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CHECK report for TPP2D on machv2

This page was generated on 2020-10-17 11:59:48 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE TPP2D PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1818/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TPP2D 1.4.1
Nils Kurzawa
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/TPP2D
Branch: RELEASE_3_11
Last Commit: 58a718f
Last Changed Date: 2020-06-20 11:06:20 -0400 (Sat, 20 Jun 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: TPP2D
Version: 1.4.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TPP2D.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TPP2D_1.4.1.tar.gz
StartedAt: 2020-10-17 06:00:05 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:02:57 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 171.3 seconds
RetCode: 0
Status:  OK 
CheckDir: TPP2D.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TPP2D.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TPP2D_1.4.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/TPP2D.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TPP2D/DESCRIPTION’ ... OK
* this is package ‘TPP2D’ version ‘1.4.1’
* package encoding: UTF-8
* 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 ‘TPP2D’ can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
getModelParamsDf       11.984  0.094  12.087
computeFStatFromParams 11.541  0.082  11.634
fitAndEvalDataset       9.916  0.093  10.014
computeFstat            8.708  0.100   8.814
competeModels           5.414  0.076   5.495
findHits                2.127  0.016   7.001
getFDR                  2.041  0.017   7.631
getPvalues              1.224  0.010   6.429
* 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: OK


Installation output

TPP2D.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TPP2D
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘TPP2D’ ...
** 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 (TPP2D)

Tests output

TPP2D.Rcheck/tests/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-apple-darwin17.0 (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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(TPP2D)
Loading required package: dplyr

Attaching package: 'dplyr'

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

> 
> test_check("TPP2D")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 15 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  9.429   0.279  13.041 

Example timings

TPP2D.Rcheck/TPP2D-Ex.timings

nameusersystemelapsed
TPP_importCheckConfigTable0.0580.0060.064
annotateDataList1.2750.0141.289
bootstrapNull0.1310.0082.604
bootstrapNullAlternativeModel3.4220.0653.489
competeModels5.4140.0765.495
computeFStatFromParams11.541 0.08211.634
computeFstat8.7080.1008.814
configWide2Long0.0110.0020.012
config_tab0.0010.0020.003
filterOutContaminants0.0590.0010.060
findHits2.1270.0167.001
fitAndEvalDataset 9.916 0.09310.014
fitH0Model0.1900.0030.193
fitH1Model1.6930.0131.706
getFDR2.0410.0177.631
getModelParamsDf11.984 0.09412.087
getPEC504Temperature0.7210.0030.723
getPvalues1.2240.0106.429
gg_qq0.0830.0020.085
import2dDataset1.0330.0081.042
import2dMain0.3950.0050.401
plot2dTppFit0.5340.0110.543
plot2dTppProfile0.4250.0030.428
plot2dTppRelProfile0.4360.0030.440
raw_dat_list0.0020.0020.004
recomputeSignalFromRatios0.0880.0010.090
renameColumns1.0050.0051.011
resolveAmbiguousProteinNames0.0430.0010.043
runTPP2D2.6690.0202.690
simulated_cell_extract_df0.0050.0010.005
tpp2dExperiment-class000