Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:51 -0400 (Fri, 15 Oct 2021).
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. |
Package 1649/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rtpca 1.2.0 (landing page) Nils Kurzawa
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: Rtpca |
Version: 1.2.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Rtpca.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Rtpca_1.2.0.tar.gz |
StartedAt: 2021-10-14 11:26:20 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:27:11 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 51.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Rtpca.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Rtpca.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Rtpca_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/Rtpca.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (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 ... OK * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/Rtpca.Rcheck/00check.log’ for details.
Rtpca.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL Rtpca ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-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)
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-pc-linux-gnu (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 3.965 0.147 4.097
Rtpca.Rcheck/Rtpca-Ex.timings
name | user | system | elapsed | |
CommonFeatures-tpcaResult-method | 0.418 | 0.020 | 0.438 | |
ComplexAnnotation-tpcaResult-method | 0.000 | 0.002 | 0.003 | |
ComplexBackgroundDistributionList-tpcaResult-method | 0.001 | 0.001 | 0.001 | |
ComplexRocTable-tpcaResult-method | 0.000 | 0.001 | 0.001 | |
ContrastCondName-tpcaResult-method | 0 | 0 | 0 | |
ContrastDistMat-tpcaResult-method | 0.000 | 0.001 | 0.001 | |
ContrastList-tpcaResult-method | 0.000 | 0.000 | 0.001 | |
CtrlCondName-tpcaResult-method | 0.000 | 0.000 | 0.001 | |
DistMat-tpcaResult-method | 0.001 | 0.000 | 0.001 | |
DistMethod-tpcaResult-method | 0.000 | 0.001 | 0.001 | |
ObjList-tpcaResult-method | 0.000 | 0.002 | 0.002 | |
PPiAnnotation-tpcaResult-method | 0.000 | 0.001 | 0.001 | |
PPiRocTable-tpcaResult-method | 0.001 | 0.000 | 0.001 | |
PPiRocTableAnno-tpcaResult-method | 0.001 | 0.000 | 0.001 | |
SetCommonFeatures-tpcaResult-method | 0.002 | 0.000 | 0.002 | |
SetComplexAnnotation-tpcaResult-method | 0.003 | 0.000 | 0.003 | |
SetComplexBackgroundDistributionList-tpcaResult-method | 0.000 | 0.002 | 0.002 | |
SetComplexRocTable-tpcaResult-method | 0.001 | 0.002 | 0.002 | |
SetContrastCondName-tpcaResult-method | 0.002 | 0.000 | 0.001 | |
SetContrastDistMat-tpcaResult-method | 0.003 | 0.000 | 0.002 | |
SetCtrlCondName-tpcaResult-method | 0.001 | 0.000 | 0.002 | |
SetDiffTpcaResultTable-tpcaResult-method | 0.001 | 0.002 | 0.003 | |
SetDistMat-tpcaResult-method | 0.000 | 0.002 | 0.002 | |
SetDistMethod-tpcaResult-method | 0.000 | 0.001 | 0.001 | |
SetPPiRocTable-tpcaResult-method | 0.000 | 0.002 | 0.002 | |
SetPPiRocTableAnno-tpcaResult-method | 0.000 | 0.002 | 0.002 | |
SetSummaryMethod-tpcaResult-method | 0.000 | 0.002 | 0.002 | |
SetTpcaResultTable-tpcaResult-method | 0.001 | 0.002 | 0.003 | |
SummaryMethod-tpcaResult-method | 0 | 0 | 0 | |
createDistMat | 0.143 | 0.004 | 0.147 | |
diffTpcaResultTable-tpcaResult-method | 0.001 | 0.000 | 0.001 | |
ori_et_al_complex_ppis | 0.041 | 0.004 | 0.044 | |
ori_et_al_complexes_df | 0.007 | 0.003 | 0.011 | |
plotComplexRoc | 0.168 | 0.003 | 0.172 | |
plotDiffTpcaVolcano | 0.216 | 0.000 | 0.216 | |
plotPPiProfiles | 1.296 | 0.068 | 1.364 | |
plotPPiRoc | 0.120 | 0.004 | 0.124 | |
plotTpcaVolcano | 0.725 | 0.008 | 0.732 | |
runDiffTPCA | 0.129 | 0.000 | 0.129 | |
runTPCA | 0.230 | 0.000 | 0.231 | |
string_ppi_df | 0.855 | 0.008 | 0.862 | |
tpcaResult-class | 0.001 | 0.000 | 0.001 | |
tpcaResultTable-tpcaResult-method | 0.002 | 0.000 | 0.002 | |