############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SARC.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SARC_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SARC.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘SARC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SARC’ version ‘1.2.0’ * 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 ‘SARC’ 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 ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... 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 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 addExonsGenes: no visible global function definition for ‘metadata’ addExonsGenes: no visible global function definition for ‘metadata<-’ anovaOnCNV: no visible global function definition for ‘metadata’ anovaOnCNV: no visible global function definition for ‘metadata<-’ cnvConfidence: no visible global function definition for ‘metadata’ cnvConfidence: no visible global function definition for ‘metadata<-’ pasteExonsGenes: no visible global function definition for ‘metadata’ pasteExonsGenes: no visible global function definition for ‘metadata<-’ phDunnetonCNV: no visible global function definition for ‘metadata’ phDunnetonCNV: no visible global function definition for ‘metadata<-’ plotCovPrep: no visible global function definition for ‘metadata’ plotCovPrep: no visible global function definition for ‘metadata<-’ prepAnova: no visible global function definition for ‘metadata’ prepAnova: no visible global function definition for ‘metadata<-’ regionGrangeMake: no visible global function definition for ‘metadata’ regionGrangeMake: no visible global function definition for ‘metadata<-’ regionMean: no visible global function definition for ‘metadata’ regionMean: no visible global function definition for ‘metadata<-’ regionQuantiles: no visible global function definition for ‘metadata’ regionQuantiles: no visible global function definition for ‘metadata<-’ regionSet: no visible global function definition for ‘sortSeqlevels’ regionSet: no visible global function definition for ‘metadata’ regionSet: no visible global function definition for ‘metadata<-’ regionSplit: no visible global function definition for ‘metadata’ regionSplit: no visible global function definition for ‘metadata<-’ setQDplot: no visible global function definition for ‘metadata’ setQDplot: no visible global function definition for ‘metadata<-’ setupCNVplot: no visible global function definition for ‘metadata’ setupCNVplot: no visible global function definition for ‘metadata<-’ Undefined global functions or variables: metadata metadata<- sortSeqlevels * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed addExonsGenes 38.105 1.970 44.634 pasteExonsGenes 22.349 0.532 22.881 plotCNV 21.898 0.429 22.327 setupCNVplot 20.732 0.432 21.164 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/SARC.Rcheck/00check.log’ for details.