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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PROPER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PROPER_1.37.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PROPER.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PROPER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PROPER’ version ‘1.37.0’
* 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 ‘PROPER’ 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 ... WARNING
'library' or 'require' call not declared from: ‘edgeR’
'library' or 'require' calls in package code:
  ‘DESeq2’ ‘DSS’ ‘edgeR’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘edgeR’
  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
RNAseq.SimOptions.2grp: no visible global function definition for
  ‘data’
RNAseq.SimOptions.2grp: no visible binding for global variable ‘cheung’
add.axis1: no visible global function definition for ‘axis’
add.axis1: no visible global function definition for ‘text’
comparePower: no visible global function definition for ‘p.adjust’
estParam: no visible global function definition for ‘exprs’
getDisp1: no visible global function definition for ‘median’
getDisp2: no visible global function definition for ‘DGEList’
getDisp2: no visible global function definition for
  ‘estimateCommonDisp’
getDisp2: no visible global function definition for
  ‘estimateTrendedDisp’
getDisp2: no visible global function definition for
  ‘estimateTagwiseDisp’
lfc.alt: no visible global function definition for ‘rnorm’
lfc.null: no visible global function definition for ‘rnorm’
plotAll: no visible global function definition for ‘par’
plotAll: no visible global function definition for ‘mtext’
plotFDR: no visible global function definition for ‘matplot’
plotFDR: no visible global function definition for ‘mtext’
plotFDR: no visible global function definition for ‘axis’
plotFDR: no visible global function definition for ‘box’
plotFDR: no visible global function definition for ‘grid’
plotFDR: no visible global function definition for ‘legend’
plotFDcost : <anonymous>: no visible global function definition for
  ‘sd’
plotFDcost: no visible global function definition for ‘matplot’
plotFDcost: no visible global function definition for ‘arrows’
plotFDcost: no visible global function definition for ‘mtext’
plotFDcost: no visible global function definition for ‘axis’
plotFDcost: no visible global function definition for ‘box’
plotFDcost: no visible global function definition for ‘grid’
plotFDcost: no visible global function definition for ‘legend’
plotPower: no visible binding for global variable ‘sd’
plotPower: no visible global function definition for ‘matplot’
plotPower: no visible global function definition for ‘arrows’
plotPower: no visible global function definition for ‘mtext’
plotPower: no visible global function definition for ‘legend’
plotPower: no visible global function definition for ‘grid’
plotPower: no visible global function definition for ‘axis’
plotPower: no visible global function definition for ‘box’
plotPowerAlpha: no visible binding for global variable ‘sd’
plotPowerAlpha: no visible global function definition for ‘matplot’
plotPowerAlpha: no visible global function definition for ‘arrows’
plotPowerAlpha: no visible global function definition for ‘mtext’
plotPowerAlpha: no visible global function definition for ‘axis’
plotPowerAlpha: no visible global function definition for ‘box’
plotPowerAlpha: no visible global function definition for ‘grid’
plotPowerAlpha: no visible global function definition for ‘abline’
plotPowerAlpha: no visible global function definition for ‘legend’
plotPowerFD: no visible binding for global variable ‘sd’
plotPowerFD: no visible global function definition for ‘matplot’
plotPowerFD: no visible global function definition for ‘arrows’
plotPowerFD: no visible global function definition for ‘mtext’
plotPowerFD: no visible global function definition for ‘axis’
plotPowerFD: no visible global function definition for ‘box’
plotPowerFD: no visible global function definition for ‘grid’
plotPowerFD: no visible global function definition for ‘legend’
plotPowerHist: no visible global function definition for ‘axis’
plotPowerTD: no visible binding for global variable ‘sd’
plotPowerTD: no visible global function definition for ‘matplot’
plotPowerTD: no visible global function definition for ‘arrows’
plotPowerTD: no visible global function definition for ‘mtext’
plotPowerTD: no visible global function definition for ‘axis’
plotPowerTD: no visible global function definition for ‘box’
plotPowerTD: no visible global function definition for ‘grid’
plotPowerTD: no visible global function definition for ‘legend’
rnegbinom: no visible global function definition for ‘rpois’
rnegbinom: no visible global function definition for ‘rgamma’
run.DESeq2: no visible global function definition for
  ‘DESeqDataSetFromMatrix’
run.DESeq2: no visible global function definition for ‘DataFrame’
run.DESeq2: no visible global function definition for ‘DESeq’
run.DESeq2: no visible global function definition for ‘results’
run.DSS: no visible global function definition for ‘newSeqCountSet’
run.DSS: no visible global function definition for ‘estNormFactors’
run.DSS: no visible global function definition for ‘estDispersion’
run.DSS: no visible global function definition for ‘waldTest’
run.edgeR: no visible global function definition for ‘DGEList’
run.edgeR: no visible global function definition for ‘calcNormFactors’
run.edgeR: no visible global function definition for
  ‘estimateCommonDisp’
run.edgeR: no visible global function definition for
  ‘estimateTagwiseDisp’
run.edgeR: no visible global function definition for ‘exactTest’
run.edgeR: no visible global function definition for ‘topTags’
runSims: no visible global function definition for ‘median’
setBaselineExpr.seqDepth: no visible global function definition for
  ‘data’
table2hist: no visible global function definition for ‘hist’
table2hist: no visible global function definition for ‘rnorm’
table2hist: no visible global function definition for ‘axis’
table2hist: no visible global function definition for ‘box’
Undefined global functions or variables:
  DESeq DESeqDataSetFromMatrix DGEList DataFrame abline arrows axis box
  calcNormFactors cheung data estDispersion estNormFactors
  estimateCommonDisp estimateTagwiseDisp estimateTrendedDisp exactTest
  exprs grid hist legend matplot median mtext newSeqCountSet p.adjust
  par results rgamma rnorm rpois sd text topTags waldTest
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "box", "grid",
             "hist", "legend", "matplot", "mtext", "par", "text")
  importFrom("stats", "median", "p.adjust", "rgamma", "rnorm", "rpois",
             "sd")
  importFrom("utils", "data")
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 ... WARNING
Codoc mismatches from Rd file 'estParam.Rd':
estParam
  Code: function(X, type = 1)
  Docs: function(X, type = c(1, 2))
  Mismatches in argument default values:
    Name: 'type' Code: 1 Docs: c(1, 2)

* 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
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
runSims 27.166  0.874  33.342
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/PROPER.Rcheck/00check.log’
for details.