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This page was generated on 2025-03-17 11:37 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1068/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iSEEtree 1.1.3  (landing page)
Giulio Benedetti
Snapshot Date: 2025-03-16 13:40 -0400 (Sun, 16 Mar 2025)
git_url: https://git.bioconductor.org/packages/iSEEtree
git_branch: devel
git_last_commit: c2698ea
git_last_commit_date: 2025-03-10 16:09:54 -0400 (Mon, 10 Mar 2025)
palomino7Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  

CHECK results for iSEEtree on palomino7

To the developers/maintainers of the iSEEtree package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iSEEtree.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: iSEEtree
Version: 1.1.3
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iSEEtree.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings iSEEtree_1.1.3.tar.gz
StartedAt: 2025-03-17 02:18:34 -0400 (Mon, 17 Mar 2025)
EndedAt: 2025-03-17 02:24:59 -0400 (Mon, 17 Mar 2025)
EllapsedTime: 384.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: iSEEtree.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iSEEtree.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings iSEEtree_1.1.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/iSEEtree.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'iSEEtree/DESCRIPTION' ... OK
* this is package 'iSEEtree' version '1.1.3'
* 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 whether package 'iSEEtree' 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
.create_visual_box_for_abund_plot: no visible global function
  definition for '.getEncodedName'
.create_visual_box_for_abund_plot: no visible global function
  definition for '.addSpecificTour'
.create_visual_box_for_abund_plot: no visible global function
  definition for 'collapseBox'
.create_visual_box_for_abund_plot: no visible global function
  definition for '.selectInput.iSEE'
.create_visual_box_for_abund_plot: no visible global function
  definition for '.checkboxInput.iSEE'
.create_visual_box_for_abunddens_plot: no visible global function
  definition for '.getEncodedName'
.create_visual_box_for_abunddens_plot: no visible global function
  definition for '.addSpecificTour'
.create_visual_box_for_abunddens_plot: no visible global function
  definition for 'collapseBox'
.create_visual_box_for_abunddens_plot: no visible global function
  definition for '.selectInput.iSEE'
.create_visual_box_for_abunddens_plot: no visible global function
  definition for '.checkboxInput.iSEE'
.create_visual_box_for_abunddens_plot: no visible global function
  definition for '.radioButtons.iSEE'
.create_visual_box_for_abunddens_plot: no visible global function
  definition for '.conditionalOnRadio'
.create_visual_box_for_graph: no visible global function definition for
  '.getEncodedName'
.create_visual_box_for_graph: no visible global function definition for
  '.addSpecificTour'
.create_visual_box_for_graph: no visible global function definition for
  'collapseBox'
.create_visual_box_for_graph: no visible global function definition for
  '.selectInput.iSEE'
.create_visual_box_for_graph: no visible global function definition for
  '.checkboxInput.iSEE'
.create_visual_box_for_graph: no visible global function definition for
  '.checkboxGroupInput.iSEE'
.create_visual_box_for_graph: no visible global function definition for
  '.conditionalOnCheckGroup'
.create_visual_box_for_loading_plot: no visible global function
  definition for '.getEncodedName'
.create_visual_box_for_loading_plot: no visible global function
  definition for '.addSpecificTour'
.create_visual_box_for_loading_plot: no visible global function
  definition for 'collapseBox'
.create_visual_box_for_loading_plot: no visible global function
  definition for '.selectInput.iSEE'
.create_visual_box_for_loading_plot: no visible global function
  definition for '.checkboxInput.iSEE'
.create_visual_box_for_rda: no visible global function definition for
  '.getEncodedName'
.create_visual_box_for_rda: no visible global function definition for
  '.addSpecificTour'
.create_visual_box_for_rda: no visible global function definition for
  'collapseBox'
.create_visual_box_for_rda: no visible global function definition for
  '.checkboxGroupInput.iSEE'
.create_visual_box_for_rda: no visible global function definition for
  '.selectInput.iSEE'
.create_visual_box_for_rda: no visible global function definition for
  '.conditionalOnCheckGroup'
.create_visual_box_for_rda: no visible global function definition for
  '.sliderInput.iSEE'
.create_visual_box_for_rda: no visible global function definition for
  '.numericInput.iSEE'
.create_visual_box_for_rda: no visible global function definition for
  '.checkboxInput.iSEE'
.create_visual_box_for_rda: no visible global function definition for
  '.conditionalOnCheckSolo'
.create_visual_box_for_scree_plot: no visible global function
  definition for '.getEncodedName'
.create_visual_box_for_scree_plot: no visible global function
  definition for '.addSpecificTour'
.create_visual_box_for_scree_plot: no visible global function
  definition for 'collapseBox'
.create_visual_box_for_scree_plot: no visible global function
  definition for '.checkboxInput.iSEE'
.create_visual_box_for_tree: no visible global function definition for
  '.getEncodedName'
.create_visual_box_for_tree: no visible global function definition for
  '.addSpecificTour'
