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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNTools_1.62.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CNTools.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNTools/DESCRIPTION’ ... OK
* this is package ‘CNTools’ version ‘1.62.0’
* 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 ‘CNTools’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
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
'library' or 'require' calls to packages already attached by Depends:
  ‘methods’ ‘tools’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘methods’ ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘genefilter:::genefilter’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getCommonSegValues’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘CNTools/R/zzz.R’:
  .onLoad calls:
    require("methods", quietly = TRUE)
    require("tools", quietly = TRUE)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

filterByMad: no visible binding for global variable ‘mad’
filterByMad: no visible global function definition for ‘quantile’
getPairCor : pair2Cor: no visible global function definition for ‘cor’
getPairDist : pair2Dist: no visible global function definition for
  ‘dist’
getPairDist: no visible global function definition for ‘as.dist’
getCor,RS: no visible global function definition for ‘cor’
getDist,RS: no visible global function definition for ‘dist’
Undefined global functions or variables:
  as.dist cor dist mad quantile
Consider adding
  importFrom("stats", "as.dist", "cor", "dist", "mad", "quantile")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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/CNTools.Rcheck/00check.log’
for details.