##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MinimumDistance.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MinimumDistance_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MinimumDistance.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 ‘MinimumDistance/DESCRIPTION’ ... OK
* this is package ‘MinimumDistance’ version ‘1.44.0’
* package encoding: UTF-8
* 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 ‘MinimumDistance’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘ff::pattern’ by ‘grid::pattern’ when loading ‘MinimumDistance’
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MinimumDistance.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 startup messages can be suppressed ... NOTE
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’

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
Namespace in Imports field not imported from: ‘MatrixGenerics’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
callDenovoSegments: no visible global function definition for
  ‘read.bsfiles’
combineRanges: no visible global function definition for ‘RangedData’
getRefGene: no visible global function definition for ‘RangedData’
overlapsCentromere: no visible global function definition for
  ‘RangedData’
pruneMD: no visible global function definition for ‘RangedDataCBS’
pruneTrioSet: no visible global function definition for
  ‘RangedDataList’
read.bsfiles2: no visible binding for global variable ‘read.bsfiles’
GenomeAnnotatedDataFrameFrom,character: no visible global function
  definition for ‘read.bsfiles’
calculateMindist,list: no visible binding for global variable ‘elt’
Undefined global functions or variables:
  RangedData RangedDataCBS RangedDataList elt read.bsfiles
* checking Rd files ... WARNING
checkRd: (5) MinimumDistance.Rd:0-7: Must have a \description
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'coerce' but not in code:
  ‘as’

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'coerce':
  ‘as’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... WARNING
Output for data("trioSetListExample", package = "MinimumDistance"):
  Warning message:
  replacing previous import ‘ff::pattern’ by ‘grid::pattern’ when loading ‘MinimumDistance’ 
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... 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
pedigreeGrid 4.016  0.148   6.353
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.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 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MinimumDistance.Rcheck/00check.log’
for details.