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This page was generated on 2025-08-21 11:40 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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

Package 2217/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TPP2D 1.24.0  (landing page)
Nils Kurzawa
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/TPP2D
git_branch: RELEASE_3_21
git_last_commit: 7f0e386
git_last_commit_date: 2025-04-15 11:46:18 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for TPP2D on merida1

To the developers/maintainers of the TPP2D package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: TPP2D
Version: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2025-08-19 12:42:37 -0400 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 12:46:53 -0400 (Tue, 19 Aug 2025)
EllapsedTime: 256.4 seconds
RetCode: 0
Status:   OK  
CheckDir: TPP2D.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/TPP2D.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TPP2D/DESCRIPTION’ ... OK
* this is package ‘TPP2D’ version ‘1.24.0’
* 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 code 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.min_RSS_h0’ ‘.min_RSS_h1_slope_pEC50’
* 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 13.945  0.098  14.794
fitAndEvalDataset      13.733  0.090  14.510
getModelParamsDf       13.594  0.086  14.394
computeFstat           11.236  0.084  11.879
plot2dTppVolcano        8.957  0.049   9.516
competeModels           7.006  0.100   7.475
findHits                2.619  0.025  10.796
getFDR                  2.563  0.023   9.636
getPvalues              1.386  0.017   9.444
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/TPP2D.Rcheck/00check.log’
for details.


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/4.5-x86_64/Resources/library’
* installing *source* package ‘TPP2D’ ...
** this is package ‘TPP2D’ version ‘1.24.0’
** 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 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
 13.740   0.473  14.714 

Example timings

TPP2D.Rcheck/TPP2D-Ex.timings

nameusersystemelapsed
TPP_importCheckConfigTable0.0340.0080.046
annotateDataList1.2540.0431.362
bootstrapNull0.1430.0304.305
bootstrapNullAlternativeModel3.6370.0493.860
bootstrapNullAlternativeModelFast4.1550.0254.352
competeModels7.0060.1007.475
computeFStatFromParams13.945 0.09814.794
computeFstat11.236 0.08411.879
configWide2Long0.0100.0030.012
filterOutContaminants0.0850.0030.094
findHits 2.619 0.02510.796
fitAndEvalDataset13.733 0.09014.510
fitH0Model0.2420.0030.257
fitH1Model2.1070.0142.248
getFDR2.5630.0239.636
getModelParamsDf13.594 0.08614.394
getPEC504Temperature0.8480.0080.897
getPvalues1.3860.0179.444
gg_qq0.1140.0030.117
import2dDataset0.9400.0100.982
import2dMain0.4300.0080.454
plot2dTppFcHeatmap0.4720.0080.498
plot2dTppFit0.7090.0070.742
plot2dTppProfile0.6960.0050.719
plot2dTppRelProfile0.6760.0060.720
plot2dTppVolcano8.9570.0499.516
recomputeSignalFromRatios0.1270.0040.136
renameColumns0.9370.0090.983
resolveAmbiguousProteinNames0.0660.0010.069
runTPP2D3.6180.0243.986
tpp2dExperiment-class0.0010.0000.001