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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 2122/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TPP2D 1.21.0  (landing page)
Nils Kurzawa
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/TPP2D
git_branch: devel
git_last_commit: 7a3f225
git_last_commit_date: 2024-04-30 11:14:51 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 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


CHECK results for TPP2D on palomino4

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: 1.21.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TPP2D.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TPP2D_1.21.0.tar.gz
StartedAt: 2024-06-10 11:23:05 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 11:30:37 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 451.5 seconds
RetCode: 0
Status:   OK  
CheckDir: TPP2D.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TPP2D.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TPP2D_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/TPP2D.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TPP2D/DESCRIPTION' ... OK
* this is package 'TPP2D' version '1.21.0'
* 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 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 5.60   0.11    5.70
getModelParamsDf       5.38   0.13    5.50
findHits               1.04   0.11   15.47
getFDR                 0.93   0.03   14.28
getPvalues             0.48   0.07   13.69
bootstrapNull          0.09   0.03   11.70
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/TPP2D.Rcheck/00check.log'
for details.


Installation output

TPP2D.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL TPP2D
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
   6.68   10.18   16.84 

Example timings

TPP2D.Rcheck/TPP2D-Ex.timings

nameusersystemelapsed
TPP_importCheckConfigTable0.030.010.05
annotateDataList0.550.110.69
bootstrapNull 0.09 0.0311.70
bootstrapNullAlternativeModel1.620.051.67
bootstrapNullAlternativeModelFast1.800.031.83
competeModels2.810.052.86
computeFStatFromParams5.600.115.70
computeFstat4.080.144.22
configWide2Long000
filterOutContaminants0.030.010.05
findHits 1.04 0.1115.47
fitAndEvalDataset4.770.114.88
fitH0Model0.100.020.12
fitH1Model0.820.030.85
getFDR 0.93 0.0314.28
getModelParamsDf5.380.135.50
getPEC504Temperature0.410.000.40
getPvalues 0.48 0.0713.69
gg_qq0.040.000.04
import2dDataset0.470.000.47
import2dMain0.220.020.23
plot2dTppFcHeatmap0.200.080.28
plot2dTppFit0.250.000.25
plot2dTppProfile0.250.000.25
plot2dTppRelProfile0.250.010.27
plot2dTppVolcano3.510.113.61
recomputeSignalFromRatios0.050.020.06
renameColumns0.50.00.5
resolveAmbiguousProteinNames0.030.000.03
runTPP2D1.620.051.67
tpp2dExperiment-class000