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CHECK report for TPP on tokay2

This page was generated on 2020-10-17 11:57:56 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE TPP PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1817/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TPP 3.16.5
Dorothee Childs
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/TPP
Branch: RELEASE_3_11
Last Commit: e18f1c3
Last Changed Date: 2020-10-06 01:47:24 -0400 (Tue, 06 Oct 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TPP
Version: 3.16.5
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TPP.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TPP_3.16.5.tar.gz
StartedAt: 2020-10-17 08:55:27 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 09:20:17 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 1490.4 seconds
RetCode: 0
Status:  OK  
CheckDir: TPP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TPP.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TPP_3.16.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/TPP.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TPP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TPP' version '3.16.5'
* 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 13.1Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
tpptrSplineFitAndTest          13.60   0.03   31.59
tpp2dCreateDRplots             12.80   0.01   12.81
tppQCPlotsCorrelateExperiments 11.70   0.05   11.75
analyze2DTPP                    9.45   0.07    9.55
tpp2dSplineFitAndTest           8.67   0.01   14.85
analyzeTPPTR                    7.78   0.06   26.79
tppccrPlotCurves                6.59   0.01    6.62
tpp2dMerge2dRef                 6.45   0.05    6.50
tpptrPlotSplines                6.06   0.00   17.43
tpp2dCurveFit                   5.95   0.00    5.96
tpptrFTest                      5.36   0.01   14.86
analyzeTPPCCR                   5.20   0.02    5.22
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
tpptrSplineFitAndTest          15.82   0.05   38.72
tppQCPlotsCorrelateExperiments 12.64   0.08   12.72
tpp2dCreateDRplots             11.29   0.03   11.31
tpp2dSplineFitAndTest          10.28   0.03   16.76
tpp2dMerge2dRef                 6.83   0.03    6.86
tpp2dCurveFit                   6.79   0.03    6.83
tppccrPlotCurves                6.44   0.02    6.45
analyzeTPPTR                    6.43   0.00   30.85
tpptrPlotSplines                6.39   0.02   29.53
tpptrFTest                      6.08   0.00   15.62
analyze2DTPP                    6.01   0.04    6.06
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/TPP.Rcheck/00check.log'
for details.



Installation output

TPP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/TPP_3.16.5.tar.gz && rm -rf TPP.buildbin-libdir && mkdir TPP.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TPP.buildbin-libdir TPP_3.16.5.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL TPP_3.16.5.zip && rm TPP_3.16.5.tar.gz TPP_3.16.5.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 44 8056k   44 3584k    0     0  5441k      0  0:00:01 --:--:--  0:00:01 5480k
100 8056k  100 8056k    0     0  5834k      0  0:00:01  0:00:01 --:--:-- 5859k

install for i386

* installing *source* package 'TPP' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TPP'
    finding HTML links ... done
    TPP-defunct                             html  
    TPP-deprecated                          html  
    TPP                                     html  
    TPPTR_reference_results_HepG2           html  
    analyze2DTPP                            html  
    finding level-2 HTML links ... done

    analyzeTPPCCR                           html  
    analyzeTPPTR                            html  
    hdacCCR_config                          html  
    hdacCCR_data                            html  
    hdacCCR_smallExample                    html  
    hdacTR_config                           html  
    hdacTR_data                             html  
    hdacTR_resultsTable_smallExample        html  
    hdacTR_smallExample                     html  
    panobinostat_2DTPP_config               html  
    panobinostat_2DTPP_data                 html  
    panobinostat_2DTPP_smallExample         html  
    resultTable                             html  
    tpp2dAddAdditionalInfo                  html  
    tpp2dCalcFractAbundance                 html  
    tpp2dComputeFoldChanges                 html  
    tpp2dCreateDRplots                      html  
    tpp2dCreateReport                       html  
    tpp2dCreateTPPTRreference               html  
    tpp2dCurveFit                           html  
    tpp2dExport                             html  
    tpp2dExportPlots                        html  
    tpp2dImport                             html  
    tpp2dMerge2dRef                         html  
    tpp2dNormalize                          html  
    tpp2dPlotQChist                         html  
    tpp2dPlotQCpEC50                        html  
    tpp2dSplineFitAndTest                   html  
    tpp2dSplinePlot                         html  
    tpp2dTRReferenceObject                  html  
    tppDefaultTheme                         html  
    tppExport                               html  
    tppQCPlotsCorrelateExperiments          html  
    tppRefData                              html  
    tppccrCurveFit                          html  
    tppccrImport                            html  
    tppccrNormalize                         html  
    tppccrNormalizeToReference              html  
    tppccrPlotCurves                        html  
    tppccrResultTable                       html  
    tppccrTransform                         html  
    tpptrAnalyzeMeltingCurves               html  
    tpptrCurveFit                           html  
    tpptrDefaultNormReqs                    html  
    tpptrFTest                              html  
    tpptrFitSplines                         html  
    tpptrImport                             html  
    tpptrNormalize                          html  
    tpptrPlotSplines                        html  
    tpptrSplineFitAndTest                   html  
    tpptrTidyUpESets                        html  
** 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

install for x64

* installing *source* package 'TPP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TPP' as TPP_3.16.5.zip
* DONE (TPP)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'TPP' successfully unpacked and MD5 sums checked

Tests output

TPP.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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]]

== testthat results  ===========================================================
[ OK: 285 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 229.32    3.82  515.62 

TPP.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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]]

== testthat results  ===========================================================
[ OK: 285 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 222.54    3.04  445.35 

Example timings

TPP.Rcheck/examples_i386/TPP-Ex.timings

nameusersystemelapsed
analyze2DTPP9.450.079.55
analyzeTPPCCR5.200.025.22
analyzeTPPTR 7.78 0.0626.79
tpp2dAddAdditionalInfo0.030.000.04
tpp2dCalcFractAbundance2.970.033.00
tpp2dComputeFoldChanges0.420.020.44
tpp2dCreateDRplots12.80 0.0112.81
tpp2dCurveFit5.950.005.96
tpp2dExport0.100.020.12
tpp2dImport0.450.000.45
tpp2dMerge2dRef6.450.056.50
tpp2dNormalize0.580.000.58
tpp2dSplineFitAndTest 8.67 0.0114.85
tpp2dSplinePlot0.020.000.01
tpp2dTRReferenceObject0.010.000.02
tppDefaultTheme0.350.000.34
tppExport0.330.050.39
tppQCPlotsCorrelateExperiments11.70 0.0511.75
tppccrCurveFit4.370.004.38
tppccrImport0.190.000.18
tppccrNormalize0.240.000.24
tppccrNormalizeToReference0.280.000.28
tppccrPlotCurves6.590.016.62
tppccrResultTable4.050.024.07
tppccrTransform0.190.000.18
tpptrAnalyzeMeltingCurves0.390.000.40
tpptrCurveFit0.80.00.8
tpptrDefaultNormReqs0.360.000.36
tpptrFTest 5.36 0.0114.86
tpptrFitSplines1.000.004.26
tpptrImport0.290.000.30
tpptrNormalize0.470.000.47
tpptrPlotSplines 6.06 0.0017.43
tpptrSplineFitAndTest13.60 0.0331.59
tpptrTidyUpESets0.760.000.76

TPP.Rcheck/examples_x64/TPP-Ex.timings

nameusersystemelapsed
analyze2DTPP6.010.046.06
analyzeTPPCCR4.030.004.03
analyzeTPPTR 6.43 0.0030.85
tpp2dAddAdditionalInfo0.030.000.04
tpp2dCalcFractAbundance2.530.022.54
tpp2dComputeFoldChanges0.400.000.41
tpp2dCreateDRplots11.29 0.0311.31
tpp2dCurveFit6.790.036.83
tpp2dExport0.050.020.06
tpp2dImport0.420.000.42
tpp2dMerge2dRef6.830.036.86
tpp2dNormalize0.700.000.71
tpp2dSplineFitAndTest10.28 0.0316.76
tpp2dSplinePlot000
tpp2dTRReferenceObject0.000.010.02
tppDefaultTheme0.410.000.41
tppExport0.780.051.06
tppQCPlotsCorrelateExperiments12.64 0.0812.72
tppccrCurveFit4.390.004.39
tppccrImport0.140.000.14
tppccrNormalize0.180.000.18
tppccrNormalizeToReference0.20.00.2
tppccrPlotCurves6.440.026.45
tppccrResultTable4.530.024.55
tppccrTransform0.170.000.17
tpptrAnalyzeMeltingCurves0.370.010.39
tpptrCurveFit0.900.000.89
tpptrDefaultNormReqs0.350.000.36
tpptrFTest 6.08 0.0015.62
tpptrFitSplines1.370.004.85
tpptrImport0.300.020.31
tpptrNormalize0.630.010.94
tpptrPlotSplines 6.39 0.0229.53
tpptrSplineFitAndTest15.82 0.0538.72
tpptrTidyUpESets0.600.010.60