| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:01 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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? 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 1148/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| microbiomeExplorer 1.5.0 (landing page) Janina Reeder
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: microbiomeExplorer |
| Version: 1.5.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:microbiomeExplorer.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings microbiomeExplorer_1.5.0.tar.gz |
| StartedAt: 2022-03-17 19:34:38 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:36:15 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 97.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: microbiomeExplorer.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:microbiomeExplorer.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings microbiomeExplorer_1.5.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/microbiomeExplorer.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'microbiomeExplorer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'microbiomeExplorer' version '1.5.0'
* 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 'microbiomeExplorer' can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.1Mb
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 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: 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/microbiomeExplorer.Rcheck/00check.log'
for details.
microbiomeExplorer.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL microbiomeExplorer
###
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* installing to library 'D:/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
converting help for package 'microbiomeExplorer'
finding HTML links ... done
abundanceHeatmap html
abundanceHeatmapUI html
addFeatData html
addPhenoData html
add_plotly_config html
add_plotly_layout html
aggFeatures html
aggregationTab html
aggregationTabUI html
alphaDiversity html
alphaDiversityUI html
avgAbundance html
avgAbundanceUI html
betaDiversity html
betaDiversityUI html
betaInput html
betaInputUI html
buildEmptyPlotlyPlot html
buildPlottingDF html
calculatePCAs html
computeCI_Interval html
computeDistMat html
corrAnalysis html
corrAnalysisUI html
corrFeature html
corrInput html
corrInputUI html
corrPhenotype html
createHeader html
dataInput html
dataInputUI html
designPairs html
diffAnalysis html
diffAnalysisUI html
diffInput html
diffInputUI html
diffTable html
diffTableUI html
extendPhenoData html
featAbundance html
featAbundanceUI html
featureAnalysis html
featureAnalysisUI html
featureCorr html
featureCorrUI html
featureInput html
featureInputUI html
featureTable html
featureTableUI html
fileUpload html
fileUploadUI html
filterByPheno html
filterMEData html
generateReport html
getFeatModCode html
getFileType html
getFilterChoices html
getLegendLevel html
getPhenoChanges html
getPhenoModCode html
getWidths html
heatmapInput html
heatmapInputUI html
interAnalysis html
interAnalysisUI html
intraAnalysis html
intraAnalysisUI html
intraInput html
intraInputUI html
longAnalysis html
longAnalysisUI html
longInput html
longInputUI html
longResults html
longResultsUI html
makeQCPlot html
normalizeData html
parseInteractionName html
phenotypeCorr html
phenotypeCorrUI html
phenotypeTable html
phenotypeTableUI html
plotAbundance html
plotAlpha html
plotAvgAbundance html
plotBeta html
plotHeatmap html
plotLongFeature html
plotSingleFeature html
plotlyHistogram html
plotlySampleBarplot html
readData html
relAbundance html
relAbundanceUI html
replaceWithUnknown html
reportList html
reportListUI html
reportRow html
reportRowUI html
rollDownFeatures html
runDiffTest html
runMicrobiomeExplorer html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'categoryCompare' is missing or broken
done
microbiomeExplorer.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(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 4.1-3
Loading required package: RColorBrewer
>
> test_check("microbiomeExplorer")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 67 ]
== Skipped tests ===============================================================
* On CRAN (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 67 ]
>
> proc.time()
user system elapsed
5.87 0.84 6.68
microbiomeExplorer.Rcheck/microbiomeExplorer-Ex.timings
| name | user | system | elapsed | |
| aggFeatures | 0.23 | 0.02 | 0.25 | |
| aggregationTabUI | 0.17 | 0.02 | 0.19 | |
| calculatePCAs | 0.22 | 0.04 | 0.26 | |
| computeDistMat | 0.19 | 0.08 | 0.27 | |
| corrAnalysisUI | 0.80 | 0.08 | 1.03 | |
| corrFeature | 0.47 | 0.01 | 0.49 | |
| corrPhenotype | 0.48 | 0.05 | 0.53 | |
| dataInputUI | 0.08 | 0.02 | 0.09 | |
| diffAnalysisUI | 0.06 | 0.00 | 0.06 | |
| featureAnalysisUI | 0.03 | 0.01 | 0.05 | |
| featureTableUI | 0.03 | 0.00 | 0.03 | |
| filterByPheno | 0.10 | 0.02 | 0.11 | |
| filterMEData | 0.90 | 0.05 | 0.95 | |
| interAnalysisUI | 0.11 | 0.01 | 0.13 | |
| intraAnalysisUI | 0.14 | 0.00 | 0.14 | |
| longAnalysisUI | 0.06 | 0.00 | 0.07 | |
| makeQCPlot | 0.11 | 0.08 | 0.18 | |
| normalizeData | 0.64 | 0.12 | 0.77 | |
| phenotypeTableUI | 0.03 | 0.00 | 0.03 | |
| plotAbundance | 0.52 | 0.05 | 0.56 | |
| plotAlpha | 0.37 | 0.06 | 0.44 | |
| plotAvgAbundance | 0.5 | 0.1 | 0.6 | |
| plotBeta | 0.25 | 0.08 | 0.32 | |
| plotHeatmap | 1.00 | 0.07 | 1.08 | |
| plotLongFeature | 0.27 | 0.03 | 0.53 | |
| plotSingleFeature | 0.22 | 0.07 | 0.28 | |
| plotlyHistogram | 0.15 | 0.04 | 0.21 | |
| plotlySampleBarplot | 0.35 | 0.07 | 0.40 | |
| replaceWithUnknown | 0.14 | 0.03 | 0.18 | |
| reportListUI | 0.01 | 0.00 | 0.01 | |
| rollDownFeatures | 0.08 | 0.00 | 0.07 | |
| runDiffTest | 0.20 | 0.01 | 0.22 | |