############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OutSplice.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OutSplice_1.0.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/OutSplice.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * 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 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OutSplice/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OutSplice’ version ‘1.0.1’ * 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 ‘OutSplice’ 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 calcBurden: no visible binding for global variable ‘FisherP2’ calcBurden: no visible binding for global variable ‘Row.names’ calcBurden: no visible global function definition for ‘na.omit’ calcBurden: no visible binding for global variable ‘FisherP1’ dotheogsa: no visible binding for global variable ‘median’ dotheogsa: no visible global function definition for ‘fisher.test’ dotheogsa: no visible global function definition for ‘p.adjust’ dotheogsa: no visible binding for global variable ‘Row.names’ outspliceAnalysis: no visible global function definition for ‘read.table’ outspliceAnalysis: no visible global function definition for ‘capture.output’ outspliceTCGA: no visible global function definition for ‘read.table’ outspliceTCGA: no visible global function definition for ‘capture.output’ plotJunctionData: no visible binding for global variable ‘FisherAnalyses’ plotJunctionData: no visible global function definition for ‘pdf’ plotJunctionData: no visible binding for global variable ‘junc.RPM’ plotJunctionData: no visible binding for global variable ‘geneAnnotations’ plotJunctionData: no visible global function definition for ‘par’ plotJunctionData: no visible binding for global variable ‘pheno’ plotJunctionData: no visible binding for global variable ‘junc.RPM.norm’ plotJunctionData: no visible global function definition for ‘barplot’ plotJunctionData: no visible global function definition for ‘title’ plotJunctionData: no visible binding for global variable ‘NORM.gene_expr.norm’ plotJunctionData: no visible binding for global variable ‘gene_expr’ plotJunctionData: no visible global function definition for ‘plot.new’ plotJunctionData: no visible global function definition for ‘dev.off’ processMatrices2: no visible binding for global variable ‘median’ saveResults: no visible global function definition for ‘write.table’ subset_overEx: no visible binding for global variable ‘FisherP2’ subset_underEx: no visible binding for global variable ‘FisherP1’ Undefined global functions or variables: FisherAnalyses FisherP1 FisherP2 NORM.gene_expr.norm Row.names barplot capture.output dev.off fisher.test geneAnnotations gene_expr junc.RPM junc.RPM.norm median na.omit p.adjust par pdf pheno plot.new read.table title write.table Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "barplot", "par", "plot.new", "title") importFrom("stats", "fisher.test", "median", "na.omit", "p.adjust") importFrom("utils", "capture.output", "read.table", "write.table") 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed outspliceAnalysis 14.308 0.668 22.731 outspliceTCGA 12.102 0.494 18.620 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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-mac-arm64/meat/OutSplice.Rcheck/00check.log’ for details.