Package: metagenomeSeq

Version: 1.24.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings metagenomeSeq_1.24.1.tar.gz

StartedAt: 2019-04-16 01:16:32 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:18:53 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 140.3 seconds

RetCode: 0

Status:  OK

CheckDir: metagenomeSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings metagenomeSeq_1.24.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 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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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL metagenomeSeq
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 18.088   0.504  18.669 

name	user	system	elapsed
MRcoefs	1.220	0.088	1.310
MRcounts	0.568	0.040	0.609
MRexperiment-class	0	0	0
MRfulltable	1.296	0.052	1.351
MRtable	1.204	0.024	1.230
aggregateBySample	0.164	0.004	0.166
aggregateByTaxonomy	0.276	0.008	0.287
biom2MRexperiment	0.456	0.004	0.485
calcNormFactors	0.792	0.008	0.800
correctIndices	0.188	0.016	0.203
correlationTest	0.412	0.032	0.442
cumNorm	0.940	0.012	0.953
cumNormMat	0.748	0.012	0.760
cumNormStat	0.748	0.000	0.751
cumNormStatFast	0.452	0.004	0.456
expSummary	0.108	0.008	0.114
exportMat	1.140	0.776	1.932
exportStats	0.440	0.024	0.463
extractMR	0.952	0.340	1.292
filterData	0.164	0.016	0.181
fitDO	0.640	0.044	3.239
fitFeatureModel	1.592	0.124	1.720
fitLogNormal	2.264	0.056	2.346
fitMultipleTimeSeries	2.396	0.032	2.427
fitPA	0.520	0.048	3.434
fitSSTimeSeries	0.944	0.036	0.982
fitTimeSeries	0.936	0.012	0.950
fitZig	2.792	0.048	2.848
libSize-set	0.384	0.024	0.411
libSize	0.392	0.024	0.412
loadBiom	0.056	0.000	0.058
loadMeta	0.032	0.000	0.043
loadMetaQ	0	0	0
loadPhenoData	0.028	0.000	0.028
makeLabels	0.000	0.000	0.001
mergeMRexperiments	2.520	0.264	2.789
newMRexperiment	0.028	0.000	0.028
normFactors-set	0.436	0.028	0.463
normFactors	0.432	0.044	0.476
plotBubble	0.436	0.060	3.407
plotClassTimeSeries	1.068	0.092	1.164
plotCorr	0.480	0.024	0.502
plotFeature	0.152	0.004	0.155
plotGenus	0.132	0.016	0.147
plotMRheatmap	2.468	0.056	2.525
plotOTU	0.236	0.000	0.236
plotOrd	0.384	0.000	0.384
plotRare	0.224	0.008	0.233
plotTimeSeries	1.248	0.056	1.307
posteriorProbs	2.628	0.060	2.692
returnAppropriateObj	0.352	0.024	0.377
ssFit	0	0	0
ssIntervalCandidate	0	0	0
ssPerm	0	0	0
ssPermAnalysis	0	0	0
trapz	0	0	0
ts2MRexperiment	2.148	0.008	2.158
uniqueFeatures	0.22	0.00	0.22
zigControl	0.000	0.000	0.001