##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scviR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scviR_1.9.11.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scviR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘scviR/DESCRIPTION’ ... OK
* this is package ‘scviR’ version ‘1.9.11’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scviR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘scviR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getCh12Sce
> ### Title: get SCE for 10k PBMC annotated as in OSCA book chapter 12
> ### Aliases: getCh12Sce
> 
> ### ** Examples
> 
> ch12sce <- getCh12Sce()
> ch12sce
class: SingleCellExperiment 
dim: 33538 7472 
metadata(2): Samples se.averaged
assays(2): counts logcounts
rownames(33538): ENSG00000243485 ENSG00000237613 ... ENSG00000277475
  ENSG00000268674
rowData names(3): ID Symbol Type
colnames(7472): AAACCCAAGATTGTGA-1 AAACCCACATCGGTTA-1 ...
  TTTGTTGTCGAGTGAG-1 TTTGTTGTCGTTCAGA-1
colData names(3): Sample Barcode sizeFactor
Loading required namespace: GenomeInfoDb
Failed with error:  ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) : 
  unable to load required package ‘GenomeInfoDb’
Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- 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:::.buildOneVignette(...)
  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
/var/cache/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")
/var/cache/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")
/var/cache/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)
/var/cache/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(
/var/cache/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)
/var/cache/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)
/var/cache/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(
/var/cache/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)
/var/cache/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)
/var/cache/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)
/var/cache/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)
/var/cache/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: False, used: False
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
/var/cache/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(
/var/cache/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.
/var/cache/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=71` in the `DataLoader` to improve performance.
/var/cache/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=71` in the `DataLoader` to improve performance.
`Trainer.fit` stopped: `max_epochs=5` reached.
GPU available: False, used: False
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
/var/cache/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(
/var/cache/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.
/var/cache/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=71` in the `DataLoader` to improve performance.
/var/cache/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=71` in the `DataLoader` to improve performance.
`Trainer.fit` stopped: `max_epochs=50` reached.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/scviR.Rcheck/vign_test/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

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/scviR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scviR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘scviR’ ...
** this is package ‘scviR’ version ‘1.9.11’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scviR)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(scviR)
Loading required package: basilisk
Loading required package: reticulate
Loading required package: shiny
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("scviR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
 17.410   0.881  18.280