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### Running command:
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###   /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_1.56.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OTUbase.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OTUbase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OTUbase’ version ‘1.56.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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 whether startup messages can be suppressed ... 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 : <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 ... NOTE
checkRd: (-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 ... 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 ... 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-3.20-bioc/meat/OTUbase.Rcheck/00check.log’
for details.