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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genomation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genomation_1.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/genomation.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 ‘genomation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomation’ version ‘1.36.0’
* package encoding: latin1
* 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 ‘genomation’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/genomation.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    in ScoreMatrixBin() function.
  Cannot process chunk/lines:
    NEW FUNCTIONS AND FEATURES
  Cannot process chunk/lines:
    The character vectors will label the x-axis of heatmaps. Examples: xcoords=c("-2kb","0","2kb")
  Cannot process chunk/lines:
    Implemented by Bozena Mika-Gospodorz.
  Cannot process chunk/lines:
    Implemented by Bozena Mika-Gospodorz.
  Cannot process chunk/lines:
    Implemented by Bozena Mika-Gospodorz.
  Cannot process chunk/lines:
    Implemented by Bozena Mika-Gospodorz.
* 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
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ScoreMatrixBin,RleList-GRangesList: no visible binding for global
  variable ‘id’
ScoreMatrixBin,RleList-GRangesList: no visible global function
  definition for ‘:=’
Undefined global functions or variables:
  := id
* checking Rd files ... NOTE
checkRd: (-1) plotMeta.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotMeta.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotMeta.Rd:59-60: 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                     user system elapsed
enrichmentMatrix-ScoreMatrixList-method             4.995  1.844  12.527
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method 4.934  0.776  10.396
enrichmentMatrix-ScoreMatrix-method                 3.828  0.246   5.288
ScoreMatrix-methods                                 3.888  0.067   6.033
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘genomation_unit_tests.R’
 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: 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/genomation.Rcheck/00check.log’
for details.