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CHECK report for metagenomeSeq on malbec2

This page was generated on 2020-10-17 11:55:06 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE metagenomeSeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1038/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagenomeSeq 1.30.0
Joseph N. Paulson
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/metagenomeSeq
Branch: RELEASE_3_11
Last Commit: 7a6db6b
Last Changed Date: 2020-04-27 14:34:03 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: metagenomeSeq
Version: 1.30.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings metagenomeSeq_1.30.0.tar.gz
StartedAt: 2020-10-17 02:58:09 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:02:31 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 262.0 seconds
RetCode: 0
Status:  OK 
CheckDir: metagenomeSeq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings metagenomeSeq_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/metagenomeSeq.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.30.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
wrenchNorm  21.335  0.091  21.431
MRfulltable  1.690  0.146   7.403
* 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

metagenomeSeq.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL metagenomeSeq
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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)

Tests output

metagenomeSeq.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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] '1.30.0'
> # 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, 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 4.0-2
Loading required package: RColorBrewer
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 15 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
105.450   1.054 106.503 

Example timings

metagenomeSeq.Rcheck/metagenomeSeq-Ex.timings

nameusersystemelapsed
MRcoefs1.8620.1161.979
MRcounts0.6580.0440.701
MRexperiment-class0.0000.0000.001
MRfulltable1.6900.1467.403
MRtable1.7990.1121.911
aggregateBySample0.2750.0040.279
aggregateByTaxonomy0.3150.0000.316
biom2MRexperiment0.5250.0200.559
calcNormFactors1.130.021.15
correctIndices0.1860.0130.198
correlationTest0.3980.0200.418
cumNorm0.7670.0080.775
cumNormMat0.7380.0110.750
cumNormStat0.5840.0040.588
cumNormStatFast0.4930.0070.499
expSummary0.1130.0010.113
exportMat1.1240.8312.035
exportStats0.4520.0280.480
extractMR1.0310.3591.390
filterData0.1800.0040.184
fitDO0.5760.0533.448
fitFeatureModel1.2230.0801.303
fitLogNormal2.1400.0562.196
fitMultipleTimeSeries2.0240.0472.072
fitPA0.5260.0983.599
fitSSTimeSeries0.5040.0520.555
fitTimeSeries0.4120.0200.432
fitZig2.1460.0522.197
libSize-set0.3670.0200.387
libSize0.3280.0200.347
loadBiom0.0440.0000.044
loadMeta0.0180.0000.031
loadMetaQ000
loadPhenoData0.0080.0000.011
makeLabels0.0000.0000.001
mergeMRexperiments1.7080.1841.892
newMRexperiment0.0280.0000.029
normFactors-set0.3450.0360.381
normFactors0.3780.0360.415
plotBubble0.4420.0694.107
plotClassTimeSeries1.3950.0951.492
plotCorr0.5970.0330.628
plotFeature0.1600.0080.168
plotGenus0.1390.0240.163
plotMRheatmap2.0510.0162.067
plotOTU0.1390.0120.152
plotOrd0.2260.0150.242
plotRare0.1330.0080.142
plotTimeSeries1.2200.0281.261
posteriorProbs1.9580.0762.034
returnAppropriateObj0.3920.0310.424
ssFit0.0010.0010.000
ssIntervalCandidate000
ssPerm000
ssPermAnalysis0.0010.0000.000
trapz0.0010.0000.001
ts2MRexperiment2.2620.0192.282
uniqueFeatures0.1940.0160.210
wrenchNorm21.335 0.09121.431
zigControl000