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###
### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scviR
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* 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
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from compch12.Rmd:44-47 [getdat]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─tools::buildVignettes(dir = ".", tangle = TRUE)
  2. │ ├─base::tryCatch(...)
  3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  4. │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5. │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  6. │ └─engine$weave(file, quiet = quiet, encoding = enc)
  7. │   └─knitr:::vweave_rmarkdown(...)
  8. │     └─rmarkdown::render(...)
  9. │       └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
 10. │         └─knitr:::process_file(text, output)
 11. │           ├─xfun:::handle_error(...)
 12. │           ├─base::withCallingHandlers(...)
 13. │           └─knitr:::process_group(group)
 14. │             └─knitr:::call_block(x)
 15. │               └─knitr:::block_exec(params)
 16. │                 └─knitr:::eng_r(options)
 17. │                   ├─knitr:::in_input_dir(...)
 18. │                   │ └─knitr:::in_dir(input_dir(), expr)
 19. │                   └─knitr (local) evaluate(...)
 20. │                     └─evaluate::evaluate(...)
 21. │                       ├─base::withRestarts(...)
 22. │                       │ └─base (local) withRestartList(expr, restarts)
 23. │                       │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 24. │                       │   │ └─base (local) doWithOneRestart(return(expr), restart)
 25. │                       │   └─base (local) withRestartList(expr, restarts[-nr])
 26. │                       │     └─base (local) withOneRestart(expr, restarts[[1L]])
 27. │                       │       └─base (local) doWithOneRestart(return(expr), restart)
 28. │                       ├─evaluate:::with_handlers(...)
 29. │                       │ ├─base::eval(call)
 30. │                       │ │ └─base::eval(call)
 31. │                       │ └─base::withCallingHandlers(...)
 32. │                       └─watcher$print_value(ev$value, ev$visible, envir)
 33. │                         ├─base::withVisible(handle_value(handler, value, visible, envir))
 34. │                         └─evaluate:::handle_value(handler, value, visible, envir)
 35. │                           └─handler$value(value, visible)
 36. │                             └─knitr (local) fun(x, options = options)
 37. │                               ├─base::withVisible(knit_print(x, ...))
 38. │                               ├─knitr::knit_print(x, ...)
 39. │                               └─knitr:::knit_print.default(x, ...)
 40. │                                 └─knitr::normal_print(x)
 41. │                                   ├─methods::show(x)
 42. │                                   └─methods::show(x)
 43. │                                     ├─S4Vectors::coolcat("reducedDimNames(%d): %s\n", reducedDimNames(object))
 44. │                                     │ └─base::ifelse(nzchar(vals), vals, "''")
 45. │                                     ├─SingleCellExperiment::reducedDimNames(object)
 46. │                                     └─SingleCellExperiment::reducedDimNames(object)
 47. │                                       └─SingleCellExperiment:::.get_internal_names(...)
 48. │                                         ├─BiocGenerics::updateObject(x)
 49. │                                         └─SingleCellExperiment::updateObject(x)
 50. │                                           ├─methods::callNextMethod()
 51. │                                           └─SummarizedExperiment (local) .nextMethod(object = object)
 52. │                                             ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 53. │                                             └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 54. │                                               ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 55. │                                               └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 56. │                                                 └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 57. └─methods:::.extendsForS3(`<chr>`)
 58.   └─methods::extends(Class, maybe = FALSE)
 59.     └─methods::getClassDef(class1)
 60.       └─methods:::.requirePackage(package)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'compch12.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building ‘compch12.Rmd’

