############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RSVSim.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RSVSim_1.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RSVSim.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RSVSim/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RSVSim’ version ‘1.46.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘RSVSim’ 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 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 dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘BSgenome.Hsapiens.UCSC.hg19’ ‘BSgenome.Hsapiens.UCSC.hg19.masked’ ‘MASS’ ‘rtracklayer’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘methods’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .compareSV: no visible global function definition for ‘wmsg’ .drawPos: no visible global function definition for ‘seqlevels’ .drawPos: no visible global function definition for ‘queryHits’ .getHG19: no visible binding for global variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’ .getHG19: no visible binding for global variable ‘Hsapiens’ .getHG19: no visible global function definition for ‘as’ .getSVSizes: no visible global function definition for ‘rbeta’ .loadFromBSGenome_TandemRepeats: no visible binding for global variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’ .loadFromBSGenome_TandemRepeats: no visible global function definition for ‘seqlevels<-’ .loadFromBSGenome_TandemRepeats: no visible global function definition for ‘as’ .loadFromUCSC_RepeatMasks: no visible global function definition for ‘browserSession’ .loadFromUCSC_RepeatMasks: no visible global function definition for ‘genome<-’ .loadFromUCSC_RepeatMasks: no visible global function definition for ‘ucscTableQuery’ .loadFromUCSC_RepeatMasks: no visible global function definition for ‘txtProgressBar’ .loadFromUCSC_RepeatMasks: no visible global function definition for ‘range<-’ .loadFromUCSC_RepeatMasks: no visible global function definition for ‘getTable’ .loadFromUCSC_RepeatMasks: no visible global function definition for ‘setTxtProgressBar’ .loadFromUCSC_RepeatMasks: no visible global function definition for ‘data’ .loadFromUCSC_SegDups: no visible global function definition for ‘browserSession’ .loadFromUCSC_SegDups: no visible global function definition for ‘genome<-’ .loadFromUCSC_SegDups: no visible global function definition for ‘getTable’ .loadFromUCSC_SegDups: no visible global function definition for ‘ucscTableQuery’ .readRepeatMaskerOutput: no visible global function definition for ‘read.table’ .readRepeatMaskerOutput: no visible global function definition for ‘data’ .simInsertionPositions: no visible global function definition for ‘txtProgressBar’ .simInsertionPositions: no visible global function definition for ‘seqlevels’ .simInsertionPositions: no visible global function definition for ‘setTxtProgressBar’ .simPositions: no visible global function definition for ‘txtProgressBar’ .simPositions: no visible global function definition for ‘setTxtProgressBar’ .simTranslocationPositions: no visible global function definition for ‘txtProgressBar’ .simTranslocationPositions: no visible global function definition for ‘seqlevels’ .simTranslocationPositions: no visible global function definition for ‘setTxtProgressBar’ .subtractIntervals: no visible global function definition for ‘seqlevels<-’ .testSVSim: no visible global function definition for ‘metadata’ compareSV,character-character: no visible global function definition for ‘read.table’ compareSV,character-data.frame: no visible global function definition for ‘read.table’ estimateSVSizes,numeric-numeric-ANY-ANY-missing: no visible global function definition for ‘fitdistr’ simulateSV,ANY: no visible global function definition for ‘data’ simulateSV,ANY: no visible global function definition for ‘txtProgressBar’ simulateSV,ANY: no visible global function definition for ‘setTxtProgressBar’ simulateSV,ANY: no visible global function definition for ‘write.table’ simulateSV,ANY: no visible global function definition for ‘metadata<-’ Undefined global functions or variables: BSgenome.Hsapiens.UCSC.hg19.masked Hsapiens as browserSession data fitdistr genome<- getTable metadata metadata<- queryHits range<- rbeta read.table seqlevels seqlevels<- setTxtProgressBar txtProgressBar ucscTableQuery wmsg write.table Consider adding importFrom("methods", "as") importFrom("stats", "rbeta") importFrom("utils", "data", "read.table", "setTxtProgressBar", "txtProgressBar", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 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 simulateSV 5.463 0.049 5.52 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/RSVSim.Rcheck/00check.log’ for details.