* using log directory ‘/srv/hornik/tmp/CRAN/S2IsoMEr.Rcheck’ * using R Under development (unstable) (2024-08-17 r87027) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘S2IsoMEr/DESCRIPTION’ ... OK * this is package ‘S2IsoMEr’ version ‘0.3.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/9s] NOTE Maintainer: ‘Bishoy Wadie ’ New submission Possibly misspelled words in DESCRIPTION: MSEA (11:109) Overrepresentation (11:35) metabolomics (11:142) Found the following (possibly) invalid URLs: URL: http://software.broadinstitute.org/gsea/doc/GSEAUserGuideTEXT.htm#_Running_a_Leading (moved to https://software.broadinstitute.org/gsea/doc/GSEAUserGuideTEXT.htm#_Running_a_Leading) From: man/simple_fgsea.Rd Status: 301 Message: Moved Permanently URL: https://academic.oup.com/bioinformatics/article/39/1/btac726/6827287 From: README.md Status: 403 Message: Forbidden URL: https://academic.oup.com/bioinformaticsadvances/article/2/1/vbac016/6544613?login=true From: man/decouple_ORA_wrapper.Rd Status: 403 Message: Forbidden URL: https://academic.oup.com/nar/article/38/suppl_2/W71/1101310 From: inst/doc/MSEA_enrichment-single_cell_metabolomics.html Status: 403 Message: Forbidden For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. The Title field should be in title case. Current version is: ‘Spatial and single-cell Isomeric metabolite enrichment in R’ In title case that is: ‘Spatial and Single-Cell Isomeric Metabolite Enrichment in R’ Size of tarball: 37988692 bytes * 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 serialization versions ... OK * checking whether package ‘S2IsoMEr’ can be installed ... [264s/264s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘Rprof.out’ ‘S2IsoMEr.Rproj’ * 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [28s/28s] NOTE .ora_analysis: no visible global function definition for ‘%>%’ .ora_analysis: no visible binding for global variable ‘condition’ .ora_analysis: no visible global function definition for ‘everything’ .ora_analysis: no visible binding for global variable ‘p_value’ .ora_analysis: no visible binding for global variable ‘statistic’ .ora_analysis: no visible binding for global variable ‘score’ .ora_analysis: no visible binding for global variable ‘TP’ .ora_analysis: no visible binding for global variable ‘FP’ .ora_analysis: no visible binding for global variable ‘FN’ .ora_analysis: no visible binding for global variable ‘TN’ .ora_analysis: no visible binding for global variable ‘TP_markers’ .ora_analysis_simple: no visible global function definition for ‘%>%’ .ora_analysis_simple: no visible binding for global variable ‘condition’ .ora_analysis_simple: no visible global function definition for ‘everything’ .ora_analysis_simple: no visible binding for global variable ‘p_value’ .ora_analysis_simple: no visible binding for global variable ‘statistic’ .ora_analysis_simple: no visible binding for global variable ‘score’ .ora_analysis_simple: no visible binding for global variable ‘TP’ .ora_analysis_simple: no visible binding for global variable ‘FP’ .ora_analysis_simple: no visible binding for global variable ‘FN’ .ora_analysis_simple: no visible binding for global variable ‘TN’ .ora_analysis_simple: no visible binding for global variable ‘TP_markers’ .ora_fisher_exact_test: no visible global function definition for ‘%>%’ Run_bootstrap_MSEA: no visible global function definition for ‘%>%’ Run_bootstrap_MSEA: no visible global function definition for ‘weighted.mean’ Run_bootstrap_MSEA : : no visible global function definition for ‘%>%’ Run_bootstrap_MSEA : : : no visible global function definition for ‘ks.test.2’ Run_bootstrap_MSEA : : no visible global function definition for ‘bind_rows’ Run_bootstrap_MSEA: no visible global function definition for ‘bind_rows’ Run_bootstrap_MSEA : : no