############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:leapR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings leapR_0.99.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/leapR.Rcheck’ * using R Under development (unstable) (2025-11-04 r88984) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.8 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘leapR/DESCRIPTION’ ... OK * this is package ‘leapR’ version ‘0.99.5’ * 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 ‘leapR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 Namespaces in Imports field not imported from: ‘gplots’ ‘methods’ ‘tibble’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE calcTTest: no visible global function definition for ‘is’ calcTTest : : no visible global function definition for ‘t.test’ cluster_enrichment: no visible global function definition for ‘is’ combine_omics: no visible global function definition for ‘as’ correlation_comparison_enrichment: no visible global function definition for ‘is’ correlation_comparison_enrichment: no visible global function definition for ‘cor’ correlation_enrichment: no visible global function definition for ‘is’ correlation_enrichment: no visible global function definition for ‘cor’ difference_enrichment_in_relationships: no visible global function definition for ‘is’ difference_enrichment_in_relationships : : no visible global function definition for ‘t.test’ difference_enrichment_in_relationships : : no visible global function definition for ‘is’ enrichment_by_fishers: no visible global function definition for ‘fisher.test’ enrichment_in_abundance: no visible global function definition for ‘is’ enrichment_in_abundance : : no visible global function definition for ‘t.test’ enrichment_in_abundance : : no visible global function definition for ‘is’ enrichment_in_groups: no visible global function definition for ‘is’ enrichment_in_groups : : no visible global function definition for ‘ks.test’ enrichment_in_relationships: no visible global function definition for ‘is’ enrichment_in_relationships : : no visible global function definition for ‘t.test’ enrichment_in_relationships : : no visible global function definition for ‘is’ leapR: no visible global function definition for ‘is’ Undefined global functions or variables: as cor fisher.test is ks.test t.test Consider adding importFrom("methods", "as", "is") importFrom("stats", "cor", "fisher.test", "ks.test", "t.test") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) leapR.Rd:35-80: Only 2 columns allowed in this table (row 3 has 1) checkRd: (-1) leapR.Rd:35-80: Only 2 columns allowed in this table (row 5 has 1) checkRd: (-1) leapR.Rd:35-80: Only 2 columns allowed in this table (row 7 has 1) checkRd: (-1) leapR.Rd:35-80: Only 2 columns allowed in this table (row 9 has 1) checkRd: (-1) leapR.Rd:35-80: Only 2 columns allowed in this table (row 11 has 1) checkRd: (-1) leapR.Rd:35-80: Only 2 columns allowed in this table (row 13 has 1) checkRd: (-1) leapR.Rd:35-80: Only 2 columns allowed in this table (row 15 has 1) checkRd: (-1) leapR.Rd:35-80: Only 2 columns allowed in this table (row 17 has 1) * 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 leapR 2.540 0.358 6.767 combine_omics 1.096 0.149 29.152 cluster_enrichment 1.123 0.037 5.530 calcTTest 0.506 0.032 5.462 * 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-3.23-bioc/meat/leapR.Rcheck/00check.log’ for details.