.create_visual_box_for_tree: no visible global function definition for
  'collapseBox'
.create_visual_box_for_tree: no visible global function definition for
  '.selectInput.iSEE'
.create_visual_box_for_tree: no visible global function definition for
  '.checkboxInput.iSEE'
.create_visual_box_for_tree: no visible global function definition for
  '.checkboxGroupInput.iSEE'
.create_visual_box_for_tree: no visible global function definition for
  '.conditionalOnCheckGroup'
.createObservers,AbundanceDensityPlot: no visible global function
  definition for '.getEncodedName'
.createObservers,AbundanceDensityPlot: no visible global function
  definition for '.createProtectedParameterObservers'
.createObservers,AbundanceDensityPlot: no visible global function
  definition for '.createUnprotectedParameterObservers'
.createObservers,AbundancePlot: no visible global function definition
  for '.getEncodedName'
.createObservers,AbundancePlot: no visible global function definition
  for '.createProtectedParameterObservers'
.createObservers,AbundancePlot: no visible global function definition
  for '.createUnprotectedParameterObservers'
.createObservers,GraphPlot: no visible global function definition for
  '.getEncodedName'
.createObservers,GraphPlot: no visible global function definition for
  '.createProtectedParameterObservers'
.createObservers,GraphPlot: no visible global function definition for
  '.createUnprotectedParameterObservers'
.createObservers,LoadingPlot: no visible global function definition for
  '.getEncodedName'
.createObservers,LoadingPlot: no visible global function definition for
  '.createProtectedParameterObservers'
.createObservers,LoadingPlot: no visible global function definition for
  '.createUnprotectedParameterObservers'
.createObservers,RDAPlot: no visible global function definition for
  '.getEncodedName'
.createObservers,RDAPlot: no visible global function definition for
  '.createProtectedParameterObservers'
.createObservers,RDAPlot: no visible global function definition for
  '.createUnprotectedParameterObservers'
.createObservers,ScreePlot: no visible global function definition for
  '.getEncodedName'
.createObservers,ScreePlot: no visible global function definition for
  '.createProtectedParameterObservers'
.createObservers,ScreePlot: no visible global function definition for
  '.createUnprotectedParameterObservers'
.createObservers,TreePlot: no visible global function definition for
  '.getEncodedName'
.createObservers,TreePlot: no visible global function definition for
  '.createProtectedParameterObservers'
.createObservers,TreePlot: no visible global function definition for
  '.createUnprotectedParameterObservers'
.defineDataInterface,AbundanceDensityPlot: no visible global function
  definition for '.getEncodedName'
.defineDataInterface,AbundanceDensityPlot: no visible global function
  definition for '.selectInput.iSEE'
.defineDataInterface,AbundanceDensityPlot: no visible global function
  definition for '.numericInput.iSEE'
.defineDataInterface,AbundanceDensityPlot: no visible global function
  definition for '.checkboxInput.iSEE'
.defineDataInterface,AbundanceDensityPlot: no visible global function
  definition for '.radioButtons.iSEE'
.defineDataInterface,AbundanceDensityPlot: no visible global function
  definition for '.conditionalOnRadio'
.defineDataInterface,AbundancePlot: no visible global function
  definition for '.getEncodedName'
.defineDataInterface,AbundancePlot: no visible global function
  definition for '.checkboxInput.iSEE'
.defineDataInterface,AbundancePlot: no visible global function
  definition for '.radioButtons.iSEE'
.defineDataInterface,AbundancePlot: no visible global function
  definition for '.conditionalOnRadio'
.defineDataInterface,AbundancePlot: no visible global function
  definition for '.selectInput.iSEE'
.defineDataInterface,ColumnTreePlot: no visible global function
  definition for '.getEncodedName'
.defineDataInterface,ColumnTreePlot: no visible global function
  definition for '.selectInput.iSEE'
.defineDataInterface,GraphPlot: no visible global function definition
  for '.getEncodedName'
.defineDataInterface,GraphPlot: no visible global function definition
  for '.selectInput.iSEE'
.defineDataInterface,GraphPlot: no visible global function definition
  for '.checkboxInput.iSEE'
.defineDataInterface,LoadingPlot: no visible global function definition
  for '.getEncodedName'
.defineDataInterface,LoadingPlot: no visible global function definition
  for '.selectInput.iSEE'
.defineDataInterface,LoadingPlot: no visible global function definition
  for '.numericInput.iSEE'
.defineDataInterface,RDAPlot: no visible global function definition for
  '.getEncodedName'
.defineDataInterface,RDAPlot: no visible global function definition for
  '.selectInput.iSEE'
.defineDataInterface,RDAPlot: no visible global function definition for
  '.sliderInput.iSEE'
.defineDataInterface,RDAPlot: no visible global function definition for
  '.checkboxInput.iSEE'
.defineDataInterface,RowTreePlot: no visible global function definition
  for '.getEncodedName'
.defineDataInterface,RowTreePlot: no visible global function definition
  for '.selectInput.iSEE'
.defineDataInterface,ScreePlot: no visible global function definition
  for '.getEncodedName'
.defineDataInterface,ScreePlot: no visible global function definition
  for '.selectInput.iSEE'
.defineDataInterface,ScreePlot: no visible global function definition
  for '.numericInput.iSEE'
