Package: metagenomeSeq

Version: 1.22.0

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_1.22.0.tar.gz

StartedAt: 2018-10-16 22:29:39 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 22:32:24 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 165.3 seconds

RetCode: 0

Status:  OK

CheckDir: metagenomeSeq.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.22.0’
* 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

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

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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] '1.22.0'
> # 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 
 16.451   2.321  18.830 

name	user	system	elapsed
MRcoefs	1.753	0.129	1.890
MRcounts	0.679	0.012	0.692
MRexperiment-class	0.001	0.000	0.001
MRfulltable	1.409	0.056	1.472
MRtable	1.383	0.033	1.425
aggregateBySample	0.204	0.014	0.219
aggregateByTaxonomy	0.197	0.015	0.216
biom2MRexperiment	0.346	0.012	0.361
calcNormFactors	0.588	0.099	0.692
correctIndices	0.162	0.026	0.189
correlationTest	0.320	0.038	0.360
cumNorm	0.700	0.098	0.803
cumNormMat	0.587	0.103	0.695
cumNormStat	0.478	0.059	0.542
cumNormStatFast	0.350	0.031	0.382
expSummary	0.139	0.012	0.150
exportMat	2.337	1.797	4.166
exportStats	0.582	0.059	0.647
extractMR	3.365	0.842	4.237
filterData	0.219	0.032	0.253
fitDO	0.682	0.046	4.171
fitFeatureModel	1.475	0.065	1.549
fitLogNormal	2.134	0.285	2.436
fitMultipleTimeSeries	2.349	0.156	2.523
fitPA	0.595	0.059	3.682
fitSSTimeSeries	1.103	0.066	1.180
fitTimeSeries	1.235	0.087	1.327
fitZig	2.191	0.309	2.516
libSize-set	0.526	0.031	0.564
libSize	0.462	0.002	0.471
loadBiom	0.061	0.000	0.063
loadMeta	0.030	0.001	0.030
loadMetaQ	0.002	0.000	0.002
loadPhenoData	0.027	0.001	0.027
makeLabels	0.001	0.000	0.001
mergeMRexperiments	2.769	0.573	3.348
newMRexperiment	0.053	0.000	0.055
normFactors-set	0.532	0.024	0.558
normFactors	0.526	0.013	0.540
plotBubble	0.437	0.076	3.741
plotClassTimeSeries	1.481	0.220	1.704
plotCorr	0.723	0.083	0.808
plotFeature	0.218	0.021	0.242
plotGenus	0.209	0.034	0.246
plotMRheatmap	4.346	0.164	4.563
plotOTU	0.209	0.017	0.228
plotOrd	0.337	0.059	0.410
plotRare	0.179	0.028	0.221
plotTimeSeries	1.177	0.113	1.310
posteriorProbs	2.218	0.450	2.670
returnAppropriateObj	0.527	0.039	0.579
ssFit	0.002	0.000	0.001
ssIntervalCandidate	0.001	0.001	0.001
ssPerm	0.001	0.000	0.001
ssPermAnalysis	0.001	0.001	0.001
trapz	0.003	0.000	0.004
ts2MRexperiment	2.367	0.219	2.601
uniqueFeatures	0.202	0.018	0.220
zigControl	0.002	0.001	0.002