############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNAR_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BioNAR.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * using platform: aarch64-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 Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BioNAR/DESCRIPTION’ ... OK * this is package ‘BioNAR’ version ‘1.7.0’ * 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 ‘BioNAR’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: extdata 6.1Mb * 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 Package in Depends field not imported from: ‘Rdpack’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘addNoise’ ‘gofs’ ‘highlightRate’ ‘plotSigmoid’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE clusterORA : forafun: no visible binding for global variable ‘pathway’ clusterORA : forafun: no visible binding for global variable ‘size’ clusterORA : forafun: no visible binding for global variable ‘overlap’ clusterORA : forafun: no visible binding for global variable ‘pval’ clusterORA : forafun: no visible binding for global variable ‘padj’ clusterORA : forafun: no visible binding for global variable ‘overlapGenes’ clusterORA : forafun: no visible binding for global variable ‘FL’ clusterORA : forafun: no visible binding for global variable ‘N’ clusterORA : forafun: no visible binding for global variable ‘Fn’ clusterORA : forafun: no visible binding for global variable ‘Cn’ clusterORA : forafun: no visible binding for global variable ‘Mu’ clusterORA : forafun: no visible binding for global variable ‘OR’ clusterORA : forafun: no visible binding for global variable ‘CIw’ clusterORA : forafun: no visible binding for global variable ‘Fe’ clusterORA : forafun: no visible binding for global variable ‘Fc’ clusterORA : forafun: no visible binding for global variable ‘palt’ plotSigmoid: no visible binding for global variable ‘yiR1’ plotSigmoid: no visible binding for global variable ‘yiR2’ plotSigmoid: no visible binding for global variable ‘yiR3’ plotSigmoid: no visible binding for global variable ‘yiR4’ plotSigmoid: no visible binding for global variable ‘yiR5’ Undefined global functions or variables: CIw Cn FL Fc Fe Fn Mu N OR overlap overlapGenes padj palt pathway pval size yiR1 yiR2 yiR3 yiR4 yiR5 * checking Rd files ... NOTE checkRd: (-1) FitDegree.Rd:34: Lost braces 34 | \item{legpos}{position of the legend @seealso{legend}} | ^ checkRd: (-1) calcEntropy.Rd:52: Lost braces; missing escapes or markup? 52 | Other {Entropy Functions}: | ^ checkRd: (-1) getEntropy.Rd:66: Lost braces; missing escapes or markup? 66 | Other {Entropy Functions}: | ^ checkRd: (-1) getEntropyRate.Rd:41: Lost braces; missing escapes or markup? 41 | Other {Entropy Functions}: | ^ checkRd: (-1) getRobustness.Rd:49: Lost braces; missing escapes or markup? 49 | Other {Robustness functions}: | ^ checkRd: (-1) makeConsensusMatrix.Rd:69: Lost braces; missing escapes or markup? 69 | Other {Robustness functions}: | ^ checkRd: (-1) plotEntropy.Rd:57: Lost braces; missing escapes or markup? 57 | Other {Entropy Functions}: | ^ * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/BioNAR.Rcheck/00check.log’ for details.