visible binding for global variable ‘pathway’ Run_bootstrap_MSEA : : no visible binding for global variable ‘bootstrap’ Run_bootstrap_MSEA : : no visible binding for global variable ‘size’ Run_bootstrap_MSEA : : no visible binding for global variable ‘ES’ Run_bootstrap_MSEA : : no visible binding for global variable ‘pval’ Run_bootstrap_MSEA : : no visible binding for global variable ‘NES’ Run_bootstrap_MSEA: no visible binding for global variable ‘Term’ Run_bootstrap_MSEA: no visible binding for global variable ‘fraction’ Run_bootstrap_MSEA: no visible binding for global variable ‘NES’ Run_bootstrap_MSEA: no visible binding for global variable ‘bootstrap’ Run_bootstrap_MSEA: no visible global function definition for ‘p.adjust’ Run_bootstrap_MSEA: no visible binding for global variable ‘p_value’ Run_bootstrap_MSEA: no visible global function definition for ‘median’ Run_bootstrap_MSEA: no visible binding for global variable ‘n’ Run_bootstrap_MSEA: no visible global function definition for ‘sd’ Run_bootstrap_MSEA: no visible binding for global variable ‘q.value’ Run_bootstrap_MSEA: no visible binding for global variable ‘q.value_combined’ Run_bootstrap_ORA: no visible global function definition for ‘%>%’ Run_enrichment: no visible global function definition for ‘%>%’ Run_enrichment: no visible binding for global variable ‘p.val’ Run_enrichment: no visible binding for global variable ‘pct.diff’ Run_simple_MSEA: no visible global function definition for ‘%>%’ Run_simple_MSEA : : no visible global function definition for ‘ks.test.2’ Run_simple_MSEA: no visible global function definition for ‘bind_rows’ Run_simple_MSEA: no visible binding for global variable ‘pathway’ Run_simple_MSEA: no visible binding for global variable ‘size’ Run_simple_MSEA: no visible binding for global variable ‘ES’ Run_simple_MSEA: no visible binding for global variable ‘pval’ Run_simple_MSEA: no visible binding for global variable ‘padj’ Run_simple_MSEA: no visible binding for global variable ‘NES’ Run_simple_MSEA: no visible binding for global variable ‘Term’ Run_simple_ORA: no visible global function definition for ‘%>%’ Run_simple_ORA : : no visible global function definition for ‘%>%’ Run_simple_ORA: no visible global function definition for ‘mutate’ Run_simple_ORA: no visible global function definition for ‘p.adjust’ Run_simple_ORA: no visible binding for global variable ‘p_value’ Run_simple_ORA: no visible binding for global variable ‘TP’ barplot_MSEA_boot.S2IsoMEr: no visible global function definition for ‘%>%’ barplot_MSEA_boot.S2IsoMEr: no visible binding for global variable ‘p_value’ barplot_MSEA_boot.S2IsoMEr: no visible binding for global variable ‘NES’ barplot_MSEA_boot.S2IsoMEr: no visible binding for global variable ‘fraction’ barplot_MSEA_boot.S2IsoMEr: no visible binding for global variable ‘Term’ barplot_MSEA_boot.S2IsoMEr: no visible binding for global variable ‘bootstrap’ barplot_MSEA_boot.S2IsoMEr: no visible binding for global variable ‘total_bootstrap’ barplot_MSEA_boot.S2IsoMEr: no visible global function definition for ‘median’ barplot_MSEA_boot.S2IsoMEr: no visible binding for global variable ‘n’ barplot_MSEA_boot.S2IsoMEr: no visible global function definition for ‘p.adjust’ barplot_MSEA_boot.S2IsoMEr: no visible binding for global variable ‘q.value’ barplot_MSEA_boot.S2IsoMEr: no visible binding for global variable ‘q.value_combined’ barplot_MSEA_boot.S2IsoMEr: no visible binding for global variable ‘.’ barplot_MSEA_boot.S2IsoMEr: no visible global function definition for ‘reorder’ barplot_MSEA_boot.S2IsoMEr: no visible global function definition for ‘element_text’ barplot_MSEA_boot.S2IsoMEr: no visible global function definition for ‘desc’ barplot_MSEA_boot.S2IsoMEr: no visible binding for global variable ‘up_down’ barplot_MSEA_boot.S2IsoMEr: no visible binding for global variable ‘q.value_clipped’ barplot_ORA_boot : : no visible global function definition for ‘%>%’ barplot_ORA_boot: no visible global function definition for ‘%>%’ barplot_ORA_boot: no visible binding for global variable ‘Term’ barplot_ORA_boot: no visible binding for global variable ‘Condition’ barplot_ORA_boot: no visible binding for global variable ‘OR’ barplot_ORA_boot: no visible binding for global variable ‘n’ barplot_ORA_boot: no visible binding for global variable ‘Term_label’ barplot_ORA_boot: no visible binding for global variable ‘ES_median’ barplot_ORA_boot: no visible binding for global variable ‘ES_max’ barplot_ORA_boot: no visible binding for global variable ‘ES_min’ barplot_ORA_boot: no visible binding for global variable ‘p.value_combined’ barplot_ORA_boot: no visible binding for global variable ‘q.value_combined’ barplot_ORA_boot: no visible global function definition for ‘position_dodge’ barplot_ORA_boot: no visible global function definition for ‘scale_fill_gradient’ barplot_ORA_simple: no visible global function definition for ‘%>%’ barplot_ORA_simple: no visible global function definition for ‘reorder’ barplot_ORA_simple: no visible binding for global variable ‘Term’ barplot_ORA_simple: no visible binding for global variable ‘score’ barplot_ORA_simple: no visible binding for global variable ‘Significance’ barplot_ORA_simple: no visible global function definition for ‘aes’ barplot_ORA_simple: no visible binding for global variable ‘TP’ barplot_ORA_simple: no visible global function definition for ‘position_dodge’ barplot_ORA_simple: no visible global function definition for ‘element_text’ collapse_ORA_boot_multi_cond: no visible global function definition for ‘%>%’ compare_metabo_distr: no visible global function definition for ‘%>%’ compare_metabo_distr: no visible binding for global variable ‘condition’ compare_metabo_distr: no visible binding for global variable ‘intens’ compare_metabo_distr: no visible global function definition for ‘median’ compare_metabo_distr: no visible binding for global variable ‘median’ compare_metabo_distr: no visible global function definition for ‘element_text’ decouple_ORA_wrapper: no visible global function definition for ‘%>%’ decouple_ORA_wrapper: no visible binding for global variable ‘condition’ decouple_ORA_wrapper: no visible binding for global variable ‘TP’ decouple_ORA_wrapper: no visible binding for global variable ‘FP’ decouple_ORA_wrapper: no visible binding for global variable ‘FN’ decouple_ORA_wrapper: no visible binding for global variable ‘TN’ decouple_ORA_wrapper: no visible binding for global variable ‘TP_markers’ decouple_ORA_wrapper: no visible binding for global variable ‘statistic’ decouple_ORA_wrapper: no visible binding for global variable ‘score’ decouple_ORA_wrapper: no visible binding for global variable ‘p_value’ dotplot_ORA: no visible global function definition for ‘%>%’ dotplot_ORA: no visible global function definition for ‘aes_string’ dotplot_ORA: no visible global function definition for ‘guide_legend’ dotplot_ORA: no visible global function definition for ‘theme’ dotplot_ORA: no visible binding for global variable ‘Enrichment_Score’ dotplot_ORA: no visible binding for global variable ‘Term’ dotplot_ORA: no visible binding for global variable ‘size’ dotplot_ORA: no visible binding for global variable ‘Score’ dotplot_ORA: no visible global function definition for ‘guides’ dotplot_ORA: no visible global function definition for ‘guide_colorbar’ dotplot_ORA: no visible global function definition for ‘element_text’ dotplot_ORA: no visible global function definition for ‘facet_wrap’ dotplot_ORA: no visible global function definition for ‘unit’ get_TP_markers_per_Term: no visible global function definition for ‘%>%’ get_TP_markers_per_Term: no visible binding for global variable ‘Term’ get_TP_markers_per_Term: no visible binding for global variable ‘TP_markers’ get_metabo_iso: no visible global function definition for ‘%>%’ get_metabo_iso : : no visible global function definition for ‘between’ initEnrichment: no visible global function definition for ‘%>%’ initEnrichment : : no visible global function definition for ‘between’ match_LUT_to_Term: no visible global function definition for ‘%>%’ match_LUT_to_Term: no visible binding for global variable ‘Term’ ora_conting_decoupleR: no visible global function definition for ‘%>%’ passed_filters_per_term: no visible global function definition for ‘%>%’ passed_filters_per_term: no visible binding for global variable ‘bootstrap’ passed_filters_per_term: no visible global function definition for ‘p.adjust’ passed_filters_per_term: no visible binding for global variable ‘p_value’ passed_filters_per_term: no visible binding for global variable ‘Term’ passed_filters_per_term: no visible global function definition for ‘median’ passed_filters_per_term: no visible binding for global variable ‘TP’ passed_filters_per_term: no visible binding for global variable ‘q.value’ passed_filters_per_term: no visible binding for global variable ‘n’ passed_filters_per_term: no visible binding for global variable ‘p.value_combined’ passed_filters_per_term: no visible binding for global variable ‘q.value_combined’ passed_filters_per_term: no visible binding for global variable ‘fraction’ passed_filters_per_term: no visible binding for global variable ‘min_TP’ passed_filters_per_term: no visible binding for global variable ‘significant_adj_boot’ passed_filters_per_term: no visible binding for global variable ‘significant_adj_terms’ passed_filters_per_term: no visible binding for global variable ‘pass_boot_fraction’ plot_MSEA_Multi_cond: no visible global function definition for ‘%>%’ plot_MSEA_Multi_cond: no visible binding for global variable ‘condition.y’ plot_MSEA_Multi_cond: no visible binding for global variable ‘condition.x’ plot_MSEA_Multi_cond: no visible binding for global variable ‘cond_label’ plot_MSEA_Multi_cond: no visible binding for global variable ‘Term’ plot_MSEA_Multi_cond: no visible binding for global variable ‘NES’ rankScore.S2IsoMEr : : no visible global function definition for ‘t.test’ rename_if_exists: no visible global function definition for ‘rename’ rename_if_exists: no visible global function definition for ‘:=’ ridge_bootstraps: no visible binding for global variable ‘TP’ ridge_bootstraps: no visible binding for global variable ‘Term’ ridge_bootstraps: no visible global function definition for ‘stat’ ridge_bootstraps: no visible binding for global variable ‘density’ seurat_wilcoxDETest : : no visible global function definition for ‘wilcox.test’ simplify_hypergeom_bootstrap: no visible global function definition for ‘%>%’ simplify_hypergeom_bootstrap: no visible global function definition for ‘p.adjust’ simplify_hypergeom_bootstrap: no visible binding for global variable ‘p_value’ simplify_hypergeom_bootstrap: no visible binding for global variable ‘Term’ simplify_hypergeom_bootstrap: no visible binding for global variable ‘fraction’ simplify_hypergeom_bootstrap: no visible binding for global variable ‘bootstrap’ simplify_hypergeom_bootstrap: no visible global function definition for ‘median’ simplify_hypergeom_bootstrap: no visible binding for global variable ‘TP’ simplify_hypergeom_bootstrap: no visible binding for global variable ‘OR’ simplify_hypergeom_bootstrap: no visible global function definition for ‘sd’ simplify_hypergeom_bootstrap: no visible binding for global variable ‘q.value’ simplify_hypergeom_bootstrap: no visible binding for global variable ‘q.value_combined’ simplify_hypergeom_bootstrap: no