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This page was generated on 2024-05-22 11:37:26 -0400 (Wed, 22 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4665
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4400
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4427
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2116/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TPP 3.33.0  (landing page)
Dorothee Childs
Snapshot Date: 2024-05-20 14:05:07 -0400 (Mon, 20 May 2024)
git_url: https://git.bioconductor.org/packages/TPP
git_branch: devel
git_last_commit: ba0b6b8
git_last_commit_date: 2024-04-30 10:43:07 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for TPP on palomino4


To the developers/maintainers of the TPP package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TPP.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: TPP
Version: 3.33.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TPP.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TPP_3.33.0.tar.gz
StartedAt: 2024-05-21 05:48:37 -0400 (Tue, 21 May 2024)
EndedAt: 2024-05-21 06:00:16 -0400 (Tue, 21 May 2024)
EllapsedTime: 698.3 seconds
RetCode: 0
Status:   OK  
CheckDir: TPP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TPP.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TPP_3.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/TPP.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TPP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TPP' version '3.33.0'
* 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 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                   46.20   0.65   46.86
tppQCPlotsCorrelateExperiments 13.17   0.30   13.47
tpp2dCreateDRplots             11.47   0.25   11.72
tpptrSplineFitAndTest          11.50   0.13   34.93
tpp2dSplineFitAndTest           9.41   0.13   15.09
tpptrPlotSplines                6.91   0.10   17.69
tpptrFTest                      6.64   0.11   18.04
tpp2dCurveFit                   6.34   0.01    6.36
tpp2dMerge2dRef                 5.86   0.09    5.95
tppccrPlotCurves                5.69   0.14    5.85
analyze2DTPP                    5.62   0.11    5.73
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/TPP.Rcheck/00check.log'
for details.


Installation output

TPP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL TPP
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'TPP' ...
** 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)

Tests output

TPP.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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, union

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

    matches

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

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

    matches

> 
> test_check("TPP")
[[1]]

[[2]]

[[3]]

[[1]]

[[2]]

[[3]]

[[1]]

[[2]]

[[3]]

[[1]]

[[2]]

[[3]]

[[1]]

[[2]]

[[3]]

[[1]]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 303 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 303 ]
> 
> proc.time()
   user  system elapsed 
 185.76    6.81  393.32 

Example timings

TPP.Rcheck/TPP-Ex.timings

nameusersystemelapsed
analyze2DTPP5.620.115.73
analyzeTPPCCR4.120.064.19
analyzeTPPTR46.20 0.6546.86
tpp2dAddAdditionalInfo0.020.000.01
tpp2dCalcFractAbundance2.730.192.92
tpp2dComputeFoldChanges0.360.020.38
tpp2dCreateDRplots11.47 0.2511.72
tpp2dCurveFit6.340.016.36
tpp2dExport0.060.020.07
tpp2dImport0.320.000.32
tpp2dMerge2dRef5.860.095.95
tpp2dNormalize0.460.000.47
tpp2dSplineFitAndTest 9.41 0.1315.09
tpp2dSplinePlot0.020.000.02
tpp2dTRReferenceObject0.000.010.03
tppDefaultTheme0.310.020.33
tppExport0.250.090.45
tppQCPlotsCorrelateExperiments13.17 0.3013.47
tppccrCurveFit3.220.053.27
tppccrImport0.090.000.09
tppccrNormalize0.140.000.15
tppccrNormalizeToReference0.160.000.15
tppccrPlotCurves5.690.145.85
tppccrResultTable3.470.053.51
tppccrTransform0.20.00.2
tpptrAnalyzeMeltingCurves0.440.000.44
tpptrCurveFit0.890.000.89
tpptrDefaultNormReqs0.310.030.35
tpptrFTest 6.64 0.1118.04
tpptrFitSplines0.950.024.97
tpptrImport0.240.000.24
tpptrNormalize0.410.000.41
tpptrPlotSplines 6.91 0.1017.69
tpptrSplineFitAndTest11.50 0.1334.93
tpptrTidyUpESets0.320.020.35