.defineDataInterface,ScreePlot: no visible global function definition
  for '.checkboxInput.iSEE'
.defineDataInterface,TreePlot: no visible global function definition
  for '.getEncodedName'
.defineDataInterface,TreePlot: no visible global function definition
  for '.checkboxInput.iSEE'
.defineDataInterface,TreePlot: no visible global function definition
  for '.sliderInput.iSEE'
.defineOutput,AbundanceDensityPlot: no visible global function
  definition for '.getEncodedName'
.defineOutput,AbundanceDensityPlot: no visible global function
  definition for '.panelColor'
.defineOutput,AbundancePlot: no visible global function definition for
  '.getEncodedName'
.defineOutput,AbundancePlot: no visible global function definition for
  '.panelColor'
.defineOutput,GraphPlot: no visible global function definition for
  '.getEncodedName'
.defineOutput,GraphPlot: no visible global function definition for
  '.panelColor'
.defineOutput,LoadingPlot: no visible global function definition for
  '.getEncodedName'
.defineOutput,LoadingPlot: no visible global function definition for
  '.panelColor'
.defineOutput,RDAPlot: no visible global function definition for
  '.getEncodedName'
.defineOutput,RDAPlot: no visible global function definition for
  '.panelColor'
.defineOutput,ScreePlot: no visible global function definition for
  '.getEncodedName'
.defineOutput,ScreePlot: no visible global function definition for
  '.panelColor'
.defineOutput,TreePlot: no visible global function definition for
  '.getEncodedName'
.defineOutput,TreePlot: no visible global function definition for
  '.panelColor'
.definePanelTour,AbundanceDensityPlot: no visible global function
  definition for '.getEncodedName'
.definePanelTour,AbundanceDensityPlot: no visible global function
  definition for '.getPanelColor'
.definePanelTour,AbundanceDensityPlot: no visible global function
  definition for '.addTourStep'
.definePanelTour,AbundancePlot: no visible global function definition
  for '.getEncodedName'
.definePanelTour,AbundancePlot: no visible global function definition
  for '.getPanelColor'
.definePanelTour,AbundancePlot: no visible global function definition
  for '.addTourStep'
.definePanelTour,GraphPlot: no visible global function definition for
  '.getEncodedName'
.definePanelTour,GraphPlot: no visible global function definition for
  '.getPanelColor'
.definePanelTour,GraphPlot: no visible global function definition for
  '.fullName'
.definePanelTour,GraphPlot: no visible global function definition for
  '.addTourStep'
.definePanelTour,LoadingPlot: no visible global function definition for
  '.getEncodedName'
.definePanelTour,LoadingPlot: no visible global function definition for
  '.getPanelColor'
.definePanelTour,LoadingPlot: no visible global function definition for
  '.addTourStep'
.definePanelTour,RDAPlot: no visible global function definition for
  '.getEncodedName'
.definePanelTour,RDAPlot: no visible global function definition for
  '.getPanelColor'
.definePanelTour,RDAPlot: no visible global function definition for
  '.addTourStep'
.definePanelTour,ScreePlot: no visible global function definition for
  '.getEncodedName'
.definePanelTour,ScreePlot: no visible global function definition for
  '.getPanelColor'
.definePanelTour,ScreePlot: no visible global function definition for
  '.addTourStep'
.definePanelTour,TreePlot: no visible global function definition for
  '.getEncodedName'
.definePanelTour,TreePlot: no visible global function definition for
  '.getPanelColor'
.definePanelTour,TreePlot: no visible global function definition for
  '.fullName'
.definePanelTour,TreePlot: no visible global function definition for
  '.addTourStep'
.exportOutput,AbundanceDensityPlot: no visible global function
  definition for '.generateOutput'
.exportOutput,AbundanceDensityPlot: no visible global function
  definition for '.getEncodedName'
.exportOutput,AbundancePlot: no visible global function definition for
  '.generateOutput'
.exportOutput,AbundancePlot: no visible global function definition for
  '.getEncodedName'
.exportOutput,GraphPlot: no visible global function definition for
  '.generateOutput'
.exportOutput,GraphPlot: no visible global function definition for
  '.getEncodedName'
.exportOutput,LoadingPlot: no visible global function definition for
  '.generateOutput'
.exportOutput,LoadingPlot: no visible global function definition for
  '.getEncodedName'
.exportOutput,RDAPlot: no visible global function definition for
  '.generateOutput'
.exportOutput,RDAPlot: no visible global function definition for
  '.getEncodedName'
.exportOutput,ScreePlot: no visible global function definition for
  '.generateOutput'
.exportOutput,ScreePlot: no visible global function definition for
  '.getEncodedName'
.exportOutput,TreePlot: no visible global function definition for
  '.generateOutput'
.exportOutput,TreePlot: no visible global function definition for
  '.getEncodedName'
.generateOutput,AbundanceDensityPlot: no visible global function
  definition for '.processMultiSelections'
.generateOutput,AbundanceDensityPlot: no visible global function
  definition for '.textEval'
.generateOutput,AbundancePlot: no visible global function definition
  for '.processMultiSelections'
.generateOutput,AbundancePlot: no visible global function definition
  for '.textEval'
.generateOutput,ColumnGraphPlot: no visible global function definition
  for '.processMultiSelections'
.generateOutput,ColumnGraphPlot: no visible global function definition
