Package: metagenomeSeq

Version: 1.28.2

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings metagenomeSeq_1.28.2.tar.gz

StartedAt: 2020-04-15 01:41:43 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:46:20 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 276.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: metagenomeSeq.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings metagenomeSeq_1.28.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.28.2’
* 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 ... WARNING
Missing link or links in documentation object 'MRihw-fitFeatureModelResults.Rd':
  ‘fitFeatureModelResults’ ‘fitZigResults’

Missing link or links in documentation object 'MRihw-fitZigResults.Rd':
  ‘fitFeatureModelResults’ ‘fitZigResults’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'MRcoefs':
  ‘IHWcov’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
Examples with CPU or elapsed time > 5s
             user system elapsed
wrenchNorm  17.90  0.100  18.084
MRfulltable  1.42  0.112   6.663
* 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: 2 WARNINGs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/metagenomeSeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL metagenomeSeq
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘metagenomeSeq’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘MRihw’ with signature ‘"fitFeatureModelResults"’: no definition for class “fitFeatureModelResults”
in method for ‘MRihw’ with signature ‘"fitZigResults"’: no definition for class “fitZigResults”
** help
*** installing help indices
** 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 (metagenomeSeq)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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] '1.28.2'
> # 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, 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, 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 3.0-2

Loading required package: RColorBrewer
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 15 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
118.756   1.376 120.467 

name	user	system	elapsed
MRcoefs	1.528	0.108	1.638
MRcounts	0.652	0.044	0.698
MRexperiment-class	0	0	0
MRfulltable	1.420	0.112	6.663
MRtable	1.320	0.088	1.428
aggregateBySample	0.156	0.008	0.167
aggregateByTaxonomy	0.240	0.016	0.258
biom2MRexperiment	0.308	0.004	0.323
calcNormFactors	0.984	0.016	1.004
correctIndices	0.204	0.004	0.207
correlationTest	0.376	0.032	0.486
cumNorm	0.680	0.016	0.694
cumNormMat	0.936	0.016	0.954
cumNormStat	0.572	0.012	0.585
cumNormStatFast	0.516	0.004	0.519
expSummary	0.132	0.008	0.142
exportMat	1.448	0.848	2.303
exportStats	0.432	0.036	0.470
extractMR	1.172	0.356	1.530
filterData	0.168	0.012	0.180
fitDO	0.644	0.056	3.917
fitFeatureModel	1.256	0.060	1.316
fitLogNormal	2.692	0.072	2.789
fitMultipleTimeSeries	2.308	0.016	2.330
fitPA	0.540	0.052	3.897
fitSSTimeSeries	0.540	0.072	0.657
fitTimeSeries	0.532	0.016	0.548
fitZig	2.936	0.084	3.024
libSize-set	0.456	0.032	0.490
libSize	0.396	0.028	0.427
loadBiom	0.036	0.000	0.037
loadMeta	0.016	0.000	0.019
loadMetaQ	0	0	0
loadPhenoData	0.028	0.000	0.032
makeLabels	0	0	0
mergeMRexperiments	2.360	0.188	2.563
newMRexperiment	0.048	0.000	0.049
normFactors-set	0.456	0.020	0.478
normFactors	0.404	0.020	0.424
plotBubble	0.372	0.052	3.926
plotClassTimeSeries	1.188	0.056	1.251
plotCorr	0.744	0.028	0.780
plotFeature	0.244	0.012	0.257
plotGenus	0.208	0.032	0.242
plotMRheatmap	2.520	0.032	2.554
plotOTU	0.132	0.000	0.136
plotOrd	0.248	0.004	0.255
plotRare	0.188	0.012	0.202
plotTimeSeries	1.312	0.004	1.319
posteriorProbs	2.216	0.040	2.261
returnAppropriateObj	0.392	0.032	0.425
ssFit	0	0	0
ssIntervalCandidate	0.000	0.000	0.001
ssPerm	0	0	0
ssPermAnalysis	0.000	0.000	0.001
trapz	0.004	0.000	0.001
ts2MRexperiment	2.548	0.048	2.598
uniqueFeatures	0.192	0.004	0.197
wrenchNorm	17.900	0.100	18.084
zigControl	0	0	0