############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:isomiRs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings isomiRs_1.31.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/isomiRs.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘isomiRs/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘isomiRs’ version ‘1.31.1’ * 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 ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘isomiRs’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .clean_noise: no visible binding for global variable ‘total’ .clean_noise: no visible binding for global variable ‘hits’ .remove_gt_n_changes: no visible binding for global variable ‘changes’ isoAnnotate: no visible binding for global variable ‘pct’ isoCounts: no visible global function definition for ‘as.tibble’ isoPlot: no visible global function definition for ‘across’ isoPlot: no visible global function definition for ‘everything’ isoPlot: no visible binding for global variable ‘iso_sample’ isoPlotPosition: no visible global function definition for ‘across’ isoPlotPosition: no visible global function definition for ‘everything’ isoPlotPosition: no visible binding for global variable ‘iso_sample’ isoSelect.IsomirDataSeq: no visible global function definition for ‘across’ isoSelect.IsomirDataSeq: no visible global function definition for ‘everything’ mirna2targetscan: no visible binding for global variable ‘targetscan.Hs.egMIRNA’ mirna2targetscan: no visible binding for global variable ‘targetscan.Hs.egMIRBASE2FAMILY’ mirna2targetscan: no visible binding for global variable ‘targetscan.Hs.egTARGETS’ mirna2targetscan: no visible binding for global variable ‘targetscan.Hs.egTARGETSFULL’ mirna2targetscan: no visible binding for global variable ‘targetscan.Mm.egMIRNA’ mirna2targetscan: no visible binding for global variable ‘targetscan.Mm.egMIRBASE2FAMILY’ mirna2targetscan: no visible binding for global variable ‘targetscan.Mm.egTARGETS’ mirna2targetscan: no visible binding for global variable ‘targetscan.Mm.egTARGETSFULL’ isoSelect,IsomirDataSeq: no visible global function definition for ‘across’ isoSelect,IsomirDataSeq: no visible global function definition for ‘everything’ Undefined global functions or variables: across as.tibble changes everything hits iso_sample pct targetscan.Hs.egMIRBASE2FAMILY targetscan.Hs.egMIRNA targetscan.Hs.egTARGETS targetscan.Hs.egTARGETSFULL targetscan.Mm.egMIRBASE2FAMILY targetscan.Mm.egMIRNA targetscan.Mm.egTARGETS targetscan.Mm.egTARGETSFULL total * 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 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 isoNetwork 9.061 0.137 9.367 isoDE 5.878 0.108 6.106 isoAnnotate 5.478 0.213 5.740 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/isomiRs.Rcheck/00check.log’ for details.