  for '.textEval'
.generateOutput,ColumnTreePlot: no visible global function definition
  for '.processMultiSelections'
.generateOutput,ColumnTreePlot: no visible global function definition
  for '.textEval'
.generateOutput,LoadingPlot: no visible global function definition for
  '.processMultiSelections'
.generateOutput,LoadingPlot: no visible global function definition for
  '.textEval'
.generateOutput,RDAPlot: no visible global function definition for
  '.processMultiSelections'
.generateOutput,RDAPlot: no visible global function definition for
  '.textEval'
.generateOutput,RowGraphPlot: no visible global function definition for
  '.processMultiSelections'
.generateOutput,RowGraphPlot: no visible global function definition for
  '.textEval'
.generateOutput,RowTreePlot: no visible global function definition for
  '.processMultiSelections'
.generateOutput,RowTreePlot: no visible global function definition for
  '.textEval'
.generateOutput,ScreePlot: no visible global function definition for
  '.textEval'
.renderOutput,AbundanceDensityPlot: no visible global function
  definition for '.getEncodedName'
.renderOutput,AbundanceDensityPlot: no visible global function
  definition for '.retrieveOutput'
.renderOutput,AbundancePlot: no visible global function definition for
  '.getEncodedName'
.renderOutput,AbundancePlot: no visible global function definition for
  '.retrieveOutput'
.renderOutput,GraphPlot: no visible global function definition for
  '.getEncodedName'
.renderOutput,GraphPlot: no visible global function definition for
  '.retrieveOutput'
.renderOutput,LoadingPlot: no visible global function definition for
  '.getEncodedName'
.renderOutput,LoadingPlot: no visible global function definition for
  '.retrieveOutput'
.renderOutput,RDAPlot: no visible global function definition for
  '.getEncodedName'
.renderOutput,RDAPlot: no visible global function definition for
  '.retrieveOutput'
.renderOutput,ScreePlot: no visible global function definition for
  '.getEncodedName'
.renderOutput,ScreePlot: no visible global function definition for
  '.retrieveOutput'
.renderOutput,TreePlot: no visible global function definition for
  '.getEncodedName'
.renderOutput,TreePlot: no visible global function definition for
  '.retrieveOutput'
initialize,AbundanceDensityPlot: no visible global function definition
  for '.emptyDefault'
initialize,AbundancePlot: no visible global function definition for
  '.emptyDefault'
initialize,GraphPlot: no visible global function definition for
  '.emptyDefault'
initialize,LoadingPlot: no visible global function definition for
  '.emptyDefault'
initialize,RDAPlot: no visible global function definition for
  '.emptyDefault'
initialize,ScreePlot: no visible global function definition for
  '.emptyDefault'
initialize,TreePlot: no visible global function definition for
  '.emptyDefault'
Undefined global functions or variables:
  .addSpecificTour .addTourStep .checkboxGroupInput.iSEE
  .checkboxInput.iSEE .conditionalOnCheckGroup .conditionalOnCheckSolo
  .conditionalOnRadio .createProtectedParameterObservers
  .createUnprotectedParameterObservers .emptyDefault .fullName
  .generateOutput .getEncodedName .getPanelColor .numericInput.iSEE
  .panelColor .processMultiSelections .radioButtons.iSEE
  .retrieveOutput .selectInput.iSEE .sliderInput.iSEE .textEval
  collapseBox
* 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:
  AbundanceDensityPlot.Rd: Panel-class
  AbundancePlot.Rd: Panel-class
  GraphPlot.Rd: Panel-class
  LoadingPlot.Rd: Panel-class
  RDAPlot.Rd: Panel-class
  ScreePlot.Rd: Panel-class
  TreePlot.Rd: Panel-class
  iSEE.Rd: SummarizedExperiment-class, Panel-class,
    ExperimentColorMap-class, shinyApp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Unknown package 'SingleSummarizedExperiment' in Rd xrefs
* 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 ... ERROR
Running examples in 'iSEEtree-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RDAPlot-class
> ### Title: RDA plot
> ### Aliases: RDAPlot-class RDAPlot
> 
> ### ** Examples
> 
> # Import TreeSE
> library(mia)
Loading required package: MultiAssayExperiment
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 1.15.32
- Online documentation and vignettes: https://microbiome.github.io/mia/
- Online book 'Orchestrating Microbiome Analysis (OMA)': https://microbiome.github.io/OMA/docs/devel/
> data("enterotype", package = "mia")
> tse <- enterotype
> 
> # Run RDA and store results into TreeSE
> tse <- runRDA(tse,
+               formula = assay ~ ClinicalStatus + Gender + Age,
+               FUN = vegan::vegdist,
+               distance = "bray",
+               na.action = na.exclude)
Error: Either 'assay.type' or 'dis.name' must be specified.
Execution halted
* 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:
  ── Error ('test-RDAPlot.R:13:3'): RDAPlot ──────────────────────────────────────
  Error: Either 'assay.type' or 'dis.name' must be specified.
  Backtrace:
      ▆
   1. └─mia::runRDA(...) at test-RDAPlot.R:13:3
   2.   ├─mia::addRDA(x, ...)
   3.   └─mia::addRDA(x, ...)
   4.     └─mia (local) .local(x, ...)
   5.       ├─mia::getRDA(y, ...)
   6.       └─mia::getRDA(y, ...)
   7.         └─mia (local) .local(x, ...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 90 ]
  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
  'E:/biocbuild/bbs-3.21-bioc/meat/iSEEtree.Rcheck/00check.log'
for details.

