############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:intansv.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings intansv_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/intansv.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘intansv/DESCRIPTION’ ... OK * this is package ‘intansv’ version ‘1.40.0’ * 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 ‘intansv’ 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 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 DellyCluster: no visible global function definition for 'subjectHits' LumpyCluster: no visible global function definition for 'subjectHits' PindelCluster: no visible global function definition for 'subjectHits' breakDancerCluster: no visible global function definition for 'subjectHits' mergeOLCNVs: no visible global function definition for 'subjectHits' methodsMerge: no visible global function definition for 'subjectHits' plotChromosome: no visible global function definition for 'queryHits' plotChromosome: no visible global function definition for 'subjectHits' plotChromosome: no visible global function definition for 'seqlengths<-' plotChromosome: no visible global function definition for 'seqlengths' plotChromosome: no visible global function definition for 'aes' plotRegion: no visible global function definition for 'seqlengths<-' plotRegion: no visible global function definition for 'subjectHits' plotRegion: no visible global function definition for 'aes' plotRegion: no visible binding for global variable 'name' readCnvnator: no visible global function definition for 'subjectHits' readDelly: no visible global function definition for 'subjectHits' readLumpy: no visible global function definition for 'subjectHits' readPindel: no visible global function definition for 'subjectHits' readSoftSearch: no visible global function definition for 'subjectHits' readSvseq: no visible global function definition for 'subjectHits' readSvseq : : no visible global function definition for 'subjectHits' softSearchCluster: no visible global function definition for 'subjectHits' tellOLPercantage: no visible global function definition for 'queryHits' tellOLPercantage: no visible global function definition for 'subjectHits' Undefined global functions or variables: aes name queryHits seqlengths seqlengths<- subjectHits * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed methodsMerge 54.127 0.730 72.495 plotChromosome 10.799 0.065 14.435 plotRegion 8.522 0.044 11.558 readLumpy 7.659 0.032 10.815 readDelly 6.881 0.034 9.904 readPindel 6.106 0.034 8.531 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.17-bioc/meat/intansv.Rcheck/00check.log’ for details.