############################################################################## ############################################################################## ### ### 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_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BioNAR.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BioNAR/DESCRIPTION’ ... OK * this is package ‘BioNAR’ version ‘1.6.0’ * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed addEdgeAtts 11.128 2.154 13.470 clusteringSummary 11.992 0.139 12.281 calcEntropy 11.021 0.913 12.075 plotEntropy 11.067 0.844 12.056 getEntropy 10.792 0.848 11.770 getGraphCentralityECDF 8.875 0.621 9.601 annotateTopOntoOVG 8.339 0.673 9.113 getCentralityMatrix 8.208 0.622 8.963 runPermDisease 6.643 0.192 6.898 annotateSCHanno 5.944 0.567 6.597 normModularity 5.431 0.556 6.065 annotateGOont 5.092 0.773 5.961 calcSparsness 5.012 0.574 5.681 FitDegree 1.094 0.047 7.218 getRandomGraphCentrality 0.562 0.029 15.527 * 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-3.19-bioc/meat/BioNAR.Rcheck/00check.log’ for details.