############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Mergeomics_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Mergeomics.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * 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 8.4Mb 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed ssea2kda 12.227 0.004 12.258 ssea2kda.analyze 11.974 0.020 12.020 kda.analyze.test 11.429 0.000 11.455 kda.prepare 11.381 0.012 11.420 kda.analyze.exec 11.281 0.091 11.401 kda.analyze.simulate 11.281 0.024 11.559 ssea2kda.import 8.695 0.020 8.736 ssea.analyze 8.548 0.012 8.586 ssea.finish.details 8.461 0.004 8.483 ssea.finish 8.409 0.016 8.445 ssea.meta 8.351 0.036 8.407 ssea.finish.genes 8.370 0.008 8.397 ssea.finish.fdr 8.347 0.012 8.378 ssea.analyze.simulate 8.217 0.016 8.252 ssea.analyze.randgenes 5.752 0.000 5.762 ssea.prepare 4.986 0.004 5.001 * 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/Mergeomics.Rcheck/00check.log’ for details.