############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-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 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 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(``) 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/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/anndata/_core/anndata.py:1758: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`. utils.warn_names_duplicates("var") /home/biocbuild/.cache/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/anndata/_core/anndata.py:1758: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`. utils.warn_names_duplicates("var") /home/biocbuild/.cache/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/mudata/_core/mudata.py:1531: 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/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/mudata/_core/mudata.py:915: UserWarning: var_names are not unique. To make them unique, call `.var_names_make_unique`. warnings.warn( /home/biocbuild/.cache/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/mudata/_core/mudata.py:1429: 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/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/mudata/_core/mudata.py:1531: 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/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/mudata/_core/mudata.py:931: UserWarning: Cannot join columns with the same name because var_names are intersecting. warnings.warn( /home/biocbuild/.cache/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/mudata/_core/mudata.py:1429: 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/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/mudata/_core/mudata.py:1531: 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/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/mudata/_core/mudata.py:1429: 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/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/docrep/decorators.py:43: SyntaxWarning: 'param_categorical_covariate_keys' is not a valid key! doc = func(self, args[0].__doc__, *args[1:], **kwargs) /home/biocbuild/.cache/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/docrep/decorators.py:43: SyntaxWarning: 'param_continuous_covariate_keys' is not a valid key! doc = func(self, args[0].__doc__, *args[1:], **kwargs) GPU available: True (cuda), used: False TPU available: False, using: 0 TPU cores HPU available: False, using: 0 HPUs /home/biocbuild/.cache/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/lightning/pytorch/trainer/setup.py:177: GPU available but not used. You can set it by doing `Trainer(accelerator='gpu')`. /home/biocbuild/.cache/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/torch/optim/lr_scheduler.py:62: UserWarning: The verbose parameter is deprecated. Please use get_last_lr() to access the learning rate. warnings.warn( /home/biocbuild/.cache/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/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/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/lightning/pytorch/trainer/connectors/data_connector.py:425: 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=7` in the `DataLoader` to improve performance. /home/biocbuild/.cache/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/lightning/pytorch/trainer/connectors/data_connector.py:425: 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=7` in the `DataLoader` to improve performance. `Trainer.fit` stopped: `max_epochs=5` reached. GPU available: True (cuda), used: True TPU available: False, using: 0 TPU cores HPU available: False, using: 0 HPUs You are using a CUDA device ('GRID A100X-10C') 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/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/torch/optim/lr_scheduler.py:62: UserWarning: The verbose parameter is deprecated. Please use get_last_lr() to access the learning rate. warnings.warn( /home/biocbuild/.cache/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/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/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/lightning/pytorch/trainer/connectors/data_connector.py:425: 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=7` in the `DataLoader` to improve performance. /home/biocbuild/.cache/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/lightning/pytorch/trainer/connectors/data_connector.py:425: 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=7` in the `DataLoader` to improve performance. `Trainer.fit` stopped: `max_epochs=50` reached. The magick package is required to crop "/tmp/RtmpRLcxRn/Rbuild378e9b6ff62/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