Multiple platform build/check report for BioC 3.8 - CHECK report for metagenomeSeq on merida1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings metagenomeSeq_1.24.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.24.1’
* 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 ‘metagenomeSeq’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL metagenomeSeq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘metagenomeSeq’ ...
** 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
* DONE (metagenomeSeq)

Tests output


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")
> packageVersion("metagenomeSeq")
[1] '1.24.1'
> # As suggested for opt-out option on testing by users, 
> # recommended by CRAN: http://adv-r.had.co.nz/Testing.html
> # Previously, best practice was to put all test files in inst/tests 
> # and ensure that R CMD check ran them by putting the following code in tests/test-all.R:  
> # >library(testthat)
> # >library(yourpackage)
> # >test_package("yourpackage")
> # Now, recommended practice is to put your tests in tests/testthat, 
> # and ensure R CMD check runs them by putting the following code in tests/test-all.R:
> # >library(testthat)
> # >test_check("yourpackage")
> # The advantage of this new structure is that the user has control over whether or not tests are installed using the –install-tests parameter to 
> # R CMD install, or INSTALL_opts = c(“–install-tests”) argument to install.packages(). I’m not sure why you wouldn’t want to install the tests, 
> # but now you have the flexibility as requested by CRAN maintainers.
> test_check("metagenomeSeq")
Loading required package: metagenomeSeq
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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
Loading required package: foreach
Loaded glmnet 2.0-16

Loading required package: RColorBrewer
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 13 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 18.047   2.582  20.829

Example timings

name	user	system	elapsed
MRcoefs	1.792	0.131	1.946
MRcounts	0.745	0.016	0.775
MRexperiment-class	0.000	0.000	0.001
MRfulltable	1.478	0.058	1.554
MRtable	1.479	0.039	1.536
aggregateBySample	0.233	0.021	0.258
aggregateByTaxonomy	0.268	0.022	0.290
biom2MRexperiment	0.429	0.013	0.449
calcNormFactors	0.611	0.103	0.726
correctIndices	0.169	0.023	0.195
correlationTest	0.362	0.025	0.392
cumNorm	0.692	0.117	0.821
cumNormMat	0.629	0.091	0.729
cumNormStat	0.584	0.061	0.650
cumNormStatFast	0.352	0.024	0.382
expSummary	0.158	0.013	0.173
exportMat	2.553	2.009	4.611
exportStats	0.637	0.066	0.716
extractMR	3.156	0.883	4.088
filterData	0.277	0.029	0.307
fitDO	0.681	0.050	4.422
fitFeatureModel	1.699	0.073	1.788
fitLogNormal	2.332	0.320	2.683
fitMultipleTimeSeries	2.418	0.177	2.617
fitPA	0.622	0.056	4.049
fitSSTimeSeries	1.359	0.061	1.428
fitTimeSeries	1.335	0.072	1.425
fitZig	2.291	0.320	2.644
libSize-set	0.483	0.026	0.512
libSize	0.486	0.006	0.503
loadBiom	0.044	0.000	0.045
loadMeta	0.022	0.001	0.024
loadMetaQ	0	0	0
loadPhenoData	0.031	0.001	0.031
makeLabels	0	0	0
mergeMRexperiments	2.413	0.507	2.941
newMRexperiment	0.034	0.000	0.034
normFactors-set	0.524	0.009	0.536
normFactors	0.462	0.023	0.486
plotBubble	0.367	0.071	3.389
plotClassTimeSeries	1.425	0.210	1.647
plotCorr	0.662	0.105	0.776
plotFeature	0.181	0.058	0.242
plotGenus	0.172	0.067	0.245
plotMRheatmap	3.933	0.154	4.135
plotOTU	0.203	0.019	0.226
plotOrd	0.313	0.043	0.359
plotRare	0.160	0.020	0.181
plotTimeSeries	1.094	0.101	1.205
posteriorProbs	2.103	0.446	2.580
returnAppropriateObj	0.503	0.029	0.538
ssFit	0	0	0
ssIntervalCandidate	0.000	0.000	0.001
ssPerm	0	0	0
ssPermAnalysis	0.001	0.000	0.000
trapz	0.000	0.000	0.001
ts2MRexperiment	2.185	0.224	2.426
uniqueFeatures	0.166	0.016	0.182
zigControl	0.001	0.000	0.001

CHECK report for metagenomeSeq on merida1

Summary

Command output

Installation output

Tests output

Example timings