##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:anndataR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings anndataR_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/anndataR.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘anndataR/DESCRIPTION’ ... OK
* this is package ‘anndataR’ version ‘1.1.2’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘anndataR’ 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 whether startup messages can be suppressed ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
read_h5ad  19.814  0.427  22.461
as_AnnData 18.178  0.637  20.132
write_h5ad  7.183  0.096   7.834
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ReticulateAnnData.R:353:3'): reticulate utility functions work ──
  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. └─reticulate::r_to_py(r_mat) at test-ReticulateAnnData.R:353:3
   2.   └─reticulate:::ensure_python_initialized()
   3.     └─reticulate:::initialize_python()
   4.       └─reticulate (local) python_not_found("Installation of Python not found, Python bindings not loaded.")
  
  [ FAIL 1 | WARN 20 | SKIP 20 | PASS 1350 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/anndataR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL anndataR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘anndataR’ ...
** this is package ‘anndataR’ version ‘1.1.2’
** using staged installation
** R
** 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 (anndataR)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> if (requireNamespace("spelling", quietly = TRUE)) {
+   spelling::spell_check_test(
+     vignettes = TRUE,
+     error = FALSE,
+     skip_on_cran = TRUE
+   )
+ }
NULL
> 
> proc.time()
   user  system elapsed 
  0.189   0.032   0.240 

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(anndataR)
> 
> test_check("anndataR")
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpSzceDi/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpzV4Sl1/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpN12cQL/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpXipjUC/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpSRToZZ/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpGZjCTC/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpZep0Da/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpQtJUi5/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpOVZ5hk/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpZ6GBnZ/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpfHo1Xb/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpGcUCzm/bin/python': No such file.
Loading required package: SeuratObject
Loading required package: sp
'SeuratObject' was built with package 'Matrix' 1.7.2 but the current
version is 1.7.3; it is recomended that you reinstall 'SeuratObject' as
the ABI for 'Matrix' may have changed

Attaching package: 'SeuratObject'

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

    intersect, t

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

Attaching package: 'IRanges'

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

    %over%

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


Attaching package: 'SummarizedExperiment'

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

    Assays

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

    Assays

Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpNCoKAu/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpmddBBH/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpVKPRVq/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpAJe4mq/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpv4YMIl/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpDnBbHe/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmp6I1Gcy/bin/python': No such file.
Error in python_config_impl(python) : 
  Error running '/home/biocbuild/.cache/R/reticulate/uv/cache/builds-v0/.tmpLEjVpt/bin/python': No such file.
[ FAIL 1 | WARN 20 | SKIP 20 | PASS 1350 ]

══ Skipped tests (20) ══════════════════════════════════════════════════════════
• Known issue for backend 'to_SCE', slot 'obsm', dtype 'pca', process
  'convert': converted sce object has dimnames(), whilst the original anndata
  does not. (1): 'test-as_SingleCellExperiment.R:200:3'
• Python anndata module not available for testing (19):
  'test-ReticulateAnnData.R:2:3', 'test-ReticulateAnnData.R:28:3',
  'test-ReticulateAnnData.R:47:3', 'test-ReticulateAnnData.R:101:3',
  'test-ReticulateAnnData.R:139:3', 'test-ReticulateAnnData.R:194:3',
  'test-ReticulateAnnData.R:229:3', 'test-ReticulateAnnData.R:248:3',
  'test-ReticulateAnnData.R:266:3', 'test-ReticulateAnnData.R:289:3',
  'test-ReticulateAnnData.R:319:3', 'test-roundtrip-X.R:1:1',
  'test-roundtrip-empty.R:1:1', 'test-roundtrip-layers.R:1:1',
  'test-roundtrip-obsmvarm.R:1:1', 'test-roundtrip-obspvarp.R:1:1',
  'test-roundtrip-obsvar.R:1:1', 'test-roundtrip-uns-nested.R:1:1',
  'test-roundtrip-uns.R:1:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ReticulateAnnData.R:353:3'): reticulate utility functions work ──
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. └─reticulate::r_to_py(r_mat) at test-ReticulateAnnData.R:353:3
 2.   └─reticulate:::ensure_python_initialized()
 3.     └─reticulate:::initialize_python()
 4.       └─reticulate (local) python_not_found("Installation of Python not found, Python bindings not loaded.")

[ FAIL 1 | WARN 20 | SKIP 20 | PASS 1350 ]
Error: Test failures
Execution halted