Installation output

iSEEtree.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL iSEEtree
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'iSEEtree' ...
** this is package 'iSEEtree' version '1.1.3'
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (iSEEtree)

Tests output

iSEEtree.Rcheck/tests/testthat.Rout.fail

R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
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> library(testthat)
> library(iSEEtree)
Loading required package: iSEE
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:grDevices':

    windows

Loading required package: GenomeInfoDb
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

Attaching package: 'iSEEtree'

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

    iSEE

> 
> test_check("iSEEtree")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 90 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-RDAPlot.R:13:3'): RDAPlot ──────────────────────────────────────
Error: Either 'assay.type' or 'dis.name' must be specified.
Backtrace:
    ▆
 1. └─mia::runRDA(...) at test-RDAPlot.R:13:3
 2.   ├─mia::addRDA(x, ...)
 3.   └─mia::addRDA(x, ...)
 4.     └─mia (local) .local(x, ...)
 5.       ├─mia::getRDA(y, ...)
 6.       └─mia::getRDA(y, ...)
 7.         └─mia (local) .local(x, ...)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 90 ]
Error: Test failures
Execution halted

Example timings

iSEEtree.Rcheck/iSEEtree-Ex.timings

nameusersystemelapsed
AbundanceDensityPlot0.550.030.65
AbundancePlot0.200.040.24
ColumnGraphPlot4.070.424.55
ColumnTreePlot0.090.030.12
LoadingPlot0.460.080.53