Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:25 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for TPP on palomino3


To the developers/maintainers of the TPP package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2029/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TPP 3.24.0  (landing page)
Dorothee Childs
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/TPP
git_branch: RELEASE_3_15
git_last_commit: de49603
git_last_commit_date: 2022-04-26 11:24:58 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TPP
Version: 3.24.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TPP.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TPP_3.24.0.tar.gz
StartedAt: 2022-10-19 04:53:03 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 05:05:51 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 768.0 seconds
RetCode: 0
Status:   OK  
CheckDir: TPP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TPP.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TPP_3.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/TPP.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '3.24.0'
* 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 ... 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                   38.61   0.53   39.15
tpptrSplineFitAndTest          13.56   0.14   34.30
tpp2dCreateDRplots             12.95   0.36   13.32
tppQCPlotsCorrelateExperiments 12.88   0.14   13.01
tpp2dSplineFitAndTest           9.95   0.11   16.78
tppccrPlotCurves                6.56   0.05    6.61
tpp2dMerge2dRef                 6.42   0.08    6.55
tpp2dCurveFit                   6.27   0.06    6.34
tpptrPlotSplines                6.03   0.18   23.92
analyze2DTPP                    5.76   0.18    5.94
tpptrFTest                      5.81   0.09   15.64
tpptrFitSplines                 1.13   0.03    5.08
* 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
  'F:/biocbuild/bbs-3.15-bioc/meat/TPP.Rcheck/00check.log'
for details.



Installation output

TPP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL TPP
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-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 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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, 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, sort, 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 1 | SKIP 0 | PASS 300 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 300 ]
> 
> proc.time()
   user  system elapsed 
 203.92    6.87  449.89 

Example timings

TPP.Rcheck/TPP-Ex.timings

nameusersystemelapsed
analyze2DTPP5.760.185.94
analyzeTPPCCR3.890.043.94
analyzeTPPTR38.61 0.5339.15
tpp2dAddAdditionalInfo0.020.000.06
tpp2dCalcFractAbundance2.000.182.18
tpp2dComputeFoldChanges0.470.000.46
tpp2dCreateDRplots12.95 0.3613.32
tpp2dCurveFit6.270.066.34
tpp2dExport0.060.010.22
tpp2dImport0.450.000.45
tpp2dMerge2dRef6.420.086.55
tpp2dNormalize0.690.000.68
tpp2dSplineFitAndTest 9.95 0.1116.78
tpp2dSplinePlot000
tpp2dTRReferenceObject0.010.000.05
tppDefaultTheme0.330.000.34
tppExport0.360.080.57
tppQCPlotsCorrelateExperiments12.88 0.1413.01
tppccrCurveFit3.620.053.69
tppccrImport0.110.010.13
tppccrNormalize0.160.000.15
tppccrNormalizeToReference0.190.020.20
tppccrPlotCurves6.560.056.61
tppccrResultTable3.790.043.85
tppccrTransform0.160.020.17
tpptrAnalyzeMeltingCurves0.380.000.37
tpptrCurveFit0.840.010.86
tpptrDefaultNormReqs0.360.020.38
tpptrFTest 5.81 0.0915.64
tpptrFitSplines1.130.035.08
tpptrImport0.250.000.25
tpptrNormalize0.470.040.50
tpptrPlotSplines 6.03 0.1823.92
tpptrSplineFitAndTest13.56 0.1434.30
tpptrTidyUpESets0.800.022.62