* using log directory ‘/srv/hornik/tmp/CRAN_pretest/UCASpatial.Rcheck’ * using R Under development (unstable) (2024-10-26 r87273) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.1 (1) Debian flang-new version 19.1.1 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘UCASpatial/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘UCASpatial’ version ‘1.0.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [2s/2s] NOTE Maintainer: ‘Yin Xu ’ New submission Non-FOSS package license (CC-BY-NC-ND 4.0) Possibly misspelled words in DESCRIPTION: Deconvolute (16:14) Deconvolution (3:8) Transcriptomics (3:34) scRNA (16:107) transcriptomics (16:38) * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘UCASpatial’ can be installed ... [20s/20s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: CC-BY-NC-ND 4.0 Standardizable: FALSE * 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 ... [6s/6s] OK * checking whether the package can be loaded with stated dependencies ... [6s/6s] OK * checking whether the package can be unloaded cleanly ... [6s/6s] OK * checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK * checking whether the namespace can be unloaded cleanly ... [6s/6s] OK * checking loading without being on the library search path ... [6s/6s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' imports not declared from: ‘tibble’ ‘tidyr’ 'library' or 'require' calls not declared from: ‘DropletUtils’ ‘Matrix’ ‘Metrics’ ‘NMF’ ‘RcppML’ ‘Seurat’ ‘cowplot’ ‘dplyr’ ‘edgeR’ ‘entropy’ ‘ggplot2’ ‘grid’ ‘jpeg’ ‘nnls’ ‘philentropy’ ‘png’ ‘purrr’ ‘reshape2’ ‘stringr’ ‘tibble’ ‘tidyr’ 'library' or 'require' calls in package code: ‘DropletUtils’ ‘Matrix’ ‘Metrics’ ‘NMF’ ‘RcppML’ ‘Seurat’ ‘cowplot’ ‘dplyr’ ‘edgeR’ ‘entropy’ ‘ggplot2’ ‘grid’ ‘jpeg’ ‘nnls’ ‘philentropy’ ‘png’ ‘purrr’ ‘reshape2’ ‘stringr’ ‘tibble’ ‘tidyr’ 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 ... [26s/26s] NOTE CalculateEntropy: no visible global function definition for ‘Idents’ CalculateEntropy: no visible global function definition for ‘WhichCells’ CalculateEntropy: no visible global function definition for ‘group_by’ CalculateEntropy: no visible binding for global variable ‘gene’ CalculateEntropy: no visible global function definition for ‘mutate’ CalculateEntropy: no visible binding for global variable ‘avg_logFC’ CalculateEntropy: no visible binding for global variable ‘pre_weight’ CalculateEntropy: no visible global function definition for ‘top_n’ CalculateEntropy: no visible binding for global variable ‘p_val’ CalculateEntropy: no visible global function definition for ‘txtProgressBar’ CalculateEntropy: no visible global function definition for ‘setTxtProgressBar’ CalculateEntropy: no visible binding for global variable ‘entropy.adjust’ CalculateEntropy: no visible binding for global variable ‘cluster’ CalculateEntropy: no visible binding for global variable ‘weight’ UCASpatial_deconv: no visible global function definition for ‘is’ UCASpatial_deconv: no visible global function definition for ‘DefaultAssay<-’ UCASpatial_deconv: no visible global function definition for ‘Idents<-’ UCASpatial_deconv: no visible global function definition for ‘rename’ UCASpatial_deconv: no visible binding for global variable ‘avg_log2FC’ UCASpatial_deconv: no visible binding for global variable ‘cluster’ UCASpatial_deconv: no visible global function definition for ‘group_by’ UCASpatial_deconv: no visible binding for global variable ‘gene’ UCASpatial_deconv: no visible global function definition for ‘filter’ UCASpatial_deconv: no visible binding for global variable ‘weight’ UCASpatial_deconv: no visible global function definition for ‘mutate’ UCASpatial_deconv: no visible binding for global variable ‘ent_weight’ UCASpatial_deconv: no visible binding for global variable ‘ent.adj’ UCASpatial_deconv: no visible binding for global variable ‘cos_weight’ UCASpatial_deconvolution_nmf: no visible global function definition for ‘txtProgressBar’ UCASpatial_deconvolution_nmf: no visible global function definition for ‘setTxtProgressBar’ UCASpatial_downsample: no visible global function definition for ‘Idents<-’ UCASpatial_downsample : : no visible global function definition for ‘WhichCells’ UCASpatial_downsample : : no visible global function definition for ‘if_else’ UCASpatial_downsample : : : no visible global function definition for ‘GetAssayData’ UCASpatial_downsample : : : no visible binding for global variable ‘var’ cosg: no visible global function definition for ‘as’ cosg: no visible global function definition for ‘select_top_n’ cut_markers2: no visible binding for global variable ‘cluster’ cut_markers2: no visible binding for global variable ‘weight’ cut_markers2: no visible binding for global variable ‘gene’ dot_plot_profiles_fun: no visible binding for global variable ‘clust_vr’ dot_plot_profiles_fun: no visible binding for global variable ‘id’ dot_plot_profiles_fun: no visible binding for global variable ‘weights’ dot_plot_profiles_fun: no visible global function definition for ‘aes’ dot_plot_profiles_fun: no visible binding for global variable ‘topics’ dot_plot_profiles_fun: no visible binding for global variable ‘median’ dot_plot_profiles_fun: no visible binding for global variable ‘.’ dot_plot_profiles_fun: no visible binding for global variable ‘Cell type’ dot_plot_profiles_fun: no visible binding for global variable ‘value’ dot_plot_profiles_fun: no visible binding for global variable ‘Topics’ init_nmf_matr: no visible binding for global variable ‘cluster’ init_nmf_matr: no visible binding for global variable ‘weight’ init_nmf_matr: no visible global function definition for ‘bind_rows’ meta_filter: no visible global function definition for ‘DefaultAssay<-’ meta_filter: no visible global function definition for ‘FindVariableFeatures’ meta_filter: no visible global function definition for ‘ScaleData’ meta_filter: no visible global function definition for ‘RunPCA’ meta_filter: no visible global function definition for ‘VariableFeatures’ meta_filter: no visible global function definition for ‘FindNeighbors’ meta_filter: no visible global function definition for ‘FindClusters’ new_simulate: no visible global function definition for ‘is’ new_simulate: no visible binding for global variable ‘n.celltype’ new_simulate: no visible binding for global variable ‘n.cell’ new_simulate: no visible global function definition for ‘txtProgressBar’ new_simulate : : no visible global function definition for ‘mutate’ new_simulate : : no visible global function definition for ‘all_of’ new_simulate : : no visible binding for global variable ‘weight’ new_simulate : : no visible global function definition for ‘sym’ new_simulate : : no visible binding for global variable ‘sum_weights’ new_simulate : : no visible global function definition for ‘setTxtProgressBar’ new_simulate: no visible binding for global variable ‘.’ predict_spatial_mixtures_nmf_weighted: no visible binding for global variable ‘sd’ predict_spatial_mixtures_nmf_weighted: no visible global function definition for ‘group_by’ predict_spatial_mixtures_nmf_weighted: no visible binding for global variable ‘gene’ predict_spatial_mixtures_nmf_weighted: no visible binding for global variable ‘weight’ prep_seobj_topic_fun: no visible global function definition for ‘is’ seed_init_mtrx_nmf: no visible global function definition for ‘bind_rows’ spatial_scatterpie: no visible global function definition for ‘is’ spatial_scatterpie: no visible binding for global variable ‘.’ spatial_scatterpie: no visible binding for global variable ‘rsum’ spatial_scatterpie: no visible binding for global variable ‘imagerow’ spatial_scatterpie: no visible binding for global variable ‘imagecol’ spatial_scatterpie: no visible binding for global variable ‘imagecol_scaled’ spatial_scatterpie: no visible binding for global variable ‘imagerow_scaled’ spatial_scatterpie: no visible global function definition for ‘scale_fill_manual’ test_MultiIndex: no visible global function definition for ‘JSD’ test_MultiIndex: no visible global function definition for ‘quantile’ test_Pearson: no visible global function definition for ‘cor’ test_Pearson_spotlevel: no visible global function definition for ‘cor’ test_RMSE: no visible global function definition for ‘rmse’ test_RMSE_spotlevel: no visible global function definition for ‘rmse’ test_Spearman: no visible global function definition for ‘cor’ test_Spearman_spotlevel: no visible global function definition for ‘cor’ topic_profile_per_cluster_nmf: no visible global function definition for ‘is’ topic_profile_per_cluster_nmf: no visible binding for global variable ‘clust_vr’ topic_profile_per_cluster_nmf: no visible binding for global variable ‘median’ train_nsnmfmod: no visible binding for global variable ‘sd’ Undefined global functions or variables: . Cell type DefaultAssay<- FindClusters FindNeighbors FindVariableFeatures GetAssayData Idents Idents<- JSD RunPCA ScaleData Topics VariableFeatures WhichCells aes all_of as avg_log2FC avg_logFC bind_rows clust_vr cluster cor cos_weight ent.adj ent_weight entropy.adjust filter gene group_by id if_else imagecol imagecol_scaled imagerow imagerow_scaled is median mutate n.cell n.celltype p_val pre_weight quantile rename rmse rsum scale_fill_manual sd select_top_n setTxtProgressBar sum_weights sym top_n topics txtProgressBar value var weight weights Consider adding importFrom("methods", "as", "is") importFrom("stats", "cor", "filter", "median", "quantile", "sd", "var", "weights") importFrom("utils", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... [0s/0s] 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 ... WARNING Undocumented arguments in Rd file 'UCASpatial_deconv.Rd' ‘output_path’ ‘min.pct’ ‘logfc.threshold’ ‘min.diff.pct’ ‘downsample_n’ ‘remove.RPL’ ‘remove.MT’ ‘cos.filter’ ‘cos.mu’ ‘cos.n_genes_user’ ‘marker.slot’ ‘unit’ ‘random.seed’ ‘meta.filter’ ‘nmf.tol’ ‘meta.assay’ ‘meta.ndims’ ‘meta.resolution’ ‘meta.purity’ ‘ent.filter.threshold’ ‘cos.filter.threshold’ ‘weight.filter.threshold’ Undocumented arguments in Rd file 'new_simulate.Rd' ‘verbose’ Undocumented arguments in Rd file 'test_MultiIndex.Rd' ‘deconv_result’ ‘synthetic_comp’ 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 examples ... NONE * checking PDF version of manual ... [3s/2s] OK * checking HTML version of manual ... [0s/0s] OK * checking for code which exercises the package ... WARNING No examples, no tests, no vignettes * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 4 WARNINGs, 2 NOTEs