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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_3.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/TPP.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TPP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TPP’ version ‘3.32.0’
* 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 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 ... 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 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
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 ... NOTE
checkRd: (-1) analyzeTPPTR.Rd:146-147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) analyzeTPPTR.Rd:148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) analyzeTPPTR.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacCCR_data.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacCCR_data.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacTR_data.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacTR_data.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacTR_data.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacTR_data.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tppccrCurveFit.Rd:42: Lost braces
42 | code{featureData(S)}.
| ^
checkRd: (-1) tppccrImport.Rd:71-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tppccrImport.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tppccrPlotCurves.Rd:45: Lost braces
45 | produced plots are stored in code{featureData(S)$plot}.
| ^
checkRd: (-1) tpptrImport.Rd:76-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tpptrImport.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tpptrImport.Rd:79: 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 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 33.294 0.384 33.996
tpptrSplineFitAndTest 23.229 0.266 30.098
tpp2dSplineFitAndTest 13.294 0.172 13.582
tppQCPlotsCorrelateExperiments 12.964 0.229 13.295
tpptrPlotSplines 12.298 0.129 12.522
tpp2dCreateDRplots 11.462 0.172 11.749
tpptrFTest 11.189 0.127 11.422
tpp2dMerge2dRef 6.463 0.114 6.637
analyze2DTPP 5.978 0.151 6.178
tppccrPlotCurves 5.823 0.089 5.980
tpp2dCurveFit 5.801 0.101 5.958
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/TPP.Rcheck/00check.log’
for details.