############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:TEKRABber.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TEKRABber_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/TEKRABber.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TEKRABber/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TEKRABber’ version ‘1.9.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘TEKRABber’ can be installed ... OK * used C++ compiler: ‘g++ (GCC) 10.3.1’ * 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 ... NOTE Problems with news in ‘NEWS.md’: No news entries found. * checking code 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 whether startup messages can be suppressed ... 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 ... NOTE File ‘TEKRABber/R/zzz.R’: .onLoad calls: packageStartupMessage(paste(messages, collapse = "\n")) See section ‘Good practice’ in '?.onAttach'. appTEKRABber: no visible global function definition for ‘grid_page’ appTEKRABber: no visible global function definition for ‘grid_card_text’ appTEKRABber: no visible global function definition for ‘grid_card’ appTEKRABber: no visible global function definition for ‘card_header’ appTEKRABber: no visible global function definition for ‘card_body’ appTEKRABber: no visible global function definition for ‘selectizeInput’ appTEKRABber: no visible global function definition for ‘actionButton’ appTEKRABber: no visible global function definition for ‘plotlyOutput’ appTEKRABber: no visible global function definition for ‘plotOutput’ appTEKRABber : server: no visible global function definition for ‘renderPlotly’ appTEKRABber : server: no visible global function definition for ‘plot_ly’ appTEKRABber : server: no visible global function definition for ‘observeEvent’ appTEKRABber : server: no visible global function definition for ‘renderPlot’ appTEKRABber : server: no visible global function definition for ‘ggplot’ appTEKRABber : server: no visible global function definition for ‘aes’ appTEKRABber : server: no visible binding for global variable ‘gene’ appTEKRABber : server: no visible binding for global variable ‘TE’ appTEKRABber : server: no visible global function definition for ‘geom_point’ appTEKRABber : server: no visible global function definition for ‘labs’ appTEKRABber : server: no visible global function definition for ‘geom_smooth’ appTEKRABber : server: no visible global function definition for ‘theme_bw’ appTEKRABber : server: no visible global function definition for ‘ggtitle’ appTEKRABber : server: no visible global function definition for ‘ggviolin’ appTEKRABber : server: no visible global function definition for ‘ylab’ appTEKRABber : server: no visible global function definition for ‘xlab’ appTEKRABber : server: no visible global function definition for ‘theme’ appTEKRABber: no visible global function definition for ‘shinyApp’ corrOrthologTE: no visible binding for global variable ‘i’ corrOrthologTE: no visible binding for global variable ‘j’ corrOrthologTE: no visible global function definition for ‘cor.test’ orthologScale: no visible global function definition for ‘desc’ orthologScale: no visible binding for global variable ‘orthologyConfidence’ orthologScale: no visible binding for global variable ‘refLength’ orthologScale: no visible binding for global variable ‘compareLength’ orthologScale: no visible global function definition for ‘across’ orthologScale: no visible binding for global variable ‘refLen’ orthologScale: no visible binding for global variable ‘compareLen’ prepareRMSK: no visible binding for global variable ‘repEnd’ prepareRMSK: no visible binding for global variable ‘repStart’ prepareRMSK: no visible binding for global variable ‘repName’ prepareRMSK: no visible binding for global variable ‘repClass’ prepareRMSK: no visible binding for global variable ‘rLen’ prepareRMSK: no visible binding for global variable ‘cLen’ Undefined global functions or variables: TE across actionButton aes cLen card_body card_header compareLen compareLength cor.test desc gene geom_point geom_smooth ggplot ggtitle ggviolin grid_card grid_card_text grid_page i j labs observeEvent orthologyConfidence plotOutput plot_ly plotlyOutput rLen refLen refLength renderPlot renderPlotly repClass repEnd repName repStart selectizeInput shinyApp theme theme_bw xlab ylab Consider adding importFrom("stats", "cor.test") to your NAMESPACE file. * checking Rd files ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘TEKRABber-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: prepareRMSK > ### Title: Prepare a table from two species RepeatMakser track from UCSC > ### genome Table > ### Aliases: prepareRMSK > > ### ** Examples > > df_rmsk <- prepareRMSK(refSpecies = "hg38", compareSpecies = "panTro6") Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [genome.ucsc.edu] SSL connection timeout Calls: prepareRMSK ... request_fetch -> request_fetch.write_memory -> Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/TEKRABber.Rcheck/00check.log’ for details.