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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TPP.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings TPP_3.28.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TPP.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘TPP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TPP’ version ‘3.28.0’
* 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 ‘TPP’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data           1.9Mb
    example_data   6.3Mb
    test_data      2.0Mb
* 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:
    Updated package vignette.
  Cannot process chunk/lines:
    Removed unit test that causes R CMD check to crash  since the latest update of package 'testthat'.
  Cannot process chunk/lines:
    Fixed bug in plotColors for the case when no comparisons are specified
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 density fitMetric
  meltcurve_plot minMetric temperature testHypothesis
Consider adding
  importFrom("stats", "density")
  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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
analyzeTPPTR                   37.270  0.324  37.612
tpptrSplineFitAndTest          16.791  0.559  17.386
tpp2dSplineFitAndTest          10.479  0.121  10.622
tppQCPlotsCorrelateExperiments 10.151  0.132  10.284
tpptrPlotSplines                9.848  0.224  10.083
tpp2dCreateDRplots              9.743  0.203   9.962
tpptrFTest                      9.455  0.264   9.730
tpp2dMerge2dRef                 5.209  0.180   5.410
analyze2DTPP                    5.194  0.182   5.398
tppccrPlotCurves                4.985  0.182   5.208
* 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 ...
  ‘NPARC_analysis_of_TPP_TR_data.Rnw’ using ‘UTF-8’... OK
  ‘TPP_introduction_1D.Rnw’ using ‘UTF-8’... OK
  ‘TPP_introduction_2D.Rnw’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/TPP.Rcheck/00check.log’
for details.