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This page was generated on 2021-10-15 15:06:51 -0400 (Fri, 15 Oct 2021).

CHECK results for Rtpca on machv2

To the developers/maintainers of the Rtpca package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rtpca.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 1649/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rtpca 1.2.0  (landing page)
Nils Kurzawa
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/Rtpca
git_branch: RELEASE_3_13
git_last_commit: acf0a22
git_last_commit_date: 2021-05-19 12:53:36 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Rtpca
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rtpca.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rtpca_1.2.0.tar.gz
StartedAt: 2021-10-14 23:27:14 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 23:28:38 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 84.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Rtpca.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rtpca.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rtpca_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/Rtpca.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 ‘Rtpca/DESCRIPTION’ ... OK
* this is package ‘Rtpca’ version ‘1.2.0’
* 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 ‘Rtpca’ 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 ... NOTE
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getRandomProteinPairs: no visible binding for global variable ‘pair’
Undefined global functions or variables:
  pair
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/Rtpca.Rcheck/00check.log’
for details.



Installation output

Rtpca.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rtpca
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘Rtpca’ ...
** 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 (Rtpca)

Tests output

Rtpca.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.

> library(testthat)
> library(Rtpca)
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

Loading required package: tidyr

Attaching package: 'tidyr'

The following object is masked from 'package:testthat':

    matches

> 
> test_check("Rtpca")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
  6.690   0.295   6.976 

Example timings

Rtpca.Rcheck/Rtpca-Ex.timings

nameusersystemelapsed
CommonFeatures-tpcaResult-method0.6420.0410.684
ComplexAnnotation-tpcaResult-method0.0020.0010.003
ComplexBackgroundDistributionList-tpcaResult-method0.0010.0000.002
ComplexRocTable-tpcaResult-method0.0020.0010.001
ContrastCondName-tpcaResult-method000
ContrastDistMat-tpcaResult-method0.0010.0010.001
ContrastList-tpcaResult-method0.0010.0000.001
CtrlCondName-tpcaResult-method000
DistMat-tpcaResult-method0.0010.0010.001
DistMethod-tpcaResult-method0.0000.0000.001
ObjList-tpcaResult-method0.0010.0010.002
PPiAnnotation-tpcaResult-method0.0020.0010.002
PPiRocTable-tpcaResult-method0.0020.0010.002
PPiRocTableAnno-tpcaResult-method0.0020.0010.002
SetCommonFeatures-tpcaResult-method0.0040.0020.005
SetComplexAnnotation-tpcaResult-method0.0040.0010.006
SetComplexBackgroundDistributionList-tpcaResult-method0.0020.0010.003
SetComplexRocTable-tpcaResult-method0.0020.0010.003
SetContrastCondName-tpcaResult-method0.0010.0000.001
SetContrastDistMat-tpcaResult-method0.0030.0010.004
SetCtrlCondName-tpcaResult-method0.0010.0010.002
SetDiffTpcaResultTable-tpcaResult-method0.0020.0020.003
SetDistMat-tpcaResult-method0.0020.0010.004
SetDistMethod-tpcaResult-method0.0020.0010.003
SetPPiRocTable-tpcaResult-method0.0020.0010.004
SetPPiRocTableAnno-tpcaResult-method0.0030.0020.004
SetSummaryMethod-tpcaResult-method0.0010.0010.002
SetTpcaResultTable-tpcaResult-method0.0030.0010.004
SummaryMethod-tpcaResult-method0.0010.0010.000
createDistMat0.2170.0070.225
diffTpcaResultTable-tpcaResult-method0.0010.0010.002
ori_et_al_complex_ppis0.0560.0050.060
ori_et_al_complexes_df0.0130.0020.015
plotComplexRoc0.2430.0060.249
plotDiffTpcaVolcano0.3500.0050.356
plotPPiProfiles1.8230.0841.909
plotPPiRoc0.1890.0080.196
plotTpcaVolcano1.3980.0351.435
runDiffTPCA0.2150.0040.220
runTPCA0.5360.0110.549
string_ppi_df1.6910.0161.711
tpcaResult-class0.0010.0000.001
tpcaResultTable-tpcaResult-method0.0030.0000.003