##############################################################################
##############################################################################
###
### 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_1.9.13.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 ‘1.9.13’
* 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
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/e6TFGpFsCuQUp7FWZLYIA/lib/python3.11/site-packages/scanpy/_utils/__init__.py:33: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  from anndata import __version__ as anndata_version
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/e6TFGpFsCuQUp7FWZLYIA/lib/python3.11/site-packages/scanpy/__init__.py:24: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(anndata.__version__) >= Version("0.11.0rc2"):
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/e6TFGpFsCuQUp7FWZLYIA/lib/python3.11/site-packages/scanpy/readwrite.py:16: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('anndata')` instead.
  if Version(anndata.__version__) >= Version("0.11.0rc2"):
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/e6TFGpFsCuQUp7FWZLYIA/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/e6TFGpFsCuQUp7FWZLYIA/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/e6TFGpFsCuQUp7FWZLYIA/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/e6TFGpFsCuQUp7FWZLYIA/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/e6TFGpFsCuQUp7FWZLYIA/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/e6TFGpFsCuQUp7FWZLYIA/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/e6TFGpFsCuQUp7FWZLYIA/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/e6TFGpFsCuQUp7FWZLYIA/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/e6TFGpFsCuQUp7FWZLYIA/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/e6TFGpFsCuQUp7FWZLYIA/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: False, used: False
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/x4XnY80EHgguSs3b_uILI/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/x4XnY80EHgguSs3b_uILI/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=71` in the `DataLoader` to improve performance.
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/x4XnY80EHgguSs3b_uILI/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=71` in the `DataLoader` to improve performance.
GPU available: False, used: False
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/x4XnY80EHgguSs3b_uILI/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/x4XnY80EHgguSs3b_uILI/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=71` in the `DataLoader` to improve performance.
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/x4XnY80EHgguSs3b_uILI/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=71` in the `DataLoader` to improve performance.
/home/biocbuild/.cache/R/reticulate/uv/cache/archive-v0/x4XnY80EHgguSs3b_uILI/lib/python3.11/site-packages/lightning/pytorch/loops/fit_loop.py:527: Found 81 module(s) in eval mode at the start of training. This may lead to unexpected behavior during training. If this is intentional, you can ignore this warning.
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 ‘1.9.13’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 
 17.122   0.819  17.932