* using log directory 'd:/RCompile/CRANincoming/R-devel/ReporterScore.Rcheck' * using R Under development (unstable) (2024-01-07 r85787 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'ReporterScore/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ReporterScore' version '0.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Peng Chen ' New submission Possibly misspelled words in DESCRIPTION: GRSA (9:27, 10:69, 12:45) Omics (3:65) RSA (8:38) ReporterScore (9:70) Uses the superseded packages: 'doSNOW', 'snow' Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. * 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 whether package 'ReporterScore' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [11s] NOTE KO_enrich_internal: no visible binding for global variable 'logFC' KO_fisher : : no visible binding for global variable 'KO_id' brite2df: no visible global function definition for 'strsplit2' brite2df2: no visible global function definition for 'strsplit2' c_means: no visible binding for global variable 'var' cm_test_k: no visible binding for global variable 'kmeans' download_org_pathway: no visible binding for global variable 'br_id' filter_report: no visible global function definition for 'na.omit' filter_report: no visible global function definition for 'setNames' filter_top_var: no visible binding for global variable 'var' filter_top_var: no visible global function definition for 'quantile' get_KOs: no visible binding for global variable 'GOlist' get_KOs : : no visible binding for global variable 'GOlist' get_facet_anno: no visible binding for global variable 'Pathway_htable' get_facet_anno: no visible binding for global variable 'Module_htable' get_features: no visible binding for global variable 'GOlist' get_features : : no visible binding for global variable 'GOlist' get_modulelist: no visible binding for global variable 'KOlist' get_modulelist: no visible binding for global variable 'CPDlist' get_modulelist: no visible binding for global variable 'GOlist' get_modulelist : : no visible binding for global variable 'GOlist' load_CARDinfo: no visible binding for global variable 'CARDinfo' load_KO_desc: no visible binding for global variable 'KO_htable' plot.cm_res: no visible global function definition for 'setNames' plot_KOs_box: no visible binding for global variable 'Compound_htable' plot_KOs_distribution: no visible global function definition for 'median' plot_KOs_distribution: no visible binding for global variable 'ReporterScore' plot_KOs_distribution: no visible binding for global variable 'p.value' plot_KOs_heatmap: no visible binding for global variable 'Compound_htable' plot_KOs_in_pathway: no visible global function definition for 'setNames' plot_enrich_res: no visible binding for global variable 'x' plot_enrich_res: no visible binding for global variable 'fill' plot_enrich_res: no visible binding for global variable 'size' plot_enrich_res: no visible binding for global variable 'size_lab' plot_enrich_res: no visible binding for global variable 'x_lab' plot_features_box: no visible binding for global variable 'Compound_htable' plot_features_distribution: no visible global function definition for 'median' plot_features_distribution: no visible binding for global variable 'ReporterScore' plot_features_distribution: no visible binding for global variable 'p.value' plot_features_heatmap: no visible binding for global variable 'Compound_htable' plot_features_in_pathway: no visible global function definition for 'setNames' plot_htable: no visible binding for global variable 'KO_id' plot_htable: no visible binding for global variable 'module2_name' plot_htable: no visible binding for global variable 'module3_name' plot_htable: no visible binding for global variable 'Module_id' plot_htable: no visible binding for global variable 'Pathway_id' plot_htable: no visible binding for global variable 'Class' plot_htable: no visible binding for global variable 'compound1_name' plot_htable: no visible binding for global variable 'compound2_name' plot_htable: no visible binding for global variable 'Compound_id' plot_htable: no visible global function definition for 'setNames' plot_report: no visible global function definition for 'setNames' plot_report_bar: no visible global function definition for 'setNames' plot_report_circle_packing: no visible global function definition for 'setNames' plot_significance: no visible global function definition for 'na.omit' plot_significance : : no visible global function definition for 'rnorm' plot_significance: no visible binding for global variable 'Z_score' plot_significance: no visible binding for global variable 'y' plot_significance: no visible binding for global variable 'ReporterScore' plot_significance: no visible binding for global variable 'p.value' pvalue2zs: no visible global function definition for 'quantile' pvalue2zs: no visible binding for global variable 'Significantly' transform_modulelist: no visible global function definition for 'setNames' up_level_KO: no visible global function definition for 'setNames' up_level_KO: no visible binding for global variable 'Module_htable' update_CARDinfo: no visible global function definition for 'download.file' update_CARDinfo: no visible global function definition for 'untar' update_GO_file: no visible global function definition for 'download.file' update_GO_file: no visible binding for global variable 'GOlist' update_GOinfo: no visible global function definition for 'download.file' update_htable: no visible global function definition for 'strsplit2' update_org_pathway: no visible binding for global variable 'br_id' Undefined global functions or variables: CARDinfo CPDlist Class Compound_htable Compound_id GOlist KO_htable KO_id KOlist Module_htable Module_id Pathway_htable Pathway_id ReporterScore Significantly Z_score br_id compound1_name compound2_name download.file fill kmeans logFC median module2_name module3_name na.omit p.value quantile rnorm setNames size size_lab strsplit2 untar var x x_lab y Consider adding importFrom("stats", "kmeans", "median", "na.omit", "quantile", "rnorm", "setNames", "var") importFrom("utils", "download.file", "untar") to your NAMESPACE file. * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [17s] ERROR Running examples in 'ReporterScore-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cm_test_k > ### Title: Test the proper clusters k for c_means > ### Aliases: cm_test_k c_means > > ### ** Examples > > data(otutab, package = "pcutils") > pcutils::hebing(otutab, metadata$Group) -> otu_group > cm_test_k(otu_group, filter_var = 0.7) ==========================Filter top 30% var and scale========================== vegan: this package haven't install, should install? yes/no(y/n)? Error in lib_ps("vegan", library = FALSE) : exit, because 'vegan' need to install Calls: cm_test_k -> filter_top_var -> -> lib_ps Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [18s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs