* using log directory 'd:/Rcompile/CRANpkg/local/4.3/cRegulome.Rcheck' * using R Under development (unstable) (2022-08-11 r82713 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: UTF-8 * checking for file 'cRegulome/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'cRegulome' version '0.3.2' * package encoding: UTF-8 * 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 'cRegulome' can be installed ... OK * checking installed package size ... OK * checking package directory ... 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 ... [8s] OK * checking Rd files ... [1s] OK * checking Rd metadata ... 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 LazyData ... NOTE 'LazyData' is specified without a 'data' directory * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [9s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [10s] OK Running 'testthat.R' [10s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [105s] ERROR Error(s) in re-building vignettes: --- re-building 'case_study.Rmd' using rmarkdown 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 v1.25.0 (2022-06-12 02:20:02 UTC) successfully loaded. See ?R.oo for help. Attaching package: 'R.oo' The following object is masked from 'package:R.methodsS3': throw The following objects are masked from 'package:methods': getClasses, getMethods The following objects are masked from 'package:base': attach, detach, load, save R.utils v2.12.0 (2022-06-28 03:20:05 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, warnings Attaching package: 'igraph' The following object is masked from 'package:R.oo': hierarchy The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:igraph': normalize, path, union The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:R.oo': trim The following object is masked from 'package:grDevices': windows clusterProfiler v4.3.4 For help: https://yulab-smu.top/biomedical-knowledge-mining-book/ If you use clusterProfiler in published research, please cite: T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141 Attaching package: 'clusterProfiler' The following object is masked from 'package:AnnotationDbi': select The following object is masked from 'package:IRanges': slice The following object is masked from 'package:S4Vectors': rename The following object is masked from 'package:igraph': simplify The following object is masked from 'package:stats': filter trying URL 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s001.xlsx' Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length 11004 bytes (10 KB) ================================================== downloaded 10 KB trying URL 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s003.xls' Content type 'application/vnd.ms-office' length 58880 bytes (57 KB) ================================================== downloaded 57 KB Picking joint bandwidth of 0.0412 Picking joint bandwidth of 0.0496 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns Warning in utils::download.file(url, quiet = TRUE, method = method, ...) : URL 'https://rest.kegg.jp/link/hsa/pathway': status was 'Failure when receiving data from the peer' Quitting from lines 240-254 (case_study.Rmd) Error: processing vignette 'case_study.Rmd' failed with diagnostics: Failed to download KEGG data. Wrong 'species' or the network is unreachable. The 'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html' --- failed re-building 'case_study.Rmd' --- re-building 'using_cRegulome.Rmd' using rmarkdown Picking joint bandwidth of 0.0445 --- finished re-building 'using_cRegulome.Rmd' SUMMARY: processing the following file failed: 'case_study.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE