############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EMDomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EMDomics_2.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/EMDomics.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘EMDomics/DESCRIPTION’ ... OK * this is package ‘EMDomics’ version ‘2.35.0’ * 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 ‘EMDomics’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Authors@R field gives more than one person with maintainer role: Sadhika Malladi [aut, cre] Daniel Schmolze [aut, cre] * 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 .cvm_pairwise_q: no visible global function definition for ‘combn’ .cvm_pairwise_q : : no visible global function definition for ‘median’ .emd_gene_pairwise: no visible global function definition for ‘hist’ .emd_pairwise_q: no visible global function definition for ‘combn’ .emd_pairwise_q : : no visible global function definition for ‘median’ .ks_pairwise_table: no visible global function definition for ‘ks.test’ calculate_cvm: no visible global function definition for ‘combn’ calculate_cvm : : no visible global function definition for ‘median’ calculate_cvm_gene: no visible global function definition for ‘combn’ calculate_emd: no visible global function definition for ‘combn’ calculate_emd : : no visible global function definition for ‘median’ calculate_emd_gene: no visible global function definition for ‘combn’ calculate_ks: no visible global function definition for ‘combn’ calculate_ks : : no visible global function definition for ‘p.adjust’ calculate_ks : : no visible global function definition for ‘median’ calculate_ks_gene: no visible global function definition for ‘combn’ calculate_ks_gene: no visible global function definition for ‘ks.test’ Undefined global functions or variables: combn hist ks.test median p.adjust Consider adding importFrom("graphics", "hist") importFrom("stats", "ks.test", "median", "p.adjust") importFrom("utils", "combn") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... NOTE Invalid package aliases in Rd file 'emdomics-package.Rd': ‘emdomics-package’ * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_cvmperms 16.429 0.131 19.343 plot_cvm_density 16.312 0.143 19.360 calculate_cvm 16.228 0.143 19.430 plot_emd_density 9.239 0.098 10.835 plot_emdperms 8.799 0.084 10.805 calculate_emd 8.288 0.103 10.141 plot_cvmnull 6.371 0.052 7.587 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/EMDomics.Rcheck/00check.log’ for details.