Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:23:14 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for metagenomeSeq on merida1


To the developers/maintainers of the metagenomeSeq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metagenomeSeq.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1129/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagenomeSeq 1.38.0  (landing page)
Joseph N. Paulson
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/metagenomeSeq
git_branch: RELEASE_3_15
git_last_commit: 50be9db
git_last_commit_date: 2022-04-26 11:14:17 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: metagenomeSeq
Version: 1.38.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metagenomeSeq_1.38.0.tar.gz
StartedAt: 2022-10-19 04:26:23 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 04:33:29 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 425.8 seconds
RetCode: 0
Status:   OK  
CheckDir: metagenomeSeq.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metagenomeSeq_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/metagenomeSeq.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.38.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
wrenchNorm  26.547  1.333  27.932
MRfulltable  1.914  0.049  10.871
fitDO        0.937  0.024   6.153
fitPA        0.696  0.043   5.775
plotBubble   0.500  0.021   5.418
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL metagenomeSeq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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] '1.38.0'
> # 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

Attaching package: 'BiocGenerics'

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.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 4.1-4
Loading required package: RColorBrewer
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 15 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
168.103   7.397 178.422 

Example timings

metagenomeSeq.Rcheck/metagenomeSeq-Ex.timings

nameusersystemelapsed
MRcoefs2.1240.1342.260
MRcounts0.8300.0360.868
MRexperiment-class0.0000.0000.001
MRfulltable 1.914 0.04910.871
MRtable1.9010.0361.939
aggregateBySample0.3110.0170.328
aggregateByTaxonomy0.3600.0170.377
biom2MRexperiment0.4300.0140.445
calcNormFactors0.9960.1271.125
correctIndices0.2280.0740.302
correlationTest0.4540.0310.487
cumNorm0.7870.1260.914
cumNormMat0.8330.1030.938
cumNormStat1.0150.0541.070
cumNormStatFast0.5440.0310.575
expSummary0.2020.0100.211
exportMat2.1381.9834.127
exportStats0.7140.0150.730
extractMR1.7260.9572.687
filterData0.3150.0150.331
fitDO0.9370.0246.153
fitFeatureModel1.9780.0522.033
fitLogNormal2.8780.1353.016
fitMultipleTimeSeries2.7420.1392.885
fitPA0.6960.0435.775
fitSSTimeSeries0.6870.0280.717
fitTimeSeries0.6990.0400.740
fitZig2.9620.0943.059
libSize-set0.6260.0460.672
libSize0.5870.0270.616
loadBiom0.0680.0000.068
loadMeta0.0320.0010.033
loadMetaQ000
loadPhenoData0.0200.0000.021
makeLabels0.0010.0000.001
mergeMRexperiments2.3960.2162.614
newMRexperiment0.0630.0000.063
normFactors-set0.6230.0290.653
normFactors0.5660.0100.576
plotBubble0.5000.0215.418
plotClassTimeSeries1.5850.1111.700
plotCorr0.8480.0430.893
plotFeature0.2780.0130.294
plotGenus0.2670.0120.280
plotMRheatmap4.4690.1084.588
plotOTU0.2680.0120.282
plotOrd0.3940.0230.418
plotRare0.2420.0190.262
plotTimeSeries1.4680.1431.613
posteriorProbs2.3550.1532.511
returnAppropriateObj0.5780.0130.593
ssFit000
ssIntervalCandidate000
ssPerm0.0000.0000.001
ssPermAnalysis000
trapz0.0000.0000.001
ts2MRexperiment2.6070.1412.753
uniqueFeatures0.2710.0120.283
wrenchNorm26.547 1.33327.932
zigControl000