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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIM_1.76.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SIM.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIM’ version ‘1.76.0’
* 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 ‘SIM’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* 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 ... 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' call to ‘biomaRt’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘quantreg’
  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
File ‘SIM/R/zzz.R’:
  .onAttach calls:
    library.dynam("SIM", pkg, lib)

See section ‘Good practice’ in '?.onAttach'.

dependent.heatmap: warning in get(as.character(adjust[[2]]), env =
  attr(adjust, ".Environment")): partial argument match of 'env' to
  'envir'
sim.plot.zoom.in: warning in eval(call, env = attr(call, "env")):
  partial argument match of 'env' to 'envir'
sim.update.chrom.table: warning in factor(table$name, level = c(1:22,
  "X", "Y")): partial argument match of 'level' to 'levels'
assemble.data: no visible binding for global variable ‘chrom.table’
convertGenomicRegion: no visible binding for global variable
  ‘chrom.table’
dependent.heatmap: no visible global function definition for ‘strwidth’
getoverlappingregions: no visible global function definition for
  ‘useMart’
getoverlappingregions: no visible global function definition for
  ‘getBM’
independent.heatmap: no visible global function definition for
  ‘strwidth’
link.metadata: no visible binding for global variable ‘expr.data’
link.metadata: no visible binding for global variable ‘hgu133plus2CHR’
link.metadata: no visible binding for global variable
  ‘hgu133plus2CHRLOC’
link.metadata: no visible binding for global variable
  ‘hgu133plus2SYMBOL’
plotCytobands: no visible binding for global variable ‘chrom.table’
sim.plot.overlapping.indep.dep.features: no visible global function
  definition for ‘box’
sim.plot.pvals.on.genome: no visible binding for global variable
  ‘chrom.table’
sim.update.chrom.table: no visible global function definition for
  ‘dbConnect’
sim.update.chrom.table: no visible global function definition for
  ‘MySQL’
sim.update.chrom.table: no visible global function definition for
  ‘dbGetQuery’
Undefined global functions or variables:
  MySQL box chrom.table dbConnect dbGetQuery expr.data getBM
  hgu133plus2CHR hgu133plus2CHRLOC hgu133plus2SYMBOL strwidth useMart
Consider adding
  importFrom("graphics", "box", "strwidth")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) integrated.analysis.Rd:116: \item in \value must have non-empty label
* 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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
SIM-package 5.645  0.216   5.919
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/SIM.Rcheck/00check.log’
for details.