Giulio Benedetti
| Snapshot Date: 2025-10-22 13:45 -0400 (Wed, 22 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/iSEEtree |
| git_branch: devel |
| git_last_commit: b1b4d6e |
| git_last_commit_date: 2025-08-29 11:35:14 -0400 (Fri, 29 Aug 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-23 12:06 -0400 (Thu, 23 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4894 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4684 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4629 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 1086/2355 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| iSEEtree 1.3.2 (landing page) Giulio Benedetti
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
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. |
| Package: iSEEtree |
| Version: 1.3.2 |
| 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_1.3.2.tar.gz |
| StartedAt: 2025-10-22 20:21:35 -0400 (Wed, 22 Oct 2025) |
| EndedAt: 2025-10-22 20:23:53 -0400 (Wed, 22 Oct 2025) |
| EllapsedTime: 137.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: iSEEtree.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.3.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/iSEEtree.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iSEEtree/DESCRIPTION’ ... OK
* this is package ‘iSEEtree’ version ‘1.3.2’
* 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 ‘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-3.22-bioc/meat/iSEEtree.Rcheck/00check.log’
for details.
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 ‘1.3.2’ ** 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)
iSEEtree.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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(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: 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
Attaching package: 'iSEEtree'
The following object is masked from 'package:iSEE':
iSEE
>
> test_check("iSEEtree")
This graph was created by an old(er) igraph version.
i Call `igraph::upgrade_graph()` on it to use with the current igraph version.
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
i Call `igraph::upgrade_graph()` on it to use with the current igraph version.
For now we convert it on the fly...
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 172 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 172 ]
>
> proc.time()
user system elapsed
11.870 0.457 12.539
iSEEtree.Rcheck/iSEEtree-Ex.timings
| name | user | system | elapsed | |
| AbundanceDensityPlot | 0.126 | 0.006 | 0.147 | |
| AbundancePlot | 0.047 | 0.003 | 0.051 | |
| ColumnGraphPlot | 1.307 | 0.031 | 1.439 | |
| ColumnTreePlot | 0.039 | 0.003 | 0.047 | |
| LoadingPlot | 0.115 | 0.006 | 0.141 | |
| PrevalencePlot | 0.069 | 0.006 | 0.086 | |
| RDAPlot | 0.513 | 0.024 | 0.560 | |
| RowGraphPlot | 1.060 | 0.021 | 1.129 | |
| RowTreePlot | 0.040 | 0.004 | 0.047 | |
| ScreePlot | 0.113 | 0.009 | 0.138 | |
| iSEE | 0.595 | 0.024 | 0.664 | |
| iSEEtree-package | 0 | 0 | 0 | |
| utils | 0.039 | 0.004 | 0.043 | |