python3.12/site-packages/mudata/_core/mudata.py:1272: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
  self._update_attr("obs", axis=1, join_common=join_common)
/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/CKhqANXmjfjFhYnlEj3Xc/lib/python3.12/site-packages/mudata/_core/mudata.py:1416: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
  self._update_attr("var", axis=0, join_common=join_common)
/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/CKhqANXmjfjFhYnlEj3Xc/lib/python3.12/site-packages/mudata/_core/mudata.py:565: UserWarning: Cannot join columns with the same name because var_names are intersecting.
  self._update_attr_legacy(attr, axis, join_common, **kwargs)
/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/CKhqANXmjfjFhYnlEj3Xc/lib/python3.12/site-packages/mudata/_core/mudata.py:1272: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
  self._update_attr("obs", axis=1, join_common=join_common)
/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/CKhqANXmjfjFhYnlEj3Xc/lib/python3.12/site-packages/mudata/_core/mudata.py:1416: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
  self._update_attr("var", axis=0, join_common=join_common)
/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/CKhqANXmjfjFhYnlEj3Xc/lib/python3.12/site-packages/mudata/_core/mudata.py:1272: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
  self._update_attr("obs", axis=1, join_common=join_common)
Downloading ml-dtypes (4.8MiB)
Downloading uvloop (4.2MiB)
Downloading tensorstore (20.0MiB)
Downloading jax (3.0MiB)
Downloading orbax-checkpoint (1.1MiB)
Downloading jaxlib (81.1MiB)
 Downloaded ml-dtypes
 Downloaded uvloop
 Downloaded tensorstore
 Downloaded jaxlib
 Downloaded jax
 Downloaded orbax-checkpoint
Installed 119 packages in 1.36s
/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/R/site-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_)
Global seed set to 0
/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/A8zkXzLjevrhg_9MKDMVj/lib/python3.12/site-packages/anndata/__init__.py:70: FutureWarning: Importing read_csv from `anndata` is deprecated. Import anndata.io.read_csv instead.
  return module_get_attr_redirect(attr_name, deprecated_mapping=_DEPRECATED)
/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/A8zkXzLjevrhg_9MKDMVj/lib/python3.12/site-packages/anndata/__init__.py:70: FutureWarning: Importing read_loom from `anndata` is deprecated. Import anndata.io.read_loom instead.
  return module_get_attr_redirect(attr_name, deprecated_mapping=_DEPRECATED)
/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/A8zkXzLjevrhg_9MKDMVj/lib/python3.12/site-packages/anndata/__init__.py:70: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.
  return module_get_attr_redirect(attr_name, deprecated_mapping=_DEPRECATED)

Quitting from new_citeseq.Rmd:101-112 [dosetup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_module_import()`:
! ModuleNotFoundError: No module named 'requests'
Run `reticulate::py_last_error()` for details.
---
Backtrace:
    ▆
 1. └─scviR::scviR()
 2.   └─reticulate::import("scvi")
 3.     └─reticulate:::py_module_import(module, convert = convert)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'new_citeseq.Rmd' failed with diagnostics:
ModuleNotFoundError: No module named 'requests'
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘new_citeseq.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted