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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 1207/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagenomeSeq 1.48.0  (landing page)
Joseph N. Paulson
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/metagenomeSeq
git_branch: RELEASE_3_20
git_last_commit: 8c1ee74
git_last_commit_date: 2024-10-29 09:45:32 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for metagenomeSeq on merida1

To the developers/maintainers of the metagenomeSeq package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: metagenomeSeq
Version: 1.48.0
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_1.48.0.tar.gz
StartedAt: 2024-12-20 05:44:26 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 05:52:26 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 480.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: metagenomeSeq.Rcheck
Warnings: NA

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_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/metagenomeSeq.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.48.0’
* 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 code 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  29.171  1.790  31.649
exportMat    2.923  7.657  10.843
extractMR    2.160  3.326   5.566
MRfulltable  1.833  0.059  11.158
fitDO        0.633  0.024   6.005
fitPA        0.608  0.031   5.858
plotBubble   0.473  0.046   5.617
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Failure ('test-fitZig.R:67:3'): `fitZig` function treats a matrix the same ──
  `fit` not equal to `fit2`.
  Component "eb": Component "df.prior": Mean relative difference: 0.01522971
  Component "eb": Component "s2.prior": Mean relative difference: 0.0208853
  Component "eb": Component "var.prior": Mean relative difference: 0.01489299
  Component "eb": Component "s2.post": Mean relative difference: 0.002818974
  Component "eb": Component "t": Mean relative difference: 0.001476944
  Component "eb": Component "df.total": Mean relative difference: 0.002226407
  Component "eb": Component "p.value": Mean relative difference: 0.001045802
  Component "eb": Component "lods": Mean relative difference: 0.002124969
  Component "eb": Component "F": Mean relative difference: 0.002818882
  
  [ FAIL 2 | WARN 6 | SKIP 0 | PASS 13 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/metagenomeSeq.Rcheck/00check.log’
for details.


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/4.4-x86_64/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.fail


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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] '1.48.0'
> # 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, aperm, 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, saveRDS, setdiff, 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 4.1-8
Loading required package: RColorBrewer
[ FAIL 2 | WARN 6 | SKIP 0 | PASS 13 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-fitZig.R:35:3'): `fitZig` function provides expected values prior to split ──
`fit` not equal to `fit2`.
Component "eb": Component "df.prior": Mean relative difference: 0.01522971
Component "eb": Component "s2.prior": Mean relative difference: 0.0208853
Component "eb": Component "var.prior": Mean relative difference: 0.01489299
Component "eb": Component "s2.post": Mean relative difference: 0.002818974
Component "eb": Component "t": Mean relative difference: 0.001476944
Component "eb": Component "df.total": Mean relative difference: 0.002226407
Component "eb": Component "p.value": Mean relative difference: 0.001045802
Component "eb": Component "lods": Mean relative difference: 0.002124969
Component "eb": Component "F": Mean relative difference: 0.002818882
── Failure ('test-fitZig.R:67:3'): `fitZig` function treats a matrix the same ──
`fit` not equal to `fit2`.
Component "eb": Component "df.prior": Mean relative difference: 0.01522971
Component "eb": Component "s2.prior": Mean relative difference: 0.0208853
Component "eb": Component "var.prior": Mean relative difference: 0.01489299
Component "eb": Component "s2.post": Mean relative difference: 0.002818974
Component "eb": Component "t": Mean relative difference: 0.001476944
Component "eb": Component "df.total": Mean relative difference: 0.002226407
Component "eb": Component "p.value": Mean relative difference: 0.001045802
Component "eb": Component "lods": Mean relative difference: 0.002124969
Component "eb": Component "F": Mean relative difference: 0.002818882

[ FAIL 2 | WARN 6 | SKIP 0 | PASS 13 ]
Error: Test failures
Execution halted

Example timings

metagