Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-17 11:37 -0400 (Mon, 17 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R 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 1068/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
iSEEtree 1.1.3 (landing page) Giulio Benedetti
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.1.3 |
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 |
############################################################################## ############################################################################## ### ### 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.
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)
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. 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 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
iSEEtree.Rcheck/iSEEtree-Ex.timings
name | user | system | elapsed | |
AbundanceDensityPlot | 0.55 | 0.03 | 0.65 | |
AbundancePlot | 0.20 | 0.04 | 0.24 | |
ColumnGraphPlot | 4.07 | 0.42 | 4.55 | |
ColumnTreePlot | 0.09 | 0.03 | 0.12 | |
LoadingPlot | 0.46 | 0.08 | 0.53 | |