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This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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

Package 1228/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiomeExplorer 1.15.0  (landing page)
Janina Reeder
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/microbiomeExplorer
git_branch: devel
git_last_commit: 3036201
git_last_commit_date: 2024-04-30 11:28:04 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 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
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for microbiomeExplorer on merida1

To the developers/maintainers of the microbiomeExplorer package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: microbiomeExplorer
Version: 1.15.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:microbiomeExplorer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings microbiomeExplorer_1.15.0.tar.gz
StartedAt: 2024-06-10 06:14:55 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 06:18:59 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 244.2 seconds
RetCode: 0
Status:   OK  
CheckDir: microbiomeExplorer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:microbiomeExplorer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings microbiomeExplorer_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/microbiomeExplorer.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microbiomeExplorer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘microbiomeExplorer’ version ‘1.15.0’
* 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   4.1Mb
    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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) plotBeta.Rd:46: Lost braces
    46 | \item{plotTitle}{Plot title. By default, becomes PCoA (code{dist.method}).}
       |                                                            ^
* 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 ... 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/microbiomeExplorer.Rcheck/00check.log’
for details.


Installation output

microbiomeExplorer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL microbiomeExplorer
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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, 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 4.1-8
Loading required package: RColorBrewer
> 
> test_check("microbiomeExplorer")
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 61 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-differential_functions.R:47:3'

[ FAIL 0 | WARN 2 | SKIP 1 | PASS 61 ]
> 
> proc.time()
   user  system elapsed 
 15.151   1.042  18.483 

Example timings

microbiomeExplorer.Rcheck/microbiomeExplorer-Ex.timings

nameusersystemelapsed
aggFeatures0.5290.0380.632
aggregationTabUI0.0730.0060.091
calculatePCAs0.7170.0470.870
computeDistMat0.7060.3161.164
corrAnalysisUI1.8560.1762.296
corrFeature1.4020.1011.697
corrPhenotype1.1860.0731.421
dataInputUI0.1570.0020.176
diffAnalysisUI0.1260.0020.143
featureAnalysisUI0.1260.0070.150
featureTableUI0.0570.0030.069
filterByPheno0.3950.0090.454
filterMEData2.1330.0532.430
interAnalysisUI0.3250.0080.381
intraAnalysisUI0.3190.0060.362
longAnalysisUI0.1510.0030.174
makeQCPlot0.4260.0680.561
normalizeData1.2080.0791.442
phenotypeTableUI0.0730.0010.086
plotAbundance1.0570.0901.300
plotAlpha0.6770.0850.872
plotAvgAbundance0.9040.0691.092
plotBeta0.5220.0790.683
plotHeatmap4.0600.1304.701
plotLongFeature0.7040.0760.919
plotSingleFeature0.6170.0720.776
plotlyHistogram0.3400.0660.462
plotlySampleBarplot0.2900.0660.398
replaceWithUnknown0.3510.3940.835
reportListUI0.0820.0010.091
rollDownFeatures0.2090.0070.244
runDiffTest1.3270.0311.518