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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miaViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miaViz_1.17.9.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/miaViz.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 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()
Warning: `aes_()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`
ℹ The deprecated feature was likely used in the ggtree package.
  Please report the issue at <https://github.com/YuLab-SMU/ggtree/issues>.
Warning in fortify(data, ...) : Arguments in `...` must be used.
✖ Problematic arguments:
• as.Date = as.Date
• yscale_mapping = yscale_mapping
• hang = hang
ℹ Did you misspell an argument name?
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
plotAbundance        25.334  0.723  27.150
plotDMN              16.034  0.101  16.440
plotBoxplot           7.051  0.107   7.275
plotAbundanceDensity  5.267  0.074   5.452
* 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 3 | WARN 5 | SKIP 0 | PASS 228 ]
  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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/miaViz.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL miaViz
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘miaViz’ ...
** this is package ‘miaViz’ version ‘1.17.9’
** using staged installation
** R
** data
** 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 (miaViz)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(miaViz)
Loading required package: ggplot2
Loading required package: ggraph
Loading required package: mia
Loading required package: MultiAssayExperiment
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

Loading required package: SingleCellExperiment
Loading required package: TreeSummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

This is mia version 1.17.9
- Online documentation and vignettes: https://microbiome.github.io/mia/
- Online book 'Orchestrating Microbiome Analysis (OMA)': https://microbiome.github.io/OMA/docs/devel/

Attaching package: 'miaViz'

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

    plotNMDS

> 
> test_check("miaViz")
initial  value 0.000000 
final  value 0.000000 
converged
[ FAIL 3 | WARN 5 | SKIP 0 | PASS 228 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-2plotSeries.R:27:5'): plot series ────────────────────────────
`miaViz:::.get_series_data(tse_sub, "counts", NULL, "DAY_ORDER")` threw an error with unexpected message.
Expected match: "argument \"group.by\" is missing, with no default"
Actual message: "argument \"facet.by\" is missing, with no default"
Backtrace:
    ▆
 1. ├─testthat::expect_error(...) at test-2plotSeries.R:27:5
 2. │ └─testthat:::quasi_capture(...)
 3. │   ├─testthat (local) .capture(...)
 4. │   │ └─base::withCallingHandlers(...)
 5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 6. └─miaViz:::.get_series_data(tse_sub, "counts", NULL, "DAY_ORDER")
── Error ('test-2plotSeries.R:43:5'): plot series ──────────────────────────────
<getvarError/missingArgError/error/condition>
Error in `miaViz:::.get_series_data(tse, assay.type = "counts", col.var = NULL, 
    time.col = "DAY_ORDER", colour.by = "Phylum", linetype.by = "Family", 
    size.by = "Kingdom", group.by = NULL)`: argument "facet.by" is missing, with no default
Backtrace:
    ▆
 1. └─miaViz:::.get_series_data(...) at test-2plotSeries.R:43:5
── Error ('test-plotLoadings.R:34:3'): plot Loadings ───────────────────────────
Error: <ggtree> object properties are invalid:
- @mapping must be <ggplot2::mapping>, not S3<data.frame>
Backtrace:
     ▆
  1. ├─miaViz::plotLoadings(...) at test-plotLoadings.R:34:3
  2. └─miaViz::plotLoadings(...)
  3.   └─miaViz (local) .local(x, ...)
  4.     └─miaViz:::.loadings_tree_plotter(mat, tree, row.var, ...)
  5.       └─S7:::Ops.S7_object(plot_out, new_scale_fill())
  6.         ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
  7.         │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  8.         │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  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 3 | WARN 5 | SKIP 0 | PASS 228 ]
Error: Test failures
Execution halted