--- re-building ‘new_citeseq.Rmd’ using rmarkdown
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/zfTTwQ31mgb8z7lRAuoQF/lib/python3.11/site-packages/muon/_core/preproc.py:31: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('scanpy')` instead
  if Version(scanpy.__version__) < Version("1.10"):
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/zfTTwQ31mgb8z7lRAuoQF/lib/python3.11/site-packages/anndata/_core/anndata.py:1794: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
  utils.warn_names_duplicates("var")
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/zfTTwQ31mgb8z7lRAuoQF/lib/python3.11/site-packages/anndata/_core/anndata.py:1794: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
  utils.warn_names_duplicates("var")
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/zfTTwQ31mgb8z7lRAuoQF/lib/python3.11/site-packages/mudata/_core/mudata.py:1598: 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)
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/zfTTwQ31mgb8z7lRAuoQF/lib/python3.11/site-packages/mudata/_core/mudata.py:947: UserWarning: var_names are not unique. To make them unique, call `.var_names_make_unique`.
  warnings.warn(
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/zfTTwQ31mgb8z7lRAuoQF/lib/python3.11/site-packages/mudata/_core/mudata.py:1461: 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)
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/zfTTwQ31mgb8z7lRAuoQF/lib/python3.11/site-packages/mudata/_core/mudata.py:1598: 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)
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/zfTTwQ31mgb8z7lRAuoQF/lib/python3.11/site-packages/mudata/_core/mudata.py:963: UserWarning: Cannot join columns with the same name because var_names are intersecting.
  warnings.warn(
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/zfTTwQ31mgb8z7lRAuoQF/lib/python3.11/site-packages/mudata/_core/mudata.py:1461: 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)
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/zfTTwQ31mgb8z7lRAuoQF/lib/python3.11/site-packages/mudata/_core/mudata.py:1598: 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)
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/zfTTwQ31mgb8z7lRAuoQF/lib/python3.11/site-packages/mudata/_core/mudata.py:1461: 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)
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/SIJrmz5ujNg3cpL6mKBBe/lib/python3.11/site-packages/torch/__init__.py:1551: UserWarning: Please use the new API settings to control TF32 behavior, such as torch.backends.cudnn.conv.fp32_precision = 'tf32' or torch.backends.cuda.matmul.fp32_precision = 'ieee'. Old settings, e.g, torch.backends.cuda.matmul.allow_tf32 = True, torch.backends.cudnn.allow_tf32 = True, allowTF32CuDNN() and allowTF32CuBLAS() will be deprecated after Pytorch 2.9. Please see https://pytorch.org/docs/main/notes/cuda.html#tensorfloat-32-tf32-on-ampere-and-later-devices (Triggered internally at /pytorch/aten/src/ATen/Context.cpp:80.)
  return _C._get_float32_matmul_precision()
You are using a CUDA device ('NVIDIA L40S') that has Tensor Cores. To properly utilize them, you should set `torch.set_float32_matmul_precision('medium' | 'high')` which will trade-off precision for performance. For more details, read https://pytorch.org/docs/stable/generated/torch.set_float32_matmul_precision.html#torch.set_float32_matmul_precision
LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [0]
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/SIJrmz5ujNg3cpL6mKBBe/lib/python3.11/site-packages/lightning/pytorch/core/optimizer.py:317: The lr scheduler dict contains the key(s) ['monitor'], but the keys will be ignored. You need to call `lr_scheduler.step()` manually in manual optimization.
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/SIJrmz5ujNg3cpL6mKBBe/lib/python3.11/site-packages/lightning/pytorch/trainer/connectors/data_connector.py:433: The 'train_dataloader' does not have many workers which may be a bottleneck. Consider increasing the value of the `num_workers` argument` to `num_workers=3` in the `DataLoader` to improve performance.
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/SIJrmz5ujNg3cpL6mKBBe/lib/python3.11/site-packages/lightning/pytorch/trainer/connectors/data_connector.py:433: The 'val_dataloader' does not have many workers which may be a bottleneck. Consider increasing the value of the `num_workers` argument` to `num_workers=3` in the `DataLoader` to improve performance.
`Trainer.fit` stopped: `max_epochs=50` reached.
The magick package is required to crop "/tmp/Rtmp0Yslm6/Rbuild20b5f1863a6/scviR/vignettes/new_citeseq_files/figure-html/lkelb-1.png" but not available.
--- finished re-building ‘new_citeseq.Rmd’

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

SUMMARY: processing the following file failed:
  ‘compch12.Rmd’

Error: Vignette re-building failed.
Execution halted