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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:miaViz.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings miaViz_1.17.9.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/miaViz.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘miaViz/DESCRIPTION’ ... OK
* this is package ‘miaViz’ version ‘1.17.9’
* 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 ‘miaViz’ 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 ... NOTE
.apply_beeswarm: no visible binding for global variable ‘.row_id’
.apply_vipor_spread: no visible binding for global variable ‘.row_id’
Undefined global functions or variables:
  .row_id
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotColTile.Rd: retrieveFeatureInfo, retrieveCellInfo
  plotGraph.Rd: ggtree
  plotPrevalence.Rd: agglomerate-methods
  plotTree.Rd: ggtree
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ‘miaViz-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotLoadings
> ### Title: Plot feature loadings for TreeSummarizedExperiment objects or
> ###   feature loadings numeric matrix.
> ### Aliases: plotLoadings plotLoadings,TreeSummarizedExperiment-method
> ###   plotLoadings,SingleCellExperiment-method plotLoadings,matrix-method
> 
> ### ** Examples
> 
> 
> library(mia)
> library(scater)
Loading required package: scuttle
> data("GlobalPatterns", package = "mia")
> tse <- GlobalPatterns
> 
> # Calculate PCA
> tse <- agglomerateByPrevalence(tse, rank="Phylum", update.tree = TRUE)
> tse <- transformAssay(tse, method = "clr", pseudocount = 1)
> tse <- runPCA(tse, ncomponents = 5, assay.type = "clr")
> 
> # Plotting feature loadings with tree
> plotLoadings(tse, dimred = "PCA", layout = "heatmap", add.tree = TRUE) |>
+     # Remove this line to see messages
+     suppressMessages()
Error: <ggtree> object properties are invalid:
- @mapping must be <ggplot2::mapping>, not S3<data.frame>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
plotDMN              30.342  0.028  30.428
plotAbundance        25.508  0.571  26.147
plotBoxplot           8.478  0.104   8.604
plotAbundanceDensity  5.780  0.043   5.840
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    9.         │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   10.         └─base_ops[[.Generic]](e1, e2)
   11.           ├─S7::S7_dispatch()
   12.           └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
   13.             └─ggplot2:::add_ggplot(e1, e2, e2name)
   14.               ├─ggplot2::ggplot_add(object, p, objectname)
   15.               └─ggnewscale:::ggplot_add.new_aes(object, p, objectname)
   16.                 ├─base::`$<-`(`*tmp*`, "mapping", value = `<df[,4]>`)
   17.                 └─ggplot2:::`$<-.ggplot2::gg`(`*tmp*`, "mapping", value = `<df[,4]>`)
   18.                   └─S7::`props<-`(`*tmp*`, value = `[[<-`(S7::props(x), i, value))
   19.                     └─S7::validate(object)
  
  [ FAIL 1 | WARN 3 | SKIP 2 | PASS 214 ]
  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: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/miaViz.Rcheck/00check.log’
for details.