############################################################################## ############################################################################## ### ### 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: 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 ‘1.6.0’ * 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 11.085 1.795 15.092 plotEntropy 11.739 0.749 17.729 calcEntropy 11.748 0.677 16.607 getEntropy 11.043 0.914 16.256 clusteringSummary 11.383 0.054 14.174 annotateTopOntoOVG 8.854 0.595 13.182 getCentralityMatrix 7.749 0.561 12.136 getGraphCentralityECDF 7.262 0.659 10.413 runPermDisease 6.726 0.137 8.361 annotateSCHanno 5.412 0.449 8.537 annotateGoBP 5.030 0.384 6.915 normModularity 4.742 0.606 6.991 annotateGOont 4.770 0.548 6.399 calcAllClustering 5.097 0.028 6.287 calcSparsness 4.219 0.590 6.384 annotateGoMF 3.430 0.246 5.167 FitDegree 1.000 0.043 7.188 getRandomGraphCentrality 0.487 0.052 15.757 * 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.