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This page was generated on 2025-09-02 12:02 -0400 (Tue, 02 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 2199/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TPP2D 1.25.0  (landing page)
Nils Kurzawa
Snapshot Date: 2025-09-01 13:45 -0400 (Mon, 01 Sep 2025)
git_url: https://git.bioconductor.org/packages/TPP2D
git_branch: devel
git_last_commit: 3734392
git_last_commit_date: 2025-04-15 11:46:18 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    NA    NA  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for TPP2D on lconway

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: 1.25.0
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_1.25.0.tar.gz
StartedAt: 2025-09-02 00:23:26 -0400 (Tue, 02 Sep 2025)
EndedAt: 2025-09-02 00:25:28 -0400 (Tue, 02 Sep 2025)
EllapsedTime: 122.2 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_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/TPP2D.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.25.0’
* 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 5.411  0.076   5.508
getModelParamsDf       5.353  0.077   5.471
fitAndEvalDataset      5.040  0.075   5.147
* 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-3.22-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 ‘1.25.0’
** 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 (2025-06-13) -- "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 
  6.295   0.293   6.633 

Example timings

TPP2D.Rcheck/TPP2D-Ex.timings

nameusersystemelapsed
TPP_importCheckConfigTable0.0170.0040.022
annotateDataList0.7070.0220.734
bootstrapNull0.0710.0152.092
bootstrapNullAlternativeModel2.0340.0352.080
bootstrapNullAlternativeModelFast2.2430.0332.289
competeModels2.5340.0412.585
computeFStatFromParams5.4110.0765.508
computeFstat4.2640.0604.348
configWide2Long0.0040.0010.006
filterOutContaminants0.0400.0010.042
findHits1.0200.0164.446
fitAndEvalDataset5.0400.0755.147
fitH0Model0.1190.0020.121
fitH1Model0.7570.0090.770
getFDR0.9740.0184.164
getModelParamsDf5.3530.0775.471
getPEC504Temperature0.3490.0040.356
getPvalues0.5600.0143.919
gg_qq0.0690.0020.072
import2dDataset0.4580.0060.468
import2dMain0.2040.0040.210
plot2dTppFcHeatmap0.2380.0050.247
plot2dTppFit0.3090.0040.315
plot2dTppProfile0.2770.0030.280
plot2dTppRelProfile0.2810.0040.288
plot2dTppVolcano4.3470.0514.428
recomputeSignalFromRatios0.0510.0010.054
renameColumns0.4650.0060.474
resolveAmbiguousProteinNames0.0290.0010.030
runTPP2D1.8000.0211.836
tpp2dExperiment-class0.0000.0000.001