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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TPP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TPP_3.22.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/TPP.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TPP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TPP’ version ‘3.22.1’
* 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 ‘TPP’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data           1.9Mb
    example_data   8.0Mb
    test_data      1.9Mb
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘broom’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘doParallel:::.options’ ‘mefa:::rep.data.frame’
  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
File ‘TPP/R/TPP.R’:
  .onLoad calls:
    packageStartupMessage(msgText, "\n")

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

fitSigmoidCCR: no visible global function definition for
  ‘capture.output’
modelSelector: no visible binding for global variable ‘testHypothesis’
modelSelector: no visible binding for global variable ‘fitMetric’
modelSelector: no visible binding for global variable ‘minMetric’
plot_fSta_distribution: no visible binding for global variable
  ‘..density..’
plot_pVal_distribution: no visible binding for global variable
  ‘..density..’
tpp2dCreateTPPTRreference: no visible binding for global variable
  ‘meltcurve_plot’
tpp2dCreateTPPTRreference: no visible binding for global variable
  ‘Protein_ID’
tpp2dExport: no visible binding for global variable ‘temperature’
tpp2dImport: no visible binding for global variable ‘temperature’
tpp2dNormalize: no visible binding for global variable ‘temperature’
Undefined global functions or variables:
  ..density.. Protein_ID capture.output fitMetric meltcurve_plot
  minMetric temperature testHypothesis
Consider adding
  importFrom("utils", "capture.output")
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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
analyzeTPPTR                   55.676  0.183  55.901
tpptrSplineFitAndTest          34.927  0.090  35.043
tpptrPlotSplines               20.379  0.055  20.451
tpptrFTest                     20.088  0.058  20.166
tpp2dSplineFitAndTest          19.882  0.078  19.974
tpp2dCreateDRplots             19.628  0.223  19.871
tppQCPlotsCorrelateExperiments 15.768  0.140  15.928
analyze2DTPP                   10.289  0.222  10.520
tpp2dMerge2dRef                 9.939  0.141  10.090
tpp2dCurveFit                   9.720  0.177   9.913
tppccrPlotCurves                8.643  0.061   8.715
tppccrCurveFit                  6.549  0.046   6.603
analyzeTPPCCR                   6.403  0.072   6.483
tppccrResultTable               6.143  0.050   6.198
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/TPP.Rcheck/00check.log’
for details.