############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iSEEu.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iSEEu_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/iSEEu.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘iSEEu/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘iSEEu’ version ‘1.19.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘iSEEu’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... NOTE Package in Depends field not imported from: ‘iSEEhex’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' calls which should be '::': ‘iSEE:::.dataParamBoxOpen’ ‘iSEE:::.multiSelectHistory’ ‘iSEE:::.noSelection’ ‘iSEE:::.organizationHeight’ ‘iSEE:::.organizationWidth’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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: AggregatedDotPlot.Rd: SummarizedExperiment-class, colData, ExperimentColorMap, Panel-class, .cacheCommonInfo, .refineParameters, .defineInterface, .defineDataInterface, .defineOutput, .panelColor, .fullName, .hideInterface, .createObservers, .generateOutput, ggplot, .renderOutput, .exportOutput, .definePanelTour, ComplexHeatmapPlot-class DynamicMarkerTable-class.Rd: rowData, RowTable-class, Table-class, Panel-class, .cacheCommonInfo, .refineParameters, .defineDataInterface, .panelColor, .fullName, .hideInterface, .createObservers, .generateTable, .definePanelTour DynamicReducedDimensionPlot-class.Rd: ColumnDotPlot-class, DotPlot-class, Panel-class, .cacheCommonInfo, .refineParameters, .defineDataInterface, .panelColor, .fullName, .createObservers, .generateDotPlotData, .multiSelectionInvalidated, .definePanelTour FeatureSetTable-class.Rd: SummarizedExperiment-class, Panel-class, .cacheCommonInfo, .refineParameters, .defineDataInterface, .panelColor, .fullName, .hideInterface, .defineOutput, datatable, .createObservers, .generateOutput, .renderOutput, .multiSelectionDimension, .multiSelectionCommands, .multiSelectionActive, .multiSelectionClear, .multiSelectionAvailable, .definePanelTour GeneSetTable-class.Rd: Panel-class, .defineDataInterface, .panelColor, .fullName, .hideInterface, .defineOutput, datatable, .createObservers, .generateOutput, .renderOutput, .multiSelectionDimension, .multiSelectionCommands, .multiSelectionActive, .multiSelectionClear, .multiSelectionAvailable LogFCLogFCPlot-class.Rd: RowDataPlot-class, rowData, RowDotPlot-class, DotPlot-class, Panel-class, SummarizedExperiment-class, .cacheCommonInfo, .refineParameters, .defineDataInterface, .panelColor, .allowableXAxisChoices, .allowableYAxisChoices, .hideInterface, .fullName, .createObservers, .generateDotPlotData, .prioritizeDotPlotData, .colorByNoneDotPlotField, .colorByNoneDotPlotScale, .generateDotPlot, ColumnDataPlot-class, ggplot, .definePanelTour, .getDotPlotColorHelp, RowDataPlot MAPlot-class.Rd: RowDataPlot-class, rowData, RowDotPlot-class, DotPlot-class, Panel-class, SummarizedExperiment-class, .cacheCommonInfo, .refineParameters, .defineDataInterface, .panelColor, .allowableXAxisChoices, .allowableYAxisChoices, .hideInterface, .fullName, .createObservers, .generateDotPlotData, .prioritizeDotPlotData, .colorByNoneDotPlotField, .colorByNoneDotPlotScale, .generateDotPlot, ColumnDataPlot-class, ggplot, .definePanelTour, .getDotPlotColorHelp, RowDataPlot MarkdownBoard-class.Rd: Panel-class, RowDataPlot-class, .defineDataInterface, .panelColor, .hideInterface, .fullName, .createObservers, .defineOutput, .renderOutput, .generateOutput, .exportOutput, .definePanelTour VolcanoPlot-class.Rd: RowDataPlot-class, RowDotPlot-class, DotPlot-class, Panel-class, rowData, SummarizedExperiment-class, .cacheCommonInfo, .refineParameters, .defineDataInterface, .panelColor, .allowableXAxisChoices, .allowableYAxisChoices, .hideInterface, .fullName, .createObservers, .generateDotPlotData, .prioritizeDotPlotData, .colorByNoneDotPlotField, .colorByNoneDotPlotScale, .generateDotPlot, ColumnDataPlot-class, ggplot, .definePanelTour, .getDotPlotColorHelp, RowDataPlot global-TableExtraFields.Rd: iSEE globals-PValuePattern.Rd: rowData, iSEE modeEmpty.Rd: iSEE modeGating.Rd: SummarizedExperiment, iSEE modeReducedDim.Rd: SingleCellExperiment, SingleCellExperiment-class, iSEE registerDEFields.Rd: Panel-class, SummarizedExperiment-class, rowData, iSEE registerFeatureSetCollections.Rd: SummarizedExperiment-class, iSEE, CharacterList-class, metadata, mcols Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... WARNING Found the following significant warnings: Warning in .setOrganism("org.Mm.eg.db") : '.setOrganism' is deprecated. Warning in GeneSetTable(PanelId = 1L) : 'GeneSetTable' is deprecated. Warning in setPValuePattern(old) : 'setPValuePattern' is deprecated. Warning in .getIdentifierType() : '.getIdentifierType' is deprecated. Warning in .setOrganism("org.Mm.eg.db") : '.setOrganism' is deprecated. Warning in .getOrganism() : '.getOrganism' is deprecated. Warning in .getOrganism() : '.getOrganism' is deprecated. Warning in .getOrganism() : '.getOrganism' is deprecated. Warning in .getIdentifierType() : '.getIdentifierType' is deprecated. Warning in .getOrganism() : '.getOrganism' is deprecated. Warning in .getOrganism() : '.getOrganism' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed AggregatedDotPlot 11.457 0.931 12.453 modeReducedDim 9.675 0.445 10.177 DynamicReducedDimensionPlot-class 4.919 0.408 5.351 * 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: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/iSEEu.Rcheck/00check.log’ for details.