############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bigmelon.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bigmelon_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/bigmelon.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * 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 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bigmelon/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘bigmelon’ version ‘1.26.0’ * 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 ‘bigmelon’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘BiocGenerics’ A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: 1.1.14 Added gdsfmt method for estimating Cell Counts, added an experimental normalisation methodology, which involves storing raw intensities as ranks and performing re-ranking steps down-stream with computed quantiles. Cannot process chunk/lines: 0.99.4 Commit to Github from svn Cannot process chunk/lines: 0.1.2 app2gds simple data appending function * checking R 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 startup messages can be suppressed ... NOTE No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘bumphunter:::greaterOrEqual’ ‘minfi:::pickCompProbes’ ‘minfi:::projectCellType’ ‘wateRmelon:::.impose’ ‘wateRmelon:::.normalizeQuantiles2’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE bumphunterEngine.gdsn: no visible binding for global variable ‘locfitByCluster’ bumphunterEngine.gdsn: no visible global function definition for ‘getDoParRegistered’ bumphunterEngine.gdsn: no visible global function definition for ‘registerDoSEQ’ bumphunterEngine.gdsn: no visible global function definition for ‘getDoParWorkers’ bumphunterEngine.gdsn: no visible global function definition for ‘getDoParName’ bumphunterEngine.gdsn: no visible global function definition for ‘getDoParVersion’ bumphunterEngine.gdsn: no visible global function definition for ‘smoother’ bumphunterEngine.gdsn: no visible global function definition for ‘regionFinder’ bumphunterEngine.gdsn: no visible global function definition for ‘%dorng%’ bumphunterEngine.gdsn: no visible global function definition for ‘foreach’ bumphunterEngine.gdsn: no visible global function definition for ‘iter’ bumphunterEngine.gdsn: no visible binding for global variable ‘regionFinder’ bumphunterEngine.gdsn : computation.tots: no visible global function definition for ‘%dorng%’ bumphunterEngine.gdsn : computation.tots: no visible global function definition for ‘foreach’ bumphunterEngine.gdsn : computation.tots: no visible global function definition for ‘iter’ bumphunterEngine.gdsn : computation.tots2: no visible global function definition for ‘%dorng%’ bumphunterEngine.gdsn : computation.tots2: no visible global function definition for ‘foreach’ bumphunterEngine.gdsn : computation.tots2: no visible global function definition for ‘iter’ es2gds: no visible global function definition for ‘colData’ estimateCellCounts.gds: no visible global function definition for ‘colData’ Undefined global functions or variables: %dorng% colData foreach getDoParName getDoParRegistered getDoParVersion getDoParWorkers iter locfitByCluster regionFinder registerDoSEQ smoother * 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 iadd 39.998 0.939 60.697 bigmelon-normalization 3.393 0.124 5.348 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/bigmelon.Rcheck/00check.log’ for details.