Package: metagenomeSeq

Version: 1.25.3

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_1.25.3.tar.gz

StartedAt: 2019-04-09 02:04:59 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:09:43 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 284.8 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_1.25.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/metagenomeSeq.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.25.3’
* 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/3.6/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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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] '1.25.3'
> # 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, 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: 21 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
124.507  10.314 136.082 

name	user	system	elapsed
MRcoefs	1.810	0.136	1.966
MRcounts	0.701	0.016	0.724
MRexperiment-class	0	0	0
MRfulltable	1.560	0.064	1.635
MRtable	1.509	0.037	1.562
aggregateBySample	0.212	0.014	0.232
aggregateByTaxonomy	0.263	0.022	0.287
biom2MRexperiment	0.468	0.013	0.483
calcNormFactors	0.643	0.104	0.755
correctIndices	0.167	0.017	0.189
correlationTest	0.340	0.026	0.368
cumNorm	0.747	0.112	0.871
cumNormMat	0.551	0.087	0.649
cumNormStat	0.763	0.064	0.842
cumNormStatFast	0.364	0.022	0.389
expSummary	0.145	0.015	0.162
exportMat	2.424	1.916	4.397
exportStats	0.605	0.061	0.674
extractMR	3.319	0.926	4.290
filterData	0.231	0.035	0.266
fitDO	0.617	0.055	4.170
fitFeatureModel	1.546	0.108	1.673
fitLogNormal	2.137	0.309	2.472
fitMultipleTimeSeries	2.126	0.146	2.311
fitPA	0.566	0.033	3.796
fitSSTimeSeries	1.303	0.132	1.448
fitTimeSeries	1.287	0.056	1.364
fitZig	2.256	0.388	2.675
libSize-set	0.527	0.034	0.568
libSize	0.471	0.012	0.502
loadBiom	0.060	0.001	0.061
loadMeta	0.027	0.001	0.028
loadMetaQ	0	0	0
loadPhenoData	0.037	0.000	0.037
makeLabels	0.000	0.001	0.000
mergeMRexperiments	2.236	0.321	2.584
newMRexperiment	0.034	0.000	0.033
normFactors-set	0.505	0.008	0.519
normFactors	0.475	0.003	0.483
plotBubble	0.371	0.079	3.562
plotClassTimeSeries	1.165	0.141	1.316
plotCorr	0.718	0.092	0.821
plotFeature	0.202	0.026	0.235
plotGenus	0.162	0.031	0.202
plotMRheatmap	3.895	0.189	4.121
plotOTU	0.169	0.019	0.191
plotOrd	0.313	0.060	0.379
plotRare	0.165	0.025	0.194
plotTimeSeries	1.084	0.086	1.181
posteriorProbs	2.030	0.396	2.458
returnAppropriateObj	0.499	0.028	0.537
ssFit	0.001	0.000	0.000
ssIntervalCandidate	0.001	0.000	0.000
ssPerm	0	0	0
ssPermAnalysis	0	0	0
trapz	0.001	0.001	0.001
ts2MRexperiment	2.148	0.133	2.309
uniqueFeatures	0.185	0.014	0.202
zigControl	0.001	0.000	0.000