* using log directory 'd:/RCompile/CRANincoming/R-devel/SmartX.Rcheck' * using R Under development (unstable) (2025-11-05 r88988 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 * checking for file 'SmartX/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'SmartX' version '0.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Haitao Xiang ' New submission License components with restrictions and base license permitting such: MIT + file LICENSE File 'LICENSE': MIT License Copyright (c) 2025 Haitao Xiang Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Possibly misspelled words in DESCRIPTION: Multiomic (3:16, 7:31) eXploration (3:60, 8:5) transcriptomics (9:29) Suggests or Enhances not in mainstream repositories: CellChat No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: person(given = "Haitao", family = "Xiang", role = c("aut", "cre"), email = "dr.haitaoxiang@gmail.com") as necessary. Package has a VignetteBuilder field but no prebuilt vignette index. * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: 'CellChat' Vignette dependency required without any vignettes: 'knitr' * 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 'SmartX' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... NOTE Non-standard file/directory found at top level: 'session_info.txt' * 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 loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING 'library' or 'require' calls not declared from: 'ggrepel' 'pals' 'patchwork' 'library' or 'require' calls in package code: 'CellChat' 'ComplexHeatmap' 'clusterProfiler' 'enrichplot' 'ggrepel' 'org.Mm.eg.db' 'pals' 'patchwork' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [20s] NOTE GOtermsOverlapJaccard: no visible binding for global variable 'p.adjust' GOtermsOverlapJaccard: no visible global function definition for 'desc' GOtermsOverlapJaccard: no visible binding for global variable 'Count' createCountsDf: no visible binding for global variable '.' createCountsDf: no visible binding for global variable 'groupID' createCountsDf: no visible binding for global variable 'cellCounts' createCountsDf: no visible binding for global variable 'percent' degOverlapJaccard: no visible global function definition for 'desc' degOverlapJaccard: no visible binding for global variable 'avg_log2FC' drawExprDotPlot: no visible global function definition for 'pdf' drawExprDotPlot: no visible global function definition for 'dev.off' drawFeatureExprVlnPlot: no visible global function definition for 'alphabet' drawFeatureExprVlnPlot: no visible global function definition for 'alphabet2' drawFeatureExprVlnPlot: no visible global function definition for 'pdf' drawFeatureExprVlnPlot: no visible global function definition for 'dev.off' drawStackBar: no visible global function definition for 'n' drawStackBar: no visible binding for global variable 'count' drawStackBar: no visible binding for global variable 'proportion' drawStackBar: no visible global function definition for 'pdf' drawStackBar: no visible global function definition for 'dev.off' drawUMAP: no visible global function definition for 'pdf' drawUMAP: no visible global function definition for 'dev.off' plot_correlation_heatmap_complex: no visible global function definition for 'colorRampPalette' plot_correlation_heatmap_complex: no visible global function definition for 'hcl.colors' plot_correlation_heatmap_complex: no visible global function definition for 'Heatmap' plot_correlation_heatmap_complex: no visible global function definition for 'pdf' plot_correlation_heatmap_complex: no visible global function definition for 'draw' plot_correlation_heatmap_complex: no visible global function definition for 'dev.off' run_DEG: no visible global function definition for 'all_of' run_DEG: no visible binding for global variable 'sampleA' run_DEG: no visible binding for global variable 'sampleB' run_DEG: no visible binding for global variable 'gene' run_DEG: no visible binding for global variable 'p_val' run_DEG: no visible binding for global variable 'p_val_adj' run_DEG: no visible binding for global variable 'avg_log2FC' run_DEG: no visible binding for global variable 'pct.1' run_DEG: no visible binding for global variable 'pct.2' run_DEG: no visible binding for global variable 'log2pctDiff' run_DEG: no visible binding for global variable 'cluster' run_GOanalysis: no visible global function definition for 'pdf' run_GOanalysis: no visible binding for global variable 'p_val' run_GOanalysis: no visible global function definition for 'desc' run_GOanalysis: no visible binding for global variable 'avg_log2FC' run_GOanalysis: no visible binding for global variable 'gene' run_GOanalysis: no visible binding for global variable 'p_val_adj' run_GOanalysis: no visible binding for global variable 'label' run_GOanalysis: no visible global function definition for 'enrichGO' run_GOanalysis: no visible binding for global variable 'org.Mm.eg.db' run_GOanalysis: no visible global function definition for 'dotplot' run_GOanalysis: no visible global function definition for 'dev.off' run_cellChat: no visible binding for global variable 'CellChatDB.mouse' run_cellChat: no visible global function definition for 'createCellChat' run_cellChat: no visible global function definition for 'subsetData' run_cellChat: no visible global function definition for 'identifyOverExpressedGenes' run_cellChat: no visible global function definition for 'identifyOverExpressedInteractions' run_cellChat: no visible global function definition for 'computeCommunProb' run_cellChat: no visible global function definition for 'filterCommunication' run_cellChat: no visible global function definition for 'computeCommunProbPathway' run_cellChat: no visible global function definition for 'aggregateNet' run_cellChat: no visible global function definition for 'write.csv' run_cellChat: no visible global function definition for 'subsetCommunication' run_cellChat: no visible global function definition for 'pdf' run_cellChat: no visible global function definition for 'layout' run_cellChat: no visible global function definition for 'par' run_cellChat: no visible global function definition for 'netVisual_circle' run_cellChat: no visible global function definition for 'dev.off' Undefined global functions or variables: . CellChatDB.mouse Count Heatmap aggregateNet all_of alphabet alphabet2 avg_log2FC cellCounts cluster colorRampPalette computeCommunProb computeCommunProbPathway count createCellChat desc dev.off dotplot draw enrichGO filterCommunication gene groupID hcl.colors identifyOverExpressedGenes identifyOverExpressedInteractions label layout log2pctDiff n netVisual_circle org.Mm.eg.db p.adjust p_val p_val_adj par pct.1 pct.2 pdf percent proportion sampleA sampleB subsetCommunication subsetData write.csv Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "hcl.colors", "pdf") importFrom("graphics", "layout", "par") importFrom("stats", "p.adjust") importFrom("utils", "write.csv") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... NOTE Invalid package aliases in Rd file 'scRNAToolkit-package.Rd': 'scRNAToolkit-package' * 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 ... OK * checking PDF version of manual ... [12s] OK * checking HTML version of manual ... OK * DONE Status: 1 WARNING, 5 NOTEs