* using log directory 'd:/RCompile/CRANincoming/R-devel/SpatialFlux.Rcheck' * using R Under development (unstable) (2026-03-19 r89661 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * current time: 2026-03-21 00:34:21 UTC * checking for file 'SpatialFlux/DESCRIPTION' ... OK * this is package 'SpatialFlux' version '1.0.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Dimitri Sokolowskei ' New submission Possibly misspelled words in DESCRIPTION: SpatialFlux (2:8) transcriptomics (3:17, 7:22) No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: c(person(given = "Dimitri", family = "Sokolowskei", role = c("aut", "cre"), email = "dimitri.sokolowskei@utsouthwestern.edu"), person(given = c("Alex", "J."), family = "Trostle", role = "aut", email = "alexander.trostle@utsouthwestern.edu"), person(given = "Achira", family = "Shah", role = "aut", email = "achira.shah@utsouthwestern.edu"), person(given = c("Robert", "J."), family = "Tower", role = "aut", email = "robert.tower@utsouthwestern.edu")) as necessary. The Title field starts with the package name. The Title field should be in title case. Current version is: 'SpatialFlux: An R package for distance gradient analysis in spatial transcriptomics' In title case that is: 'SpatialFlux: An R Package for Distance Gradient Analysis in Spatial Transcriptomics' * 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 serialization versions ... OK * checking whether package 'SpatialFlux' can be installed ... WARNING Found the following significant warnings: Note: possible error in 'layout(clickmode = "event+select", ': unused arguments (clickmode = "event+select", title = "Click spots to select/deselect", xaxis = list(title = "X coordinate", scaleanchor = "y", scaleratio = 1), yaxis = list(title = "Y coordinate"), dragmode = "zoom", legend = list(title = list(text = "Clusters"), itemsizing = "constant")) Note: possible error in 'layout(p, xaxis = list(range = current_view$xaxis$range), ': unused arguments (xaxis = list(range = current_view$xaxis$range), yaxis = list(range = current_view$yaxis$range)) See 'd:/RCompile/CRANincoming/R-devel/SpatialFlux.Rcheck/00install.out' for details. Information on the location(s) of code generating the 'Note's can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to 'yes'. * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. Non-standard files/directories found at top level: 'docs' 'images' * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in 'NEWS.md': No news entries found. * 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 loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' imports not declared from: 'fs' 'readr' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE CoordMerge: no visible global function definition for 'str_sort' CoordMerge: no visible global function definition for 'str_detect' CoordMergeHD: no visible global function definition for 'str_sort' CoordMergeHD: no visible global function definition for 'str_detect' GeneGet: no visible global function definition for 'is' GeneGet: no visible global function definition for 'cutree' GeneVis: no visible global function definition for 'FetchData' GeneVis: no visible global function definition for '%>%' GeneVis: no visible global function definition for 'mutate' GeneVis: no visible global function definition for 'Cells' GeneVis: no visible global function definition for 'select' GeneVis: no visible global function definition for 'melt' GeneVis: no visible global function definition for 'ggplot' GeneVis: no visible global function definition for 'aes' GeneVis: no visible binding for global variable 'st' GeneVis: no visible binding for global variable 'value' GeneVis: no visible binding for global variable 'variable' GeneVis: no visible global function definition for 'geom_smooth' GeneVis: no visible global function definition for 'theme_classic' Pseudo2Flux: no visible global function definition for 'is' Pseudo2Flux: no visible global function definition for 'as' Pseudo2Flux: no visible global function definition for 'new' Pseudo2Flux: no visible global function definition for 'newCellDataSet' Pseudo2Flux: no visible global function definition for 'negbinomial.size' Pseudo2Flux: no visible global function definition for 'estimateSizeFactors' Pseudo2Flux: no visible global function definition for 'estimateDispersions' Pseudo2Flux: no visible global function definition for 'detectGenes' Pseudo2Flux: no visible binding for global variable 'num_cells_expressed' Pseudo2Flux: no visible global function definition for 'dispersionTable' Pseudo2Flux: no visible binding for global variable 'mean_expression' Pseudo2Flux: no visible binding for global variable 