############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPseqR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPseqR_1.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ChIPseqR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChIPseqR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChIPseqR’ version ‘1.46.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ChIPseqR’ 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 .fixCounts: no visible global function definition for ‘runLength’ .fixCounts: no visible global function definition for ‘runValue’ getBindLen: no visible global function definition for ‘window’ pickPeak: no visible global function definition for ‘start’ pickPeak: no visible global function definition for ‘runLength’ pickPeak : : no visible global function definition for ‘window’ [[,BindScore-ANY-numeric: no visible global function definition for ‘window’ decompress,Rle: no visible global function definition for ‘runValue’ decompress,RleList : : no visible global function definition for ‘runValue’ initialize,RLEBindScore : : no visible global function definition for ‘Rle’ initialize,RLEBindScore : : no visible global function definition for ‘runValue’ initialize,RLEBindScore : : no visible global function definition for ‘runValue<-’ plot,RLEReadCounts-missing : : no visible global function definition for ‘window’ Undefined global functions or variables: Rle runLength runValue runValue<- start window Consider adding importFrom("stats", "start", "window") 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * 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 alignFeature 11.630 2.529 14.184 BindScore 6.948 0.222 7.177 RLEBindScore-class 6.035 0.232 6.275 simpleNucCall 5.417 0.188 5.607 callBindingSites 5.455 0.122 5.577 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/ChIPseqR.Rcheck/00check.log’ for details.