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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:TPP.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings TPP_3.39.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/TPP.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-23 09:06:29 UTC
* checking for file ‘TPP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TPP’ version ‘3.39.1’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... INFO
  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 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘rlang’
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'.

eSetsToLongTable_fData: no visible binding for global variable ‘id’
eSetsToLongTable_fc: no visible binding for global variable ‘id’
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’
plotPerID: no visible binding for global variable ‘textString’
plotPerID: no visible binding for global variable ‘uniqueID’
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’
tppccrCurveFit: no visible binding for global variable ‘id’
tppccrPlotCurves: no visible binding for global variable ‘id’
tpptrTidyUpESets: no visible binding for global variable ‘id’
Undefined global functions or variables:
  ..density.. Protein_ID capture.output density fitMetric id
  meltcurve_plot minMetric temperature testHypothesis textString
  uniqueID
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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  analyze2DTPP.Rd: brewer.pal
  tpp2dCreateDRplots.Rd: brewer.pal
  tpptrFTest.Rd: squeezeVar
  tpptrFitSplines.Rd: AICc
  tpptrPlotSplines.Rd: AICc
  tpptrSplineFitAndTest.Rd: AICc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'tppccrPlotCurves.Rd':
tppccrPlotCurves
  Code: function(data = NULL, fcTable = NULL, curvePars = NULL,
                 resultPath = NULL, ggplotTheme = tppDefaultTheme(),
                 nCores = NULL, verbose = FALSE)
  Docs: function(data = NULL, fcTable = NULL, curvePars = NULL,
                 resultPath = NULL, ggplotTheme = tppDefaultTheme(),
                 nCores = "max", verbose = FALSE)
  Mismatches in argument default values:
    Name: 'nCores' Code: NULL Docs: "max"

Codoc mismatches from Rd file 'tpptrFitSplines.Rd':
tpptrFitSplines
  Code: function(data, factorsH1, factorsH0 = character(0), splineDF =
                 3:7, computeAUC = NULL, returnModels = TRUE, nCores =
                 NULL)
  Docs: function(data, factorsH1, factorsH0 = character(0), splineDF =
                 3:7, computeAUC = NULL, returnModels = TRUE, nCores =
                 "max")
  Mismatches in argument default values:
    Name: 'nCores' Code: NULL Docs: "max"

* 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’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
analyzeTPPTR                   40.276  0.584  40.867
tpp2dCreateDRplots             16.937  0.252  17.190
tpptrSplineFitAndTest          16.595  0.270  16.866
tppQCPlotsCorrelateExperiments 12.594  0.285  12.879
tpptrFTest                      9.480  0.411   9.889
tpptrPlotSplines                9.323  0.206   9.523
tpp2dSplineFitAndTest           9.082  0.239   9.325
tppccrPlotCurves                5.873  0.013   5.885
tpp2dCurveFit                   5.296  0.095   5.390
analyze2DTPP                    4.998  0.333   5.331
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/TPP.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL TPP
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘TPP’ ...
** this is package ‘TPP’ version ‘3.39.1’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TPP)

R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(TPP)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:Biobase':

    combine

The following objects are masked from 'package:BiocGenerics':

    combine, intersect, setdiff, setequal, union

The following object is masked from 'package:generics':

    explain

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: magrittr

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not

Loading required package: tidyr

Attaching package: 'tidyr'

The following object is masked from 'package:magrittr':

    extract

> 
> test_check("TPP")
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[ FAIL 0 | WARN 4 | SKIP 0 | PASS 303 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 303 ]
> 
> proc.time()
   user  system elapsed 
243.095   2.673 251.316