##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc-gpu/R/bin/R CMD check --install=check:scviR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc-gpu/R/site-library --timings scviR_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/scviR.Rcheck’
* using R Under development (unstable) (2025-11-17 r89032)
* 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 ‘1.11.0’
* 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: muonR
> ### Title: basic interface to muon
> ### Aliases: muonR
> 
> ### ** Examples
> 
> md <- muonR()
Error in py_module_import(module, convert = convert) : 
  ImportError: Numba needs NumPy 2.3 or less. Got NumPy 2.4.
Run `reticulate::py_last_error()` for details.
Calls: muonR -> <Anonymous> -> py_module_import
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
getSubclLM               9.284  0.999  10.306
getSubclusteringFeatures 5.307  1.064   6.385
* 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
Installed 19 packages in 48ms
The magick package is required to crop "/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/scviR.Rcheck/vign_test/scviR/vignettes/compch12_files/figure-html/lkkey-1.png" but not available.
The magick package is required to crop "/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/scviR.Rcheck/vign_test/scviR/vignettes/compch12_files/figure-html/lkadt-1.png" but not available.
The magick package is required to crop "/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/scviR.Rcheck/vign_test/scviR/vignettes/compch12_files/figure-html/dosubcl-1.png" but not available.
The magick package is required to crop "/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/scviR.Rcheck/vign_test/scviR/vignettes/compch12_files/figure-html/lkgra-1.png" but not available.
The magick package is required to crop "/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/scviR.Rcheck/vign_test/scviR/vignettes/compch12_files/figure-html/lktotumap-1.png" but not available.
The magick package is required to crop "/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/scviR.Rcheck/vign_test/scviR/vignettes/compch12_files/figure-html/domattot-1.png" but not available.
The magick package is required to crop "/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/scviR.Rcheck/vign_test/scviR/vignettes/compch12_files/figure-html/lkconc-1.png" but not available.
The magick package is required to crop "/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/scviR.Rcheck/vign_test/scviR/vignettes/compch12_files/figure-html/lksubsss-1.png" but not available.
The magick package is required to crop "/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/scviR.Rcheck/vign_test/scviR/vignettes/compch12_files/figure-html/lkgradvi-1.png" but not available.
--- finished re-building ‘compch12.Rmd’

--- re-building ‘new_citeseq.Rmd’ using rmarkdown
Downloading scanpy (1.9MiB)
   Building llvmlite==0.36.0
 Downloading scanpy
   Building numba==0.53.1
  × Failed to build `numba==0.53.1`
  ├─▶ The build backend returned an error
  ╰─▶ Call to `setuptools.build_meta:__legacy__.build_wheel` failed (exit
      status: 1)

      [stderr]
      /media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/sdists-v9/pypi/numba/0.53.1/lburqqmnhjcuj5NL45xTN/src/versioneer.py:415:
      SyntaxWarning: invalid escape sequence '\s'
        mo = re.search(r'=\s*"(.*)"', line)
      Traceback (most recent call last):
        File "<string>", line 14, in <module>
        File
      "/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpAYBw86/lib/python3.12/site-packages/setuptools/build_meta.py",
      line 331, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File
      "/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpAYBw86/lib/python3.12/site-packages/setuptools/build_meta.py",
      line 301, in _get_build_requires
          self.run_setup()
        File
      "/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpAYBw86/lib/python3.12/site-packages/setuptools/build_meta.py",
      line 512, in run_setup
          super().run_setup(setup_script=setup_script)
        File
      "/media/volume/biocgpu2/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpAYBw86/lib/python3.12/site-packages/setuptools/build_meta.py",
      line 317, in run_setup
          exec(code, locals())
        File "<string>", line 50, in <module>
        File "<string>", line 47, in _guard_py_ver
      RuntimeError: Cannot install on Python version 3.12.12; only versions
      >=3.6,<3.10 are supported.

      hint: This usually indicates a problem with the package or the build
      environment.
  help: `numba` (v0.53.1) was included because `muon` (v0.1.7) depends on
        `numba`
uv error code: 1
-- Current requirements -------------------------------------------------
 Python:   3.12.12 (reticulate default)
 Packages: numpy, muon
-------------------------------------------------------------------------

Quitting from new_citeseq.Rmd:41-48 [doe44]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Installation of Python not found, Python bindings not loaded.
See the Python "Order of Discovery" here: https://rstudio.github.io/reticulate/articles/versions.html#order-of-discovery.
---
Backtrace:
    ▆
 1. └─scviR::muonR()
 2.   └─reticulate::import("muon")
 3.     └─reticulate:::ensure_python_initialized(required_module = module)
 4.       └─reticulate:::initialize_python()
 5.         └─reticulate (local) python_not_found("Installation of Python not found, Python bindings not loaded.")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'new_citeseq.Rmd' failed with diagnostics:
Installation of Python not found, Python bindings not loaded.
See the Python "Order of Discovery" here: https://rstudio.github.io/reticulate/articles/versions.html#order-of-discovery.
--- 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

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

Status: 2 ERRORs, 1 NOTE
See
  ‘/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/scviR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc-gpu/R/bin/R CMD INSTALL scviR
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/R/site-library’
* installing *source* package ‘scviR’ ...
** this is package ‘scviR’ version ‘1.11.0’
** 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 Under development (unstable) (2025-11-17 r89032) -- "Unsuffered Consequences"
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 
 24.163   0.967  25.183