* using log directory ‘/srv/hornik/tmp/CRAN_pretest/SIOSSAR.Rcheck’ * using R Under development (unstable) (2026-03-27 r89733) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.8 (3+b1) Debian flang version 21.1.8 (3+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * current time: 2026-03-28 08:33:06 UTC * checking for file ‘SIOSSAR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SIOSSAR’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Jia Qing ’ New submission Possibly misspelled words in DESCRIPTION: hotspots (12:69) transcriptomic (12:91) Suggests or Enhances not in mainstream repositories: SeuratData Size of tarball: 21556366 bytes * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: ‘SeuratData’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: SIOSSAR/.Rbuildignore These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. CRAN-pack does not know about SIOSSAR/.Rbuildignore * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘SIOSSAR’ can be installed ... [16s/16s] WARNING Found the following significant warnings: Warning: replacing previous import ‘Matrix::cov2cor’ by ‘stats::cov2cor’ when loading ‘SIOSSAR’ Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘SIOSSAR’ Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘SIOSSAR’ Warning: replacing previous import ‘Matrix::toeplitz’ by ‘stats::toeplitz’ when loading ‘SIOSSAR’ Warning: replacing previous import ‘Matrix::update’ by ‘stats::update’ when loading ‘SIOSSAR’ Warning: replacing previous import ‘Matrix::unpack’ by ‘tidyr::unpack’ when loading ‘SIOSSAR’ Warning: replacing previous import ‘Matrix::expand’ by ‘tidyr::expand’ when loading ‘SIOSSAR’ Warning: replacing previous import ‘magrittr::extract’ by ‘tidyr::extract’ when loading ‘SIOSSAR’ Warning: replacing previous import ‘Matrix::pack’ by ‘tidyr::pack’ when loading ‘SIOSSAR’ See ‘/srv/hornik/tmp/CRAN_pretest/SIOSSAR.Rcheck/00install.out’ for details. * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. Non-standard file/directory found at top level: ‘SIOSSAR’ * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... WARNING Found the following file with non-ASCII characters: R/SIOSSAR_functions.R Portable packages must use only ASCII characters in their R code and NAMESPACE directives, except perhaps in comments. Use \uxxxx escapes for other characters. Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII characters in files. * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [4s/4s] OK * checking whether the package can be loaded with stated dependencies ... [3s/3s] OK * checking whether the package can be unloaded cleanly ... [3s/3s] OK * checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK * checking whether the namespace can be unloaded cleanly ... [3s/3s] OK * checking loading without being on the library search path ... [3s/3s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘scales’ 'library' or 'require' calls not declared from: ‘Seurat’ ‘dplyr’ ‘ggalluvial’ ‘ggplot2’ ‘pheatmap’ 'library' or 'require' calls in package code: ‘Seurat’ ‘dplyr’ ‘ggalluvial’ ‘ggplot2’ ‘pheatmap’ 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 ... [15s/15s] NOTE compute_siossar: no visible global function definition for ‘data’ compute_siossar: no visible binding for global variable ‘from’ compute_siossar: no visible binding for global variable ‘distance’ compute_siossar: no visible global function definition for ‘txtProgressBar’ compute_siossar: no visible global function definition for ‘setTxtProgressBar’ construct_adj_wide: no visible binding for global variable ‘from’ construct_adj_wide: no visible binding for global variable ‘value’ hot_region_plot: no visible global function definition for ‘theme’ hot_region_plot: no visible global function definition for ‘element_text’ hot_region_plot: no visible global function definition for ‘element_rect’ hot_region_plot: no visible global function definition for ‘scale_fill_manual’ hplot: no visible global function definition for ‘scale_fill_manual’ hplot: no visible global function definition for ‘theme’ hplot: no visible global function definition for ‘element_text’ hplot: no visible global function definition for ‘element_rect’ norm: no visible global function definition for ‘packageVersion’ norm: no visible global function definition for ‘LayerData’ plot_PPI_sankey: no visible binding for global variable ‘ligand’ plot_PPI_sankey: no visible binding for global variable ‘receptor’ plot_PPI_sankey: no visible global function definition for ‘ggplot’ plot_PPI_sankey: no visible global function definition for ‘aes’ plot_PPI_sankey: no visible binding for global variable ‘freq’ plot_PPI_sankey: no visible global function definition for ‘geom_alluvium’ plot_PPI_sankey: no visible global function definition for ‘geom_stratum’ plot_PPI_sankey: no visible global function definition for ‘geom_text’ plot_PPI_sankey: no visible global function definition for ‘after_stat’ plot_PPI_sankey: no visible binding for global variable ‘stratum’ plot_PPI_sankey: no visible global function definition for ‘scale_x_discrete’ plot_PPI_sankey: no visible global function definition for ‘theme_bw’ plot_PPI_sankey: no visible global function definition for ‘theme’ plot_PPI_sankey: no visible global function definition for ‘element_blank’ plot_top_pathway_heatmap: no visible global function definition for ‘pheatmap’ score_plot: no visible global function definition for ‘theme’ score_plot: no visible global function definition for ‘element_text’ score_plot: no visible global function definition for ‘element_rect’ score_plot: no visible global function definition for ‘scale_fill_gradientn’ Undefined global functions or variables: LayerData aes after_stat data distance element_blank element_rect element_text freq from geom_alluvium geom_stratum geom_text ggplot ligand packageVersion pheatmap receptor scale_fill_gradientn scale_fill_manual scale_x_discrete setTxtProgressBar stratum theme theme_bw txtProgressBar value Consider adding importFrom("utils", "data", "packageVersion", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'compute_siossar.Rd': \usage lines wider than 90 characters: compute_siossar(object, LR_PPI = "high_ppi_list", pathway, norm="NormalizeData" ,verbose = TRUE) These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘high_ppi_list’ ‘low_ppi_list’ ‘medium_ppi_list’ Undocumented data sets: ‘high_ppi_list’ ‘low_ppi_list’ ‘medium_ppi_list’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'ISs.Rd' ‘aa’ ‘topn_sm’ ‘SM_exp’ Documented arguments not in \usage in Rd file 'ISs.Rd': ‘aa:’ ‘SM_exp:’ ‘topn_sm:’ Undocumented arguments in Rd file 'RandomWalk2igraph.Rd' ‘igraphM’ ‘VertexWeight’ ‘EdgeWeight’ ‘gamma’ Documented arguments not in \usage in Rd file 'RandomWalk2igraph.Rd': ‘igraphM:’ ‘VertexWeight:’ ‘EdgeWeight:’ ‘gamma:’ Undocumented arguments in Rd file 'compute_siossar.Rd' ‘object’ ‘LR_PPI’ ‘pathway’ ‘norm’ ‘verbose’ Documented arguments not in \usage in Rd file 'compute_siossar.Rd': ‘object:’ ‘LR_PPI:’ ‘pathway:’ ‘norm:’ ‘verbose:’ Undocumented arguments in Rd file 'construct_adj_long.Rd' ‘M’ Documented arguments not in \usage in Rd file 'construct_adj_long.Rd': ‘M:’ Undocumented arguments in Rd file 'construct_adj_wide.Rd' ‘dist_long_sub’ Documented arguments not in \usage in Rd file 'construct_adj_wide.Rd': ‘dist_long_sub:’ Undocumented arguments in Rd file 'hplot.Rd' ‘show_layers’ ‘layer_colors’ Documented arguments not in \usage in Rd file 'hplot.Rd': ‘level’ Undocumented arguments in Rd file 'membrane_mean.Rd' ‘exp’ ‘gene’ Documented arguments not in \usage in Rd file 'membrane_mean.Rd': ‘exp:’ ‘gene:’ Undocumented arguments in Rd file 'norm.Rd' ‘object’ ‘norm’ Documented arguments not in \usage in Rd file 'norm.Rd': ‘object:’ ‘norm:’ Undocumented arguments in Rd file 'run_rwr.Rd' ‘Network’ ‘all_spot’ ‘topn_sm’ Documented arguments not in \usage in Rd file 'run_rwr.Rd': ‘Network:’ ‘all_spot:’ ‘topn_sm:’ Undocumented arguments in Rd file 'secret_mean.Rd' ‘exp’ ‘gene’ Documented arguments not in \usage in Rd file 'secret_mean.Rd': ‘exp:’ ‘gene:’ Undocumented arguments in Rd file 'top_secret.Rd' ‘SM_exp’ Documented arguments not in \usage in Rd file 'top_secret.Rd': ‘SM_exp:’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [3s/3s] OK * checking LazyData ... WARNING LazyData DB of 11.0 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [4s/4s] ERROR Running examples in ‘SIOSSAR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ISs > ### Title: Integrated scores > ### Aliases: ISs > > ### ** Examples > > IS <- ISs(aa,topn_sm,SM_exp) Error: object 'aa' not found Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [7s/7s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘spatial_analysis_tutorial.Rmd’ using rmarkdown Warning in eng_r(options) : Failed to tidy R code in chunk 'setup'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Quitting from spatial_analysis_tutorial.Rmd:77-108 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `norm()`: ! no slot of name "data" for this object of class "Assay5" --- Backtrace: ▆ 1. └─SIOSSAR::compute_siossar(...) 2. └─SIOSSAR::norm(object, norm) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'spatial_analysis_tutorial.Rmd' failed with diagnostics: no slot of name "data" for this object of class "Assay5" --- failed re-building ‘spatial_analysis_tutorial.Rmd’ SUMMARY: processing the following file failed: ‘spatial_analysis_tutorial.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [2s/2s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 6 WARNINGs, 5 NOTEs