################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:OTUbase.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings OTUbase_1.60.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OTUbase.Rcheck’* using R version 4.5.2 (2025-10-31)* using platform: x86_64-pc-linux-gnu* R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0* running under: Ubuntu 24.04.3 LTS* using session charset: UTF-8* checking for file ‘OTUbase/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘OTUbase’ version ‘1.60.0’* 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 ... NOTEMalformed 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 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 loading without being on the library search path ... OK* checking whether startup messages can be suppressed ... OK* checking dependencies in R code ... NOTEPackage 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 : <anonymous>: 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 ... NOTEcheckRd: (-1) abundance.Rd:24: Lost braces in \itemize; meant \describe ?checkRd: (-1) abundance.Rd:25: Lost braces in \itemize; meant \describe ?checkRd: (-1) abundance.Rd:26: Lost braces in \itemize; meant \describe ?checkRd: (-1) abundance.Rd:27: Lost braces in \itemize; meant \describe ?checkRd: (-1) abundance.Rd:28: Lost braces in \itemize; meant \describe ?checkRd: (-1) clusterSamples.Rd:27: Lost braces in \itemize; meant \describe ?checkRd: (-1) clusterSamples.Rd:28: Lost braces in \itemize; meant \describe ?checkRd: (-1) clusterSamples.Rd:29: Lost braces in \itemize; meant \describe ?checkRd: (-1) clusterSamples.Rd:30: Lost braces in \itemize; meant \describe ?checkRd: (-1) clusterSamples.Rd:31: Lost braces in \itemize; meant \describe ?checkRd: (-1) other_functions.Rd:36: Lost braces in \itemize; meant \describe ?checkRd: (-1) other_functions.Rd:38: Lost braces in \itemize; meant \describe ?checkRd: (-1) other_functions.Rd:40: Lost braces in \itemize; meant \describe ?checkRd: (-1) other_functions.Rd:42: Lost braces in \itemize; meant \describe ?checkRd: (-1) other_functions.Rd:44: Lost braces in \itemize; meant \describe ?checkRd: (-1) other_functions.Rd:46: Lost braces in \itemize; meant \describe ?checkRd: (-1) other_functions.Rd:48: Lost braces in \itemize; meant \describe ?checkRd: (-1) other_functions.Rd:50: Lost braces in \itemize; meant \describe ?checkRd: (-1) other_functions.Rd:52: Lost braces in \itemize; meant \describe ?checkRd: (-1) other_functions.Rd:54: Lost braces in \itemize; meant \describe ?* checking Rd metadata ... OK* checking Rd cross-references ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors: accessors.Rd: ShortRead clusterSamples.Rd: vegdistPlease provide package anchors for all Rd \link{} targets not in thepackage itself and the base packages.* 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* checking for unstated dependencies in vignettes ... OK* checking package vignettes ... OK* checking re-building of vignette outputs ... OK* checking PDF version of manual ... OK* DONEStatus: 5 NOTEsSee ‘/home/biocbuild/bbs-3.22-bioc/meat/OTUbase.Rcheck/00check.log’for details.################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL OTUbase###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘OTUbase’ ...** this is package ‘OTUbase’ version ‘1.60.0’** using staged installation** R** inst** byte-compile and prepare package for lazy loading** help*** installing help indices** building package indices** installing vignettes** testing if installed package can be loaded from temporary location** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (OTUbase)
