* using log directory ‘/srv/hornik/tmp/CRAN/TOmicsVis.Rcheck’ * using R Under development (unstable) (2023-07-01 r84626) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 16.0.6 (1) GNU Fortran (Debian 12.2.0-14) 12.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘TOmicsVis/DESCRIPTION’ ... OK * this is package ‘TOmicsVis’ version ‘1.1.5’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Benben Miao ’ New submission Possibly misspelled words in DESCRIPTION: Omics (2:19, 8:25) Unknown, possibly misspelled, fields in DESCRIPTION: ‘News’ Found the following (possibly) invalid URLs: URL: https://github.com/BioSciTools/BioSciTools.github.io (moved to https://github.com/OmicsSuite/OmicsSuite.github.io) From: inst/doc/Introduction.html README.md Status: 301 Message: Moved Permanently * 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 ‘TOmicsVis’ can be installed ... [19s/19s] WARNING Found the following significant warnings: Warning: replacing previous import ‘GGally::ggtable’ by ‘enrichplot::ggtable’ when loading ‘TOmicsVis’ Warning: replacing previous import ‘enrichplot::color_palette’ by ‘ggpubr::color_palette’ when loading ‘TOmicsVis’ Warning: replacing previous import ‘dplyr::as_data_frame’ by ‘igraph::as_data_frame’ when loading ‘TOmicsVis’ Warning: replacing previous import ‘dplyr::groups’ by ‘igraph::groups’ when loading ‘TOmicsVis’ Warning: replacing previous import ‘clusterProfiler::simplify’ by ‘igraph::simplify’ when loading ‘TOmicsVis’ Warning: replacing previous import ‘dplyr::union’ by ‘igraph::union’ when loading ‘TOmicsVis’ Warning: replacing previous import ‘circlize::degree’ by ‘igraph::degree’ when loading ‘TOmicsVis’ Warning: replacing previous import ‘ComplexHeatmap::pheatmap’ by ‘pheatmap::pheatmap’ when loading ‘TOmicsVis’ Warning: replacing previous import ‘WGCNA::cor’ by ‘stats::cor’ when loading ‘TOmicsVis’ Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘TOmicsVis’ Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘TOmicsVis’ Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘TOmicsVis’ Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘TOmicsVis’ Warning: replacing previous import ‘igraph::crossing’ by ‘tidyr::crossing’ when loading ‘TOmicsVis’ Warning: replacing previous import ‘igraph::diversity’ by ‘vegan::diversity’ when loading ‘TOmicsVis’ Warning: replacing previous import ‘stats::filter’ by ‘dplyr::filter’ when loading ‘TOmicsVis’ See ‘/srv/hornik/tmp/CRAN/TOmicsVis.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 Non-standard file/directory found at top level: ‘README.Rmd’ * 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 ... [6s/6s] OK * checking whether the package can be loaded with stated dependencies ... [5s/5s] OK * checking whether the package can be unloaded cleanly ... [5s/5s] OK * checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK * checking whether the namespace can be unloaded cleanly ... [5s/5s] OK * checking loading without being on the library search path ... [5s/5s] 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 ... [25s/25s] NOTE go_enrich_bar: no visible binding for global variable ‘Count’ go_enrich_bar: no visible binding for global variable ‘GeneRatio’ go_enrich_stat: no visible binding for global variable ‘Description’ go_enrich_stat: no visible binding for global variable ‘Count’ go_enrich_stat: no visible binding for global variable ‘Ontology’ kegg_enrich_bar: no visible binding for global variable ‘Count’ kegg_enrich_bar: no visible binding for global variable ‘GeneRatio’ tsne_plot: no visible binding for global variable ‘tSNE1’ tsne_plot: no visible binding for global variable ‘tSNE2’ Undefined global functions or variables: Count Description GeneRatio Ontology tSNE1 tSNE2 * 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 ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [92s/92s] ERROR Running examples in ‘TOmicsVis-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: venn_plot > ### Title: Venn plot for stat common and unique gene among multiple sets. > ### Aliases: venn_plot > > ### ** Examples > > # 1. Library TOmicsVis package > library(TOmicsVis) > > # 2. Use example dataset > data(venn_plot) Warning in data(venn_plot) : data set ‘venn_plot’ not found > > # 3. Default parameters > venn_plot(venn_data) Error: Packages "ggplot2" and "ggpolypath" are needed to make this work, please install. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [12s/12s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] NOTE Found the following HTML validation problems: box_plot.html:60:171 (box_plot.Rd:28): Warning: nested emphasis violin_plot.html:61:171 (violin_plot.Rd:29): Warning: nested emphasis * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 WARNING, 4 NOTEs