Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:31 -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 microbiomeExplorer on nebbiolo1


To the developers/maintainers of the microbiomeExplorer package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/microbiomeExplorer.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 1173/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiomeExplorer 1.6.1  (landing page)
Janina Reeder
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/microbiomeExplorer
git_branch: RELEASE_3_15
git_last_commit: 17f323d
git_last_commit_date: 2022-09-01 16:28:09 -0400 (Thu, 01 Sep 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: microbiomeExplorer
Version: 1.6.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:microbiomeExplorer.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings microbiomeExplorer_1.6.1.tar.gz
StartedAt: 2022-10-18 20:34:30 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 20:36:09 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 99.4 seconds
RetCode: 0
Status:   OK  
CheckDir: microbiomeExplorer.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:microbiomeExplorer.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings microbiomeExplorer_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/microbiomeExplorer.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microbiomeExplorer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘microbiomeExplorer’ version ‘1.6.1’
* 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 ‘microbiomeExplorer’ 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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: OK


Installation output

microbiomeExplorer.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL microbiomeExplorer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘microbiomeExplorer’ ...
** using staged installation
** R
** 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 (microbiomeExplorer)

Tests output

microbiomeExplorer.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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(microbiomeExplorer)
Loading required package: shiny
Loading required package: magrittr

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not

Loading required package: metagenomeSeq
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.1-4
Loading required package: RColorBrewer
> 
> test_check("microbiomeExplorer")
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 61 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (1)

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 61 ]
> 
> proc.time()
   user  system elapsed 
  8.032   0.479   8.500 

Example timings

microbiomeExplorer.Rcheck/microbiomeExplorer-Ex.timings

nameusersystemelapsed
aggFeatures0.4700.0200.491
aggregationTabUI0.0420.0040.045
calculatePCAs0.3000.0560.355
computeDistMat0.2240.1520.377
corrAnalysisUI0.8670.0480.915
corrFeature0.6590.0280.686
corrPhenotype0.7840.0320.817
dataInputUI0.1010.0120.112
diffAnalysisUI0.0540.0000.055
featureAnalysisUI0.0490.0000.049
featureTableUI0.0240.0000.024
filterByPheno0.1890.0160.204
filterMEData0.8370.0280.866
interAnalysisUI0.1240.0040.128
intraAnalysisUI0.1290.0040.132
longAnalysisUI0.0550.0000.055
makeQCPlot0.1780.0230.201
normalizeData0.8160.0760.892
phenotypeTableUI0.0330.0000.033
plotAbundance0.4990.0360.535
plotAlpha0.3190.0120.331
plotAvgAbundance0.3740.0200.393
plotBeta0.2220.0240.246
plotHeatmap1.2240.0521.262
plotLongFeature0.6660.0520.719
plotSingleFeature0.2830.0280.311
plotlyHistogram0.1630.0040.167
plotlySampleBarplot0.1280.0200.148
replaceWithUnknown0.1420.1880.331
reportListUI0.0240.0030.027
rollDownFeatures0.0910.0170.108
runDiffTest0.5830.0340.617