visible binding for global variable ‘n’ simplify_hypergeom_bootstrap: no visible binding for global variable ‘p.value_combined’ to_ORA_query: no visible global function definition for ‘%>%’ to_ORA_query: no visible binding for global variable ‘condition’ to_ORA_query: no visible binding for global variable ‘markers’ Undefined global functions or variables: %>% . := Condition ES ES_max ES_median ES_min Enrichment_Score FN FP NES OR Score Significance TN TP TP_markers Term Term_label aes aes_string between bind_rows bootstrap cond_label condition condition.x condition.y density desc element_text everything facet_wrap fraction guide_colorbar guide_legend guides intens ks.test.2 markers median min_TP mutate n p.adjust p.val p.value_combined p_value padj pass_boot_fraction pathway pct.diff position_dodge pval q.value q.value_clipped q.value_combined rename reorder scale_fill_gradient score sd significant_adj_boot significant_adj_terms size stat statistic t.test theme total_bootstrap unit up_down weighted.mean wilcox.test Consider adding importFrom("stats", "density", "median", "p.adjust", "reorder", "sd", "t.test", "weighted.mean", "wilcox.test") to your NAMESPACE file. * checking Rd files ... [0s/0s] NOTE checkRd: (-1) Load_background.Rd:18: Lost braces in \itemize; meant \describe ? checkRd: (-1) Load_background.Rd:19: Lost braces in \itemize; meant \describe ? checkRd: (-1) Load_background.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) Load_background.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) Load_background.Rd:22: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'build_iso_bg.Rd': \examples lines wider than 100 characters: custom_db <- data.frame(ID = 1:3, Name = c("Met1", "Met2", "Met3"), Endogenous = "Yes", Pathway_assoc = "Yes", HMDB_status = "known") Rd file 'decouple_ORA_wrapper.Rd': \examples lines wider than 100 characters: results <- decouple_ORA_wrapper(marker_list, term_list, universe, pass_adjust = TRUE, seed = 42, ORA_boot = FALSE) Rd file 'get_metabo_iso.Rd': \examples lines wider than 100 characters: results <- get_metabo_iso(sf_vec, consider_isobars = TRUE, polarization_mode = "positive", mass_range_ppm = 5) Rd file 'passed_filters_per_term.Rd': \examples lines wider than 100 characters: enrich_ORA_summary = passed_filters_per_term(unfiltered_df = ORA_res$upregulated$unfiltered_enrich_res, These lines will be truncated in the PDF manual. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [2s/2s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [0s/0s] ERROR Running examples in ‘S2IsoMEr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: Run_enrichment > ### Title: Run Metabolite/Lipids enrichment analysis for single cell > ### metabolomics > ### Aliases: Run_enrichment > > ### ** Examples > > ## Not run: > ##D data("example_ORA_obj") > ##D data("example_ORA_custom_universe") > ##D input_scm = example_ORA_obj$scmatrix > ##D conds = example_ORA_obj$conditions > ##D cond_x = "U" > ##D cond_y = "F" > ##D ORA_obj <- initEnrichment( > ##D scmatrix = input_scm, > ##D conditions = conds, > ##D enrichment_type = "ORA", > ##D annot_db = "HMDB", > ##D consider_isomers = TRUE, > ##D consider_isobars = TRUE, > ##D polarization_mode = "positive", > ##D background_type = "sub_class", > ##D molecule_type = "Metabo", > ##D condition.x = cond_x, > ##D condition.y = cond_y > ##D ) > ##D ORA_res <- Run_enrichment( > ##D object = ORA_obj, > ##D custom_universe = example_ORA_custom_universe, > ##D report_ambiguity_scores = TRUE, > ##D DE_LFC_cutoff = 0, > ##D min.pct.diff = 0 > ##D ) > ## End(Not run) > myTestRun <- + Run_enrichment(object = object, + Run_DE = TRUE) Error: object 'object' not found Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [2s/2s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 5 NOTEs