* using log directory ‘/srv/hornik/tmp/CRAN_pretest/XYlabmiR.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘XYlabmiR/DESCRIPTION’ ... OK * this is package ‘XYlabmiR’ version ‘0.0.0.9000’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Xuyang Yi <627251009@qq.com>’ New submission Version contains large components (0.0.0.9000) Possibly misspelled words in DESCRIPTION: mRNA (2:14) miRNA (2:8, 10:53) The Title field should be in title case. Current version is: ‘miRNA-mRNA-protein analysis’ In title case that is: ‘miRNA-mRNA-Protein Analysis’ Size of tarball: 87050993 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 ‘XYlabmiR’ can be installed ... [1s/1s] OK * checking package directory ... OK * checking for future file timestamps ... 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 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 ... [2s/2s] NOTE calculate_final_weights: no visible global function definition for ‘:=’ calculate_final_weights: no visible binding for global variable ‘final_weight’ calculate_final_weights: no visible binding for global variable ‘centrality’ calculate_final_weights: no visible binding for global variable ‘mirna_count’ calculate_node_importance: no visible global function definition for ‘as.data.table’ calculate_node_importance: no visible global function definition for ‘:=’ calculate_node_importance: no visible binding for global variable ‘protein1’ calculate_node_importance: no visible binding for global variable ‘protein2’ calculate_node_importance: no visible global function definition for ‘useEnsembl’ calculate_node_importance: no visible global function definition for ‘getBM’ calculate_node_importance: no visible global function definition for ‘setnames’ calculate_node_importance: no visible binding for global variable ‘gene1’ calculate_node_importance: no visible binding for global variable ‘gene2’ calculate_node_importance: no visible global function definition for ‘graph_from_data_frame’ calculate_node_importance: no visible global function definition for ‘.’ calculate_node_importance: no visible binding for global variable ‘combined_score’ calculate_node_importance: no visible global function definition for ‘graph.strength’ calculate_node_importance: no visible global function definition for ‘data.table’ calculate_node_importance: no visible binding for global variable ‘gene’ get_mirna_gene_relationship: no visible global function definition for ‘fread’ get_mirna_gene_relationship: no visible binding for global variable ‘.N’ get_mirna_gene_relationship: no visible binding for global variable ‘mRNA’ get_mirna_gene_relationship: no visible global function definition for ‘setnames’ visualize_network: no visible global function definition for ‘fread’ visualize_network: no visible global function definition for ‘:=’ visualize_network: no visible binding for global variable ‘protein1’ visualize_network: no visible binding for global variable ‘protein2’ visualize_network: no visible global function definition for ‘useEnsembl’ visualize_network: no visible global function definition for ‘getBM’ visualize_network: no visible global function definition for ‘setnames’ visualize_network: no visible binding for global variable ‘gene1’ visualize_network: no visible binding for global variable ‘gene2’ visualize_network: no visible global function definition for ‘graph_from_data_frame’ visualize_network: no visible global function definition for ‘.’ visualize_network: no visible binding for global variable ‘combined_score’ visualize_network: no visible global function definition for ‘V’ visualize_network: no visible global function definition for ‘V<-’ visualize_network: no visible global function definition for ‘E’ visualize_network: no visible global function definition for ‘E<-’ visualize_network: no visible global function definition for ‘ggraph’ visualize_network: no visible global function definition for ‘geom_edge_link’ visualize_network: no visible global function definition for ‘aes’ visualize_network: no visible binding for global variable ‘width’ visualize_network: no visible global function definition for ‘geom_node_point’ visualize_network: no visible binding for global variable ‘size’ visualize_network: no visible global function definition for ‘geom_node_text’ visualize_network: no visible binding for global variable ‘label’ visualize_network: no visible binding for global variable ‘mirna_count’ visualize_network: no visible global function definition for ‘scale_size’ visualize_network: no visible global function definition for ‘labs’ visualize_network: no visible global function definition for ‘theme_void’ Undefined global functions or variables: . .N := E E<- V V<- aes as.data.table centrality combined_score data.table final_weight fread gene gene1 gene2 geom_edge_link geom_node_point geom_node_text getBM ggraph graph.strength graph_from_data_frame label labs mRNA mirna_count protein1 protein2 scale_size setnames size theme_void useEnsembl width * 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 examples ... [19s/34s] ERROR Running examples in ‘XYlabmiR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: calculate_final_weights > ### Title: Title > ### Aliases: calculate_final_weights > > ### ** Examples > > library(data.table) # 用于读取数据 > library(igraph) # 用于网络分析 Attaching package: ‘igraph’ The following objects are masked from ‘package:stats’: decompose, spectrum The following object is masked from ‘package:base’: union > library(biomaRt) # 用于基因ID转换 > library(ggraph) Loading required package: ggplot2 > library(R.utils)# # 读取 protein_file 和 mirna_file Loading required package: R.oo Loading required package: R.methodsS3 R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help. R.oo v1.26.0 (2024-01-24 05:12:50 UTC) successfully loaded. See ?R.oo for help. Attaching package: ‘R.oo’ The following object is masked from ‘package:R.methodsS3’: throw The following object is masked from ‘package:igraph’: hierarchy The following objects are masked from ‘package:methods’: getClasses, getMethods The following objects are masked from ‘package:base’: attach, detach, load, save R.utils v2.12.3 (2023-11-18 01:00:02 UTC) successfully loaded. See ?R.utils for help. Attaching package: ‘R.utils’ The following object is masked from ‘package:utils’: timestamp The following objects are masked from ‘package:base’: cat, commandArgs, getOption, isOpen, nullfile, parse, use, warnings > protein_file <- system.file("extdata", "9606.protein.links.v12.0.txt.gz", package = "XYlabmiR") > mirna_file <- system.file("extdata", "miRTarget.csv", package = "XYlabmiR")# > # 假设 gene_list 是一个已有的基因列表 > gene_list <- c("EGFR", "EPCAM", "VIM")# > calculate_final_weights(gene_list, protein_file, mirna_file, use_full_data = TRUE) Error in `req_perform()`: ! Failed to perform HTTP request. Caused by error in `curl::curl_fetch_memory()`: ! Timeout was reached: [www.ensembl.org] Operation timed out after 10002 milliseconds with 0 bytes received Backtrace: ▆ 1. └─XYlabmiR::calculate_final_weights(...) 2. └─XYlabmiR::calculate_node_importance(...) 3. └─biomaRt::useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl") 4. └─biomaRt:::.listEnsembl(version = version, GRCh = GRCh, mirror = mirror) 5. └─biomaRt:::.currentEnsemblVersion() 6. └─biomaRt::listEnsemblArchives() 7. └─biomaRt:::.listEnsemblArchives(https = https, http_config = list()) 8. └─biomaRt:::.checkArchiveList(https, http_config) 9. └─biomaRt:::.getArchiveList(https = https, http_config = http_config) 10. └─httr2::req_perform(html_request) 11. └─base::tryCatch(...) 12. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. └─value[[3L]](cond) Execution halted * checking PDF version of manual ... [4s/3s] WARNING LaTeX errors when creating PDF version. 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Type H for immediate help. * checking PDF version of manual without index ... ERROR * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘XYlabmiR-manual.tex’ * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 1 WARNING, 3 NOTEs