Mac ARM64 build report for BioC 3.19 - CHECK results for HELP on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4461
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: HELP

Version: 1.62.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HELP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HELP_1.62.0.tar.gz

StartedAt: 2024-05-06 22:09:43 -0400 (Mon, 06 May 2024)

EndedAt: 2024-05-06 22:09:59 -0400 (Mon, 06 May 2024)

EllapsedTime: 16.2 seconds

RetCode: 0

Status: OK

CheckDir: HELP.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HELP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HELP_1.62.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/HELP.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HELP/DESCRIPTION’ ... OK
* this is package ‘HELP’ 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 ‘HELP’ can be installed ... OK
* 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 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
  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
calcTm: no visible global function definition for ‘data’
calcTm: no visible binding for global variable
  ‘base.stacking.thermodynamics’
readSampleKey: no visible global function definition for ‘read.table’
calcGC,ExpressionSet: no visible global function definition for
  ‘validObject’
calcGC,ExpressionSet: no visible global function definition for
  ‘callGeneric’
calcGC,ExpressionSet: no visible global function definition for ‘new’
calcPrototype,ExpressionSet: no visible global function definition for
  ‘validObject’
calcPrototype,ExpressionSet: no visible global function definition for
  ‘callGeneric’
calcPrototype,vector: no visible global function definition for
  ‘callGeneric’
calcTm,character: no visible binding for global variable
  ‘base.stacking.thermodynamics’
calcTm,ExpressionSet: no visible global function definition for
  ‘validObject’
calcTm,ExpressionSet: no visible global function definition for
  ‘callGeneric’
calcTm,ExpressionSet: no visible global function definition for ‘new’
combineData,ExpressionSet-missing-missing: no visible global function
  definition for ‘validObject’
combineData,ExpressionSet-missing-missing: no visible global function
  definition for ‘callGeneric’
combineData,ExpressionSet-vector-missing: no visible global function
  definition for ‘validObject’
combineData,ExpressionSet-vector-missing: no visible global function
  definition for ‘callGeneric’
combineData,matrix-vector-missing: no visible global function
  definition for ‘callGeneric’
combineData,vector-missing-missing: no visible global function
  definition for ‘callGeneric’
combineData,vector-missing-vector: no visible global function
  definition for ‘callGeneric’
combineData,vector-vector-missing: no visible global function
  definition for ‘callGeneric’
combineData,vector-vector-vector: no visible global function definition
  for ‘callGeneric’
createWiggle,ExpressionSet-matrix: no visible global function
  definition for ‘validObject’
createWiggle,ExpressionSet-matrix: no visible global function
  definition for ‘callGeneric’
createWiggle,ExpressionSet-missing: no visible global function
  definition for ‘validObject’
createWiggle,ExpressionSet-missing: no visible global function
  definition for ‘callGeneric’
createWiggle,matrix-matrix: no visible global function definition for
  ‘rainbow’
createWiggle,matrix-matrix: no visible global function definition for
  ‘col2rgb’
createWiggle,vector-matrix: no visible global function definition for
  ‘callGeneric’
getFeatures,AnnotatedDataFrame-missing: no visible global function
  definition for ‘validObject’
getFeatures,AnnotatedDataFrame-NULL: no visible global function
  definition for ‘validObject’
getFeatures,AnnotatedDataFrame-vector: no visible global function
  definition for ‘validObject’
getFeatures,AnnotatedDataFrame-vector: no visible global function
  definition for ‘callGeneric’
getFeatures,ExpressionSet-missing: no visible global function
  definition for ‘validObject’
getFeatures,ExpressionSet-NULL: no visible global function definition
  for ‘validObject’
getFeatures,ExpressionSet-vector: no visible global function definition
  for ‘validObject’
getFeatures,ExpressionSet-vector: no visible global function definition
  for ‘callGeneric’
getFeatures,vector-vector: no visible global function definition for
  ‘callGeneric’
getSamples,ExpressionSet-missing: no visible global function definition
  for ‘validObject’
getSamples,ExpressionSet-NULL: no visible global function definition
  for ‘validObject’
getSamples,ExpressionSet-vector: no visible global function definition
  for ‘validObject’
getSamples,ExpressionSet-vector: no visible global function definition
  for ‘callGeneric’
getSamples,vector-vector: no visible global function definition for
  ‘callGeneric’
plotBins,ExpressionSet-ExpressionSet: no visible global function
  definition for ‘validObject’
plotBins,ExpressionSet-ExpressionSet: no visible global function
