############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OTUbase.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OTUbase_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/OTUbase.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OTUbase/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OTUbase’ version ‘1.48.0’ * 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 ‘OTUbase’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * 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 dependencies in R code ... NOTE Package in Depends field not imported from: ‘vegan’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .onAttach: warning in packageDescription("OTUbase", field = "Version"): partial argument match of 'field' to 'fields' .readADF: warning in read.table(file.path(dirPath, ADF), sep = "\t", head = T): partial argument match of 'head' to 'header' .readRDP: warning in read.table(file.path(dirPath, ADF), head = F, sep = "\t", stringsAsFactors = F): partial argument match of 'head' to 'header' .readrdpfix: warning in read.table(file.path(dirPath, rdpfile), head = F, stringsAsFactors = F, sep = "\t"): partial argument match of 'head' to 'header' readTAXset: warning in read.table(file.path(dirPath, namefile), head = F, stringsAsFactors = F, sep = "\t"): partial argument match of 'head' to 'header' o_diversity: no visible global function definition for ‘diversity’ o_estimateR : : no visible global function definition for ‘estimateR’ clusterSamples,.OTUset: no visible global function definition for ‘vegdist’ clusterSamples,.TAXset: no visible global function definition for ‘vegdist’ Undefined global functions or variables: diversity estimateR vegdist * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.16-bioc/meat/OTUbase.Rcheck/00check.log’ for details.