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This page was generated on 2025-03-20 11:45 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4777
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" 4458
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 1.1.4  (landing page)
Giulio Benedetti
Snapshot Date: 2025-03-19 13:40 -0400 (Wed, 19 Mar 2025)
git_url: https://git.bioconductor.org/packages/iSEEtree
git_branch: devel
git_last_commit: be032f4
git_last_commit_date: 2025-03-19 06:44:00 -0400 (Wed, 19 Mar 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for iSEEtree on kjohnson3

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: 1.1.4
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iSEEtree.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iSEEtree_1.1.4.tar.gz
StartedAt: 2025-03-19 20:01:12 -0400 (Wed, 19 Mar 2025)
EndedAt: 2025-03-19 20:03:22 -0400 (Wed, 19 Mar 2025)
EllapsedTime: 130.6 seconds
RetCode: 0
Status:   OK  
CheckDir: iSEEtree.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iSEEtree.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iSEEtree_1.1.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/iSEEtree.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iSEEtree/DESCRIPTION’ ... OK
* this is package ‘iSEEtree’ version ‘1.1.4’
* 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 ‘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_prev_plot: no visible global function definition
  for ‘.getEncodedName’
.create_visual_box_for_prev_plot: no visible global function definition
  for ‘collapseBox’
.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,PrevalencePlot: no visible global function definition
  for ‘.getEncodedName’
.createObservers,PrevalencePlot: no visible global function definition
  for ‘.createProtectedParameterObservers’
.createObservers,PrevalencePlot: 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,PrevalencePlot: no visible global function
  definition for ‘.getEncodedName’
.defineDataInterface,PrevalencePlot: no visible global function
  definition for ‘.selectInput.iSEE’
.defineDataInterface,PrevalencePlot: no visible global function
  definition for ‘.sliderInput.iSEE’
.defineDataInterface,PrevalencePlot: no visible global function
  definition for ‘.checkboxInput.iSEE’
.defineDataInterface,PrevalencePlot: no visible global function
  definition for ‘.conditionalOnCheckSolo’
.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,PrevalencePlot: no visible global function definition for
  ‘.getEncodedName’
.defineOutput,PrevalencePlot: 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,PrevalencePlot: no visible global function definition
  for ‘.getEncodedName’
.definePanelTour,PrevalencePlot: no visible global function definition
  for ‘.getPanelColor’
.definePanelTour,PrevalencePlot: 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,PrevalencePlot: no visible global function definition for
  ‘.generateOutput’
.exportOutput,PrevalencePlot: 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,PrevalencePlot: no visible global function definition
  for ‘.processMultiSelections’
.generateOutput,PrevalencePlot: 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,PrevalencePlot: no visible global function definition for
  ‘.getEncodedName’
.renderOutput,PrevalencePlot: 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,PrevalencePlot: 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:
  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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/iSEEtree.Rcheck/00check.log’
for details.


Installation output

iSEEtree.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL iSEEtree
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘iSEEtree’ ...
** this is package ‘iSEEtree’ version ‘1.1.4’
** using staged installation
** R
** inst
** 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


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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
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 0 | WARN 0 | SKIP 0 | PASS 107 ]
> 
> proc.time()
   user  system elapsed 
  9.348   0.432   9.902 

Example timings

iSEEtree.Rcheck/iSEEtree-Ex.timings

nameusersystemelapsed
AbundanceDensityPlot0.1690.0060.189
AbundancePlot0.0530.0050.058
ColumnGraphPlot1.3720.0311.437
ColumnTreePlot0.0400.0040.044
LoadingPlot0.1450.0080.156
PrevalencePlot0.0800.0040.086
RDAPlot0.5030.0200.524
RowGraphPlot1.1600.0241.198
RowTreePlot0.0410.0040.044
ScreePlot0.1110.0100.124
iSEE0.6220.0190.653
iSEEtree-package000
utils0.0380.0040.043