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This page was generated on 2021-10-15 15:06:56 -0400 (Fri, 15 Oct 2021).

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? here 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 1940/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TPP2D 1.8.0  (landing page)
Nils Kurzawa
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/TPP2D
git_branch: RELEASE_3_13
git_last_commit: 432c4fa
git_last_commit_date: 2021-05-19 12:43:43 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: TPP2D
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TPP2D.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TPP2D_1.8.0.tar.gz
StartedAt: 2021-10-15 00:50:27 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 00:53:16 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 168.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TPP2D.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TPP2D.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TPP2D_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/TPP2D.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.8.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... WARNING
Codoc mismatches from documentation object 'plot2dTppFit':
plot2dTppFit
  Code: function(df, name, model_type = "H0", optim_fun = .min_RSS_h0,
                 optim_fun_2 = NULL, maxit = 500, xlab =
                 "-log10(conc.)", ylab = "log2(summed intensities)",
                 dot_size = 1, line_type = "solid", fit_color =
                 "gray30")
  Docs: function(df, name, model_type = "H0", optim_fun = .min_RSS_h0,
                 optim_fun_2 = NULL, maxit = 500, xlab =
                 "-log10(conc.)", ylab = "log2(summed intensities)",
                 dot_size = 0.5, line_type = "dashed", fit_color =
                 "darkgray")
  Mismatches in argument default values:
    Name: 'dot_size' Code: 1 Docs: 0.5
    Name: 'line_type' Code: "solid" Docs: "dashed"
    Name: 'fit_color' Code: "gray30" Docs: "darkgray"

* 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 10.239  0.085  10.329
getModelParamsDf       10.239  0.067  10.314
fitAndEvalDataset       8.695  0.076   8.775
computeFstat            7.741  0.052   7.798
plot2dTppVolcano        7.298  0.063   7.368
competeModels           5.241  0.066   5.310
findHits                2.128  0.015   6.678
getFDR                  2.017  0.020   6.804
getPvalues              1.154  0.008   6.091
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/TPP2D.Rcheck/00check.log’
for details.



Installation output

TPP2D.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 
  8.414   0.260   8.661 

Example timings

TPP2D.Rcheck/TPP2D-Ex.timings

nameusersystemelapsed
TPP_importCheckConfigTable0.0450.0060.052
annotateDataList0.8590.0390.899
bootstrapNull0.1260.0082.561
bootstrapNullAlternativeModel3.0050.0333.040
competeModels5.2410.0665.310
computeFStatFromParams10.239 0.08510.329
computeFstat7.7410.0527.798
configWide2Long0.0100.0010.010
filterOutContaminants0.0490.0010.050
findHits2.1280.0156.678
fitAndEvalDataset8.6950.0768.775
fitH0Model0.2290.0040.232
fitH1Model1.3270.0081.335
getFDR2.0170.0206.804
getModelParamsDf10.239 0.06710.314
getPEC504Temperature0.6620.0060.668
getPvalues1.1540.0086.091
gg_qq0.0540.0010.055
import2dDataset0.7460.0040.750
import2dMain0.4070.0030.411
plot2dTppFcHeatmap0.3320.0070.340
plot2dTppFit0.3730.0030.376
plot2dTppProfile0.3850.0020.387
plot2dTppRelProfile0.3630.0030.366
plot2dTppVolcano7.2980.0637.368
recomputeSignalFromRatios0.0540.0010.055
renameColumns0.8320.0050.838
resolveAmbiguousProteinNames0.0590.0000.059
runTPP2D2.4070.0152.426
tpp2dExperiment-class000