############################################################################## ############################################################################## ### ### 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_1.9.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BioNAR.Rcheck’ * using R Under development (unstable) (2025-01-22 r87618) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BioNAR/DESCRIPTION’ ... OK * this is package ‘BioNAR’ version ‘1.9.1’ * 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 ‘BioNAR’ can be installed ... OK * checking installed package size ... INFO 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 ... NOTE Unknown package ‘clusterCons’ in Rd xrefs * 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 annotateTopOntoOVG 10.040 4.058 31.379 addEdgeAtts 10.093 3.876 14.524 calcEntropy 12.220 1.198 13.601 plotEntropy 12.169 0.989 13.290 getEntropy 11.822 1.084 13.028 clusteringSummary 12.360 0.076 12.576 getCentralityMatrix 10.606 0.835 11.557 getGraphCentralityECDF 10.165 0.792 11.058 runPermDisease 6.750 0.287 7.123 normModularity 5.985 0.798 6.870 annotateGoMF 4.134 2.550 7.947 calcSparsness 5.533 0.833 6.457 annotateGOont 4.131 1.783 10.912 annotateSCHanno 4.639 1.266 7.026 annotateGoBP 4.691 1.036 6.059 FitDegree 1.006 0.058 6.857 getRandomGraphCentrality 0.674 0.027 16.145 * 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-3.21-bioc/meat/BioNAR.Rcheck/00check.log’ for details.