  definition for ‘callGeneric’
plotBins,ExpressionSet-missing: no visible global function definition
  for ‘validObject’
plotBins,ExpressionSet-missing: no visible global function definition
  for ‘callGeneric’
plotBins,ExpressionSet-vector: no visible global function definition
  for ‘validObject’
plotBins,ExpressionSet-vector: no visible global function definition
  for ‘callGeneric’
plotBins,matrix-missing: no visible global function definition for
  ‘callGeneric’
plotBins,vector-ExpressionSet: no visible global function definition
  for ‘validObject’
plotBins,vector-ExpressionSet: no visible global function definition
  for ‘callGeneric’
plotBins,vector-vector: no visible global function definition for
  ‘rainbow’
plotBins,vector-vector: no visible global function definition for
  ‘quantile’
plotBins,vector-vector: no visible global function definition for
  ‘layout’
plotBins,vector-vector: no visible global function definition for
  ‘axis’
plotBins,vector-vector: no visible global function definition for
  ‘rect’
plotBins,vector-vector: no visible global function definition for
  ‘density’
plotBins,vector-vector: no visible global function definition for
  ‘lines’
plotChip,ExpressionSet-ExpressionSet-missing: no visible global
  function definition for ‘validObject’
plotChip,ExpressionSet-ExpressionSet-missing: no visible global
  function definition for ‘callGeneric’
plotChip,ExpressionSet-missing-missing: no visible global function
  definition for ‘validObject’
plotChip,ExpressionSet-missing-missing: no visible global function
  definition for ‘callGeneric’
plotChip,ExpressionSet-vector-missing: no visible global function
  definition for ‘validObject’
plotChip,ExpressionSet-vector-missing: no visible global function
  definition for ‘callGeneric’
plotChip,matrix-missing-missing: no visible global function definition
  for ‘callGeneric’
plotChip,vector-vector-ExpressionSet: no visible global function
  definition for ‘validObject’
plotChip,vector-vector-ExpressionSet: no visible global function
  definition for ‘callGeneric’
plotChip,vector-vector-vector: no visible global function definition
  for ‘rainbow’
plotChip,vector-vector-vector: no visible global function definition
  for ‘quantile’
plotChip,vector-vector-vector: no visible global function definition
  for ‘rect’
plotFeature,ExpressionSet-missing: no visible global function
  definition for ‘callGeneric’
plotFeature,ExpressionSet-vector: no visible global function definition
  for ‘validObject’
plotFeature,ExpressionSet-vector: no visible global function definition
  for ‘callGeneric’
plotFeature,matrix-vector: no visible global function definition for
  ‘par’
plotFeature,matrix-vector: no visible global function definition for
  ‘median’
plotFeature,matrix-vector: no visible global function definition for
  ‘mad’
plotFeature,matrix-vector: no visible global function definition for
  ‘layout’
plotFeature,matrix-vector: no visible global function definition for
  ‘density’
plotFeature,matrix-vector: no visible global function definition for
  ‘points’
plotFeature,matrix-vector: no visible global function definition for
  ‘abline’
plotPairs,ExpressionSet: no visible global function definition for
  ‘validObject’
plotPairs,ExpressionSet: no visible global function definition for
  ‘callGeneric’
plotPairs,matrix: no visible global function definition for ‘par’
plotPairs,matrix: no visible global function definition for ‘hclust’
plotPairs,matrix: no visible global function definition for ‘dist’
plotPairs,matrix: no visible global function definition for ‘cutree’
plotPairs,matrix: no visible global function definition for ‘rainbow’
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for ‘par’
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for ‘points’
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for ‘cor’
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for ‘lowess’
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for ‘lines’
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for ‘text’
plotPairs,matrix: no visible global function definition for ‘layout’
plotPairs,matrix: no visible global function definition for ‘pairs’
plotPairs,matrix: no visible global function definition for ‘points’
plotPairs,matrix: no visible global function definition for ‘abline’
plotPairs,matrix: no visible global function definition for ‘text’
plotPairs,matrix : draw.tree: no visible global function definition for
  ‘points’
plotPairs,matrix: no visible global function definition for
  ‘as.dendrogram’
quantileNormalize,ExpressionSet-ExpressionSet: no visible global
  function definition for ‘validObject’
quantileNormalize,ExpressionSet-ExpressionSet: no visible global
  function definition for ‘callGeneric’
quantileNormalize,ExpressionSet-missing: no visible global function
  definition for ‘validObject’
quantileNormalize,ExpressionSet-missing: no visible global function
  definition for ‘callGeneric’
quantileNormalize,ExpressionSet-vector: no visible global function
  definition for ‘validObject’
quantileNormalize,ExpressionSet-vector: no visible global function
  definition for ‘callGeneric’
quantileNormalize,matrix-missing: no visible global function definition
  for ‘callGeneric’
quantileNormalize,vector-ExpressionSet: no visible global function
  definition for ‘validObject’
quantileNormalize,vector-ExpressionSet: no visible global function
  definition for ‘callGeneric’
quantileNormalize,vector-vector: no visible global function definition
  for ‘quantile’
readDesign,character-character-ExpressionSet: no visible global
  function definition for ‘validObject’
readDesign,character-character-ExpressionSet: no visible global
  function definition for ‘read.table’
readDesign,character-character-ExpressionSet: no visible global
  function definition for ‘new’
readDesign,vector-missing-missing: no visible global function
  definition for ‘callGeneric’
readDesign,vector-missing-missing: no visible global function
  definition for ‘new’
readDesign,vector-vector-missing: no visible global function definition
  for ‘callGeneric’
readDesign,vector-vector-missing: no visible global function definition
  for ‘new’
readPairs,character-character-ExpressionSet: no visible global function
  definition for ‘validObject’
readPairs,character-character-ExpressionSet: no visible global function
  definition for ‘read.table’
readPairs,character-character-ExpressionSet: no visible global function
  definition for ‘new’
readPairs,vector-missing-missing: no visible global function definition
  for ‘callGeneric’
readPairs,vector-missing-missing: no visible global function definition
  for ‘new’
readPairs,vector-vector-missing: no visible global function definition
  for ‘callGeneric’
readPairs,vector-vector-missing: no visible global function definition
  for ‘new’
Undefined global functions or variables:
  abline as.dendrogram axis base.stacking.thermodynamics callGeneric
  col2rgb cor cutree data density dist hclust layout lines lowess mad
  median new pairs par points quantile rainbow read.table rect text
  validObject
Consider adding
  importFrom("graphics", "abline", "axis", "layout", "lines", "pairs",
             "par", "points", "rect", "text")
  importFrom("grDevices", "col2rgb", "rainbow")
  importFrom("methods", "callGeneric", "new", "validObject")
  importFrom("stats", "as.dendrogram", "cor", "cutree", "density",
             "dist", "hclust", "lowess", "mad", "median", "quantile")
  importFrom("utils", "data", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) combineData-methods.Rd:36: Lost braces
    36 | \item{x = "ExpressionSet", y = "vector", w = "missing"}{ Handle input of an object of class \code{ExpressionSet} and a vector specifying grouping information. Derive weighting data from code{AssayDataElement}. }
       |                                                                                                                                                                                               ^
checkRd: (-1) fuzzyMatches.Rd:22: Lost braces
    22 |         \item{\option{nomatch}}{ numerical, specifying a value for non-matching values in code{x} when \code{strict = FALSE}, \code{keep = TRUE}, and \code{alias = FALSE}.}
       |                                                                                               ^
checkRd: (-1) fuzzyMatches.Rd:23: Lost braces
    23 |         \item{\option{na.rm}}{ a logical value indicating whether NA values should be stripped before the computation proceeds (default is \option{TRUE}). If \option{FALSE} any missing values in \code{x} will cause an error and missing values in code{y} may cause unexpected behavior. }
       |                                                                                                                                                                                                                                                           ^
* 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 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/HELP.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HELP
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘HELP’ ...
** using staged installation
** R
** data
** demo
** 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 (HELP)

name	user	system	elapsed
base.stacking.thermodynamics	0.006	0.002	0.008
calcGC	0.000	0.001	0.000
calcPrototype	0.012	0.002	0.013
calcTm	0.013	0.002	0.015
combineData	0.019	0.001	0.020
createWiggle	0.001	0.000	0.002
exprs2	0	0	0
fuzzyMatches	0.017	0.000	0.017
getFeatures	0.017	0.001	0.019
getSamples	0.010	0.000	0.011
plotBins	0.019	0.002	0.021
plotChip	0.053	0.002	0.055
plotFeature	0.027	0.002	0.028
plotPairs	0.179	0.006	0.187
quantileNormalize	0.081	0.001	0.081
readDesign	0.016	0.001	0.017
readPairs	0.027	0.001	0.028
readSampleKey	0.000	0.000	0.001

CHECK results for HELP on kjohnson3

Summary

Command output

Installation output

Tests output

Example timings