############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Mergeomics_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Mergeomics.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Mergeomics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Mergeomics’ version ‘1.35.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Mergeomics’ can be installed ... OK * checking installed package size ... INFO installed size is 8.3Mb sub-directories of 1Mb or more: extdata 7.5Mb * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE kda.analyze: no visible global function definition for ‘p.adjust’ kda.analyze.exec: no visible global function definition for ‘pnorm’ kda.analyze.simulate: no visible global function definition for ‘rnorm’ kda.prepare: no visible global function definition for ‘quantile’ kda.prepare: no visible global function definition for ‘object.size’ kda.prepare.screen: no visible global function definition for ‘quantile’ kda.prepare.screen: no visible global function definition for ‘median’ kda.start: no visible global function definition for ‘object.size’ kda2cytoscape: no visible global function definition for ‘write.table’ kda2cytoscape.colormap: no visible global function definition for ‘rainbow’ kda2cytoscape.colormap: no visible global function definition for ‘col2rgb’ kda2himmeli: no visible global function definition for ‘quantile’ kda2himmeli: no visible global function definition for ‘write.table’ kda2himmeli.colormap: no visible global function definition for ‘rainbow’ kda2himmeli.colormap: no visible global function definition for ‘col2rgb’ ssea.analyze: no visible global function definition for ‘qnorm’ ssea.analyze: no visible global function definition for ‘approx’ ssea.analyze: no visible global function definition for ‘pnorm’ ssea.analyze.simulate: no visible global function definition for ‘quantile’ ssea.control: no visible global function definition for ‘median’ ssea.control: no visible global function definition for ‘object.size’ ssea.meta: no visible global function definition for ‘qnorm’ ssea.meta: no visible global function definition for ‘quantile’ ssea.meta: no visible global function definition for ‘pnorm’ ssea.meta: no visible global function definition for ‘median’ ssea.meta: no visible global function definition for ‘na.omit’ ssea.prepare: no visible global function definition for ‘median’ ssea.prepare: no visible global function definition for ‘object.size’ ssea.start: no visible global function definition for ‘na.omit’ ssea.start: no visible global function definition for ‘object.size’ ssea.start.configure: no visible global function definition for ‘write.table’ ssea2kda: no visible global function definition for ‘na.omit’ ssea2kda.import: no visible global function definition for ‘na.omit’ tool.aggregate: no visible global function definition for ‘na.omit’ tool.cluster: no visible global function definition for ‘as.dist’ tool.cluster: no visible global function definition for ‘hclust’ tool.fdr.bh: no visible global function definition for ‘qnorm’ tool.fdr.bh: no visible global function definition for ‘p.adjust’ tool.fdr.bh: no visible global function definition for ‘approx’ tool.fdr.empirical: no visible global function definition for ‘qnorm’ tool.fdr.empirical: no visible global function definition for ‘approx’ tool.metap: no visible global function definition for ‘qnorm’ tool.metap: no visible global function definition for ‘pnorm’ tool.normalize: no visible global function definition for ‘sd’ tool.normalize: no visible global function definition for ‘median’ tool.normalize: no visible global function definition for ‘optim’ tool.normalize: no visible global function definition for ‘ks.test’ tool.normalize.quality: no visible global function definition for ‘sd’ tool.normalize.quality: no visible global function definition for ‘ks.test’ tool.overlap: no visible global function definition for ‘phyper’ tool.read: no visible global function definition for ‘read.delim’ tool.read: no visible global function definition for ‘na.omit’ tool.save: no visible global function definition for ‘write.table’ tool.unify: no visible global function definition for ‘sd’ tool.unify: no visible global function definition for ‘quantile’ tool.unify: no visible global function definition for ‘approx’ Undefined global functions or variables: approx as.dist col2rgb hclust ks.test median na.omit object.size optim p.adjust phyper pnorm qnorm quantile rainbow read.delim rnorm sd write.table Consider adding importFrom("grDevices", "col2rgb", "rainbow") importFrom("stats", "approx", "as.dist", "hclust", "ks.test", "median", "na.omit", "optim", "p.adjust", "phyper", "pnorm", "qnorm", "quantile", "rnorm", "sd") importFrom("utils", "object.size", "read.delim", "write.table") 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * 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 kda.analyze.test 8.815 0.313 9.171 kda.analyze.exec 8.679 0.365 9.090 kda.analyze.simulate 8.484 0.304 8.822 kda.prepare 8.432 0.316 8.784 ssea2kda 6.260 0.240 6.546 ssea2kda.analyze 6.161 0.249 6.452 ssea.meta 5.369 0.133 5.545 ssea.finish.genes 5.092 0.162 5.290 ssea2kda.import 5.079 0.155 5.272 ssea.analyze 5.029 0.183 5.243 ssea.finish.fdr 5.028 0.153 5.225 ssea.finish 4.931 0.151 5.122 ssea.finish.details 4.917 0.159 5.109 ssea.analyze.simulate 4.790 0.173 5.003 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/Mergeomics.Rcheck/00check.log’ for details.