'dispersion_empirical' Pseudo2Flux: no visible binding for global variable 'dispersion_fit' Pseudo2Flux: no visible global function definition for 'setOrderingFilter' Pseudo2Flux: no visible global function definition for 'reduceDimension' Pseudo2Flux: no visible global function definition for 'orderCells' Pseudo2Flux: no visible global function definition for 'differentialGeneTest' Pseudo2FluxHD: no visible global function definition for 'is' Pseudo2FluxHD: no visible global function definition for 'as' Pseudo2FluxHD: no visible global function definition for 'new' Pseudo2FluxHD: no visible global function definition for 'newCellDataSet' Pseudo2FluxHD: no visible global function definition for 'negbinomial.size' Pseudo2FluxHD: no visible global function definition for 'estimateSizeFactors' Pseudo2FluxHD: no visible global function definition for 'estimateDispersions' Pseudo2FluxHD: no visible global function definition for 'detectGenes' Pseudo2FluxHD: no visible binding for global variable 'num_cells_expressed' Pseudo2FluxHD: no visible global function definition for 'dispersionTable' Pseudo2FluxHD: no visible binding for global variable 'mean_expression' Pseudo2FluxHD: no visible binding for global variable 'dispersion_empirical' Pseudo2FluxHD: no visible binding for global variable 'dispersion_fit' Pseudo2FluxHD: no visible global function definition for 'setOrderingFilter' Pseudo2FluxHD: no visible global function definition for 'reduceDimension' Pseudo2FluxHD: no visible global function definition for 'orderCells' Pseudo2FluxHD: no visible global function definition for 'differentialGeneTest' PseudoFlux: no visible global function definition for 'is' PseudoFlux: no visible global function definition for 'as' PseudoFlux: no visible global function definition for 'new' PseudoFlux: no visible global function definition for 'newCellDataSet' PseudoFlux: no visible global function definition for 'negbinomial.size' PseudoFlux: no visible global function definition for 'estimateSizeFactors' PseudoFlux: no visible global function definition for 'estimateDispersions' PseudoFlux: no visible global function definition for 'detectGenes' PseudoFlux: no visible binding for global variable 'num_cells_expressed' PseudoFlux: no visible global function definition for 'dispersionTable' PseudoFlux: no visible binding for global variable 'mean_expression' PseudoFlux: no visible binding for global variable 'dispersion_empirical' PseudoFlux: no visible binding for global variable 'dispersion_fit' PseudoFlux: no visible global function definition for 'setOrderingFilter' PseudoFlux: no visible global function definition for 'reduceDimension' PseudoFlux: no visible global function definition for 'orderCells' PseudoFlux: no visible global function definition for 'differentialGeneTest' PseudoM3Flux: no visible global function definition for 'is' PseudoM3Flux: no visible global function definition for 'as' PseudoM3Flux: no visible global function definition for 'new_cell_data_set' PseudoM3Flux: no visible global function definition for 'preprocess_cds' PseudoM3Flux: no visible global function definition for 'reduce_dimension' PseudoM3Flux: no visible global function definition for 'cluster_cells' PseudoM3Flux: no visible global function definition for 'learn_graph' PseudoM3Flux: no visible global function definition for 'order_cells' PseudoM3Flux: no visible global function definition for 'pseudotime' PseudoM3Flux: no visible global function definition for 'graph_test' PseudoM3Flux: no visible binding for global variable 'q_value' PseudoM3Flux: no visible binding for global variable 'morans_I' PseudoM3Flux: no visible global function definition for 'exprs' PseudoM3Flux: no visible global function definition for 'rowData' PseudoM3Flux : : no visible global function definition for 'smooth.spline' PseudoM3Flux : : no visible global function definition for 'sd' ScaleRatio: no visible global function definition for 'GetTissueCoordinates' ShinySelection: no visible global function definition for 'GetTissueCoordinates' ShinySelection: no visible global function definition for 'rainbow' ShinySelection: no visible global function definition for 'setNames' ShinySelection : server: no visible global function definition for 'reactiveVal' ShinySelection : server: no visible global function definition for 'renderPlotly' ShinySelection : server: no visible global function definition for '%>%' ShinySelection : server: no visible global function definition for 'plot_ly' ShinySelection : server: no visible global function definition for 'layout' ShinySelection : server: no visible global function definition for 'config' ShinySelection : server: no visible global function definition for 'event_register' ShinySelection : server: no visible global function definition for 'observeEvent' ShinySelection : server: no visible global function definition for 'event_data' ShinySelection : server: no visible global function definition for 'reactive' ShinySelection : server: no visible global function definition for 'renderText' ShinySelection : server: no visible global function definition for 'renderUI' ShinySelection : server: no visible global function definition for 'actionButton' ShinySelection : server: no visible global function definition for 'write.csv' ShinySelection: no visible global function definition for 'fluidPage' ShinySelection: no visible global function definition for 'plotlyOutput' ShinySelection: no visible global function definition for 'verbatimTextOutput' ShinySelection: no visible global function definition for 'fluidRow' ShinySelection: no visible global function definition for 'column' ShinySelection: no visible global function definition for 'uiOutput' ShinySelection: no visible global function definition for 'textOutput' ShinySelection: no visible global function definition for 'shinyApp' ShinySpots: no visible global function definition for 'is' ShinySpots: no visible global function definition for 'read.csv' ShinySpots: no visible binding for global variable 'barcode' Spatial2Flux: no visible global function definition for '%>%' Spatial2Flux: no visible global function definition for 'mutate' Spatial2Flux: no visible binding for global variable '...1' Spatial2Flux: no visible global function definition for 'select' Spatial2Flux: no visible binding for global variable 'imagerow' Spatial2Flux: no visible binding for global variable 'imagecol' Spatial2Flux: no visible binding for global variable 'barcode' Spatial2Flux: no visible global function definition for 'rowwise' Spatial2Flux: no visible global function definition for 'ungroup' Spatial2Flux: no visible binding for global variable 'st_abs' Spatial2FluxHD: no visible global function definition for '%>%' Spatial2FluxHD: no visible global function definition for 'mutate' Spatial2FluxHD: no visible binding for global variable '...1' Spatial2FluxHD: no visible global function definition for 'select' Spatial2FluxHD: no visible binding for global variable 'x' Spatial2FluxHD: no visible binding for global variable 'y' Spatial2FluxHD: no visible binding for global variable 'barcode' Spatial2FluxHD: no visible global function definition for 'rowwise' Spatial2FluxHD: no visible global function definition for 'ungroup' Spatial2FluxHD: no visible binding for global variable 'st_abs' SpatialCalc: no visible global function definition for 'read_csv' SpatialCalc: no visible global function definition for 'fromJSON' SpatialCalc: no visible global function definition for 'str_to_title' SpatialCalc: no visible global function definition for '%>%' SpatialCalc: no visible global function definition for 'arrange' SpatialCalc: no visible global function definition for 'desc' SpatialCalc: no visible global function definition for 'mutate' SpatialCalc: no visible global function definition for ':=' SpatialCalc: no visible global function definition for 'case_when' SpatialCalc: no visible global function definition for 'filter_at' SpatialCalc: no visible global function definition for 'vars' SpatialCalc: no visible global function definition for 'ends_with' SpatialCalc: no visible global function definition for 'any_vars' SpatialCalc: no visible binding for global variable '.' SpatialFlux: no visible global function definition for '%>%' SpatialFlux: no visible global function definition for 'mutate' SpatialFlux: no visible binding for global variable 'X' SpatialFlux: no visible global function definition for 'select' SpatialFlux: no visible binding for global variable 'imagerow' SpatialFlux: no visible binding for global variable 'imagecol' SpatialFlux: no visible binding for global variable 'barcode' SpatialFlux: no visible global function definition for 'contains' SpatialFlux: no visible global function definition for 'filter_if' SpatialFlux: no visible global function definition for 'all_vars' SpatialFlux: no visible binding for global variable '.' SpatialFlux: no visible global function definition for 'rowwise' SpatialFlux: no visible global function definition for 'ungroup' SpatialFlux: no visible binding for global variable 'st_abs' SpatialFluxHD: no visible global function definition for '%>%' SpatialFluxHD: no visible global function definition for 'rename' SpatialFluxHD: no visible binding for global variable 'x' SpatialFluxHD: no visible binding for global variable 'y' SpatialFluxHD: no visible global function definition for 'mutate' SpatialFluxHD: no visible binding for global variable 'X' SpatialFluxHD: no visible global function definition for 'select' SpatialFluxHD: no visible binding for global variable 'imagerow' SpatialFluxHD: no visible binding for global variable 'imagecol' SpatialFluxHD: no visible binding for global variable 'barcode' SpatialFluxHD: no visible global function definition for 'contains' SpatialFluxHD: no visible global function definition for 'filter_if' SpatialFluxHD: no visible global function definition for 'all_vars' SpatialFluxHD: no visible binding for global variable '.' SpatialFluxHD: no visible global function definition for 'rowwise' SpatialFluxHD: no visible global function definition for 'ungroup' SpatialFluxHD: no visible binding for global variable 'st_abs' SpatialShinyFlux: no visible global function definition for '%>%' SpatialShinyFlux: no visible global function definition for 'mutate' SpatialShinyFlux: no visible binding for global variable '...1' SpatialShinyFlux: no visible global function definition for 'select' SpatialShinyFlux: no visible binding for global variable 'imagerow' SpatialShinyFlux: no visible binding for global variable 'imagecol' SpatialShinyFlux: no visible binding for global variable 'barcode' SpatialShinyFlux: no visible global function definition for 'rowwise' SpatialShinyFlux: no visible global function definition for 'ungroup' SpatialShinyFlux: no visible binding for global variable 'st_abs' SpatialVis: no visible global function definition for 'Cells' SpatialVis: no visible binding for global variable 'st' SpatialVis: no visible global function definition for 'SpatialFeaturePlot' gradient_heatmap: no visible global function definition for 'colorRampPalette' gradient_heatmap: no visible global function definition for 'brewer.pal' gradient_heatmap: no visible global function definition for 'hclust' gradient_heatmap: no visible global function definition for 'dist' gradient_heatmap: no visible global function definition for 'cutree' gradient_heatmap: no visible global function definition for 'pheatmap' subset2Labels: no visible global function definition for 'Idents' subset2Labels: no visible global function definition for 'write.csv' subset2LabelsHD: no visible global function definition for 'Idents' subset2LabelsHD: no visible global function definition for 'GetTissueCoordinates' subset2LabelsHD: no visible global function definition for 'write.csv' subsetLabels: no visible global function definition for 'is' subsetLabels: no visible global function definition for 'Idents' subsetLabels: no visible global function definition for 'write.csv' Undefined global functions or variables: %>% . ...1 := Cells FetchData GetTissueCoordinates Idents SpatialFeaturePlot X actionButton aes all_vars any_vars arrange as barcode brewer.pal case_when cluster_cells colorRampPalette column config contains cutree desc detectGenes differentialGeneTest dispersionTable dispersion_empirical dispersion_fit dist ends_with estimateDispersions estimateSizeFactors event_data event_register exprs filter_at filter_if fluidPage fluidRow fromJSON geom_smooth ggplot graph_test hclust imagecol imagerow is layout learn_graph mean_expression melt morans_I mutate negbinomial.size new newCellDataSet new_cell_data_set num_cells_expressed observeEvent orderCells order_cells pheatmap plot_ly plotlyOutput preprocess_cds pseudotime q_value rainbow reactive reactiveVal read.csv read_csv reduceDimension reduce_dimension rename renderPlotly renderText renderUI rowData rowwise sd select setNames setOrderingFilter shinyApp smooth.spline st st_abs str_detect str_sort str_to_title textOutput theme_classic uiOutput ungroup value variable vars verbatimTextOutput write.csv x y Consider adding importFrom("grDevices", "colorRampPalette", "rainbow") importFrom("graphics", "layout") importFrom("methods", "as", "is", "new") importFrom("stats", "cutree", "dist", "hclust", "sd", "setNames", "smooth.spline") importFrom("utils", "read.csv", "write.csv") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). Found if() conditions comparing class() to string: File 'SpatialFlux/R/SpatialVis.R': if (is.null(file) || class(file) != "Seurat") ... File 'SpatialFlux/R/SpatialVis.R': if (is.null(object) || class(object) != "Seurat") ... Use inherits() (or maybe is()) instead. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * 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 examples ... NONE * checking for unstated dependencies in 'tests' ... OK * checking tests ... OK Running 'testthat.R' * checking PDF version of manual ... [13s] OK * checking HTML version of manual ... OK * DONE Status: 2 WARNINGs, 5 NOTEs