Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2022-10-19 13:20:59 -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 TPP2D on nebbiolo1


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 2030/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TPP2D 1.12.0  (landing page)
Nils Kurzawa
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/TPP2D
git_branch: RELEASE_3_15
git_last_commit: 80a0003
git_last_commit_date: 2022-04-26 11:55:55 -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: TPP2D
Version: 1.12.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TPP2D.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TPP2D_1.12.0.tar.gz
StartedAt: 2022-10-18 22:11:28 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 22:13:27 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 119.4 seconds
RetCode: 0
Status:   OK  
CheckDir: TPP2D.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TPP2D.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TPP2D_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/TPP2D.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TPP2D/DESCRIPTION’ ... OK
* this is package ‘TPP2D’ version ‘1.12.0’
* 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
computeFStatFromParams 7.591  0.044   7.635
getModelParamsDf       7.278  0.004   7.282
fitAndEvalDataset      6.897  0.004   6.901
plot2dTppVolcano       5.982  0.024   6.006
computeFstat           5.857  0.032   5.890
getFDR                 1.814  0.016   5.378
findHits               1.669  0.008   5.845
* 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL TPP2D
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 2 | SKIP 0 | PASS 18 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 18 ]
> 
> proc.time()
   user  system elapsed 
  6.982   0.224   7.192 

Example timings

TPP2D.Rcheck/TPP2D-Ex.timings

nameusersystemelapsed
TPP_importCheckConfigTable0.1780.0160.194
annotateDataList0.7010.0510.752
bootstrapNull0.0980.0001.849
bootstrapNullAlternativeModel2.6940.0602.754
competeModels3.5820.0203.603
computeFStatFromParams7.5910.0447.635
computeFstat5.8570.0325.890
configWide2Long0.0110.0000.011
filterOutContaminants0.0430.0000.043
findHits1.6690.0085.845
fitAndEvalDataset6.8970.0046.901
fitH0Model0.2630.0000.264
fitH1Model1.1770.0361.214
getFDR1.8140.0165.378
getModelParamsDf7.2780.0047.282
getPEC504Temperature0.3510.0000.351
getPvalues0.8090.0004.865
gg_qq0.0600.0000.061
import2dDataset0.6380.0070.647
import2dMain0.3210.0010.321
plot2dTppFcHeatmap0.1960.0000.197
plot2dTppFit0.2550.0040.258
plot2dTppProfile0.2470.0000.247
plot2dTppRelProfile0.2770.0000.277
plot2dTppVolcano5.9820.0246.006
recomputeSignalFromRatios0.0650.0030.069
renameColumns0.6900.0050.694
resolveAmbiguousProteinNames0.0470.0040.051
runTPP2D2.3690.0152.386
tpp2dExperiment-class000