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This page was generated on 2023-04-12 11:05:10 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 nebbiolo2


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 1195/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiomeExplorer 1.8.0  (landing page)
Janina Reeder
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/microbiomeExplorer
git_branch: RELEASE_3_16
git_last_commit: a1ed081
git_last_commit_date: 2022-11-01 11:23:06 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: microbiomeExplorer
Version: 1.8.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:microbiomeExplorer.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings microbiomeExplorer_1.8.0.tar.gz
StartedAt: 2023-04-10 21:56:59 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:59:14 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 135.8 seconds
RetCode: 0
Status:   OK  
CheckDir: microbiomeExplorer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:microbiomeExplorer.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings microbiomeExplorer_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/microbiomeExplorer.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘microbiomeExplorer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘microbiomeExplorer’ 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 ... 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 ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
    shiny     2.9Mb
* 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 loading without being on the library search path ... 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 ...
  ‘exploreMouseData.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/microbiomeExplorer.Rcheck/00check.log’
for details.



Installation output

microbiomeExplorer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL microbiomeExplorer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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, aperm, 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 4.1-7
Loading required package: RColorBrewer
> 
> test_check("microbiomeExplorer")
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 61 ]

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

[ FAIL 0 | WARN 2 | SKIP 1 | PASS 61 ]
> 
> proc.time()
   user  system elapsed 
  8.863   0.512   9.358 

Example timings

microbiomeExplorer.Rcheck/microbiomeExplorer-Ex.timings

nameusersystemelapsed
aggFeatures0.5350.0160.551
aggregationTabUI0.0420.0000.042
calculatePCAs0.2980.0680.366
computeDistMat0.2440.0430.288
corrAnalysisUI1.2150.0391.256
corrFeature0.6870.0760.763
corrPhenotype0.8000.0510.851
dataInputUI0.0610.0000.061
diffAnalysisUI0.0580.0040.062
featureAnalysisUI0.0490.0000.049
featureTableUI0.0210.0000.022
filterByPheno0.1900.0120.202
filterMEData1.0660.0161.083
interAnalysisUI0.1090.0000.110
intraAnalysisUI0.1230.0040.127
longAnalysisUI0.0530.0000.052
makeQCPlot0.2150.0080.223
normalizeData0.9150.0360.951
phenotypeTableUI0.0270.0000.027
plotAbundance0.9150.1041.019
plotAlpha0.3440.0160.360
plotAvgAbundance0.4310.0080.439
plotBeta0.2560.0200.276
plotHeatmap1.3810.0151.381
plotLongFeature0.3990.0200.420
plotSingleFeature0.3630.0250.386
plotlyHistogram0.1870.0270.215
plotlySampleBarplot0.2010.0200.221
replaceWithUnknown0.1550.0320.186
reportListUI0.0310.0000.032
rollDownFeatures0.1200.0130.132
runDiffTest1.1470.0041.152