Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:12 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for Rtpca on palomino3


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? 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 1721/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rtpca 1.6.0  (landing page)
Nils Kurzawa
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/Rtpca
git_branch: RELEASE_3_15
git_last_commit: 8f5d600
git_last_commit_date: 2022-04-26 12:06:23 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Rtpca
Version: 1.6.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rtpca.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Rtpca_1.6.0.tar.gz
StartedAt: 2022-10-19 03:45:25 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 03:46:50 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 85.0 seconds
RetCode: 0
Status:   OK  
CheckDir: Rtpca.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rtpca.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Rtpca_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/Rtpca.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Rtpca/DESCRIPTION' ... OK
* this is package 'Rtpca' version '1.6.0'
* 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 '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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.15-bioc/meat/Rtpca.Rcheck/00check.log'
for details.



Installation output

Rtpca.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Rtpca
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   5.01    0.35    5.39 

Example timings

Rtpca.Rcheck/Rtpca-Ex.timings

nameusersystemelapsed
CommonFeatures-tpcaResult-method0.470.080.58
ComplexAnnotation-tpcaResult-method0.010.000.02
ComplexBackgroundDistributionList-tpcaResult-method000
ComplexRocTable-tpcaResult-method000
ContrastCondName-tpcaResult-method000
ContrastDistMat-tpcaResult-method0.020.000.01
ContrastList-tpcaResult-method000
CtrlCondName-tpcaResult-method000
DistMat-tpcaResult-method000
DistMethod-tpcaResult-method000
ObjList-tpcaResult-method000
PPiAnnotation-tpcaResult-method000
PPiRocTable-tpcaResult-method000
PPiRocTableAnno-tpcaResult-method000
SetCommonFeatures-tpcaResult-method000
SetComplexAnnotation-tpcaResult-method000
SetComplexBackgroundDistributionList-tpcaResult-method000
SetComplexRocTable-tpcaResult-method000
SetContrastCondName-tpcaResult-method000
SetContrastDistMat-tpcaResult-method000
SetCtrlCondName-tpcaResult-method000
SetDiffTpcaResultTable-tpcaResult-method000
SetDistMat-tpcaResult-method000
SetDistMethod-tpcaResult-method000
SetPPiRocTable-tpcaResult-method000
SetPPiRocTableAnno-tpcaResult-method000
SetSummaryMethod-tpcaResult-method000
SetTpcaResultTable-tpcaResult-method0.010.000.01
SummaryMethod-tpcaResult-method000
createDistMat0.140.020.16
diffTpcaResultTable-tpcaResult-method000
ori_et_al_complex_ppis0.080.170.25
ori_et_al_complexes_df0.010.050.06
plotComplexRoc0.170.010.19
plotDiffTpcaVolcano0.300.000.29
plotPPiProfiles1.470.061.53
plotPPiRoc0.100.000.09
plotTpcaVolcano0.890.111.00
runDiffTPCA0.190.000.19
runTPCA0.280.020.30
string_ppi_df0.830.000.83
tpcaResult-class000
tpcaResultTable-tpcaResult-method0.010.000.01