Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:56 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 TPP2D on machv2


To the developers/maintainers of the TPP2D package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TPP2D.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 1977/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TPP2D 1.10.0  (landing page)
Nils Kurzawa
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/TPP2D
git_branch: RELEASE_3_14
git_last_commit: 2456623
git_last_commit_date: 2021-10-26 12:51:59 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TPP2D
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TPP2D.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TPP2D_1.10.0.tar.gz
StartedAt: 2022-04-12 19:29:53 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 19:33:49 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 235.4 seconds
RetCode: 0
Status:   OK  
CheckDir: TPP2D.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TPP2D.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TPP2D_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/TPP2D.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.10.0’
* 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              17.665  0.104  17.786
computeFStatFromParams        17.283  0.099  17.399
fitAndEvalDataset             16.271  0.090  16.375
computeFstat                  12.628  0.073  12.711
plot2dTppVolcano              11.610  0.091  11.713
competeModels                  8.425  0.092   8.520
bootstrapNullAlternativeModel  5.739  0.062   5.807
findHits                       3.612  0.022  10.888
getFDR                         3.357  0.027  10.419
getPvalues                     1.866  0.013   9.050
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TPP2D
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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")
[1] "Warning: You have specificed B < 20, it is recommended to use at least B = 20 in order to obtain reliable results."

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
> 
> proc.time()
   user  system elapsed 
 13.508   0.363  13.863 

Example timings

TPP2D.Rcheck/TPP2D-Ex.timings

nameusersystemelapsed
TPP_importCheckConfigTable0.1490.0060.156
annotateDataList1.4570.0601.517
bootstrapNull0.1610.0083.063
bootstrapNullAlternativeModel5.7390.0625.807
competeModels8.4250.0928.520
computeFStatFromParams17.283 0.09917.399
computeFstat12.628 0.07312.711
configWide2Long0.0140.0010.015
filterOutContaminants0.0840.0030.087
findHits 3.612 0.02210.888
fitAndEvalDataset16.271 0.09016.375
fitH0Model0.5940.0110.616
fitH1Model3.0170.0243.044
getFDR 3.357 0.02710.419
getModelParamsDf17.665 0.10417.786
getPEC504Temperature0.7600.0050.766
getPvalues1.8660.0139.050
gg_qq0.1100.0020.112
import2dDataset1.2560.0121.268
import2dMain0.6250.0090.636
plot2dTppFcHeatmap0.3490.0080.357
plot2dTppFit0.4190.0040.423
plot2dTppProfile0.3820.0030.385
plot2dTppRelProfile0.4940.0030.498
plot2dTppVolcano11.610 0.09111.713
recomputeSignalFromRatios0.0910.0010.093
renameColumns1.1330.0121.145
resolveAmbiguousProteinNames0.0970.0010.097
runTPP2D4.6880.0414.777
tpp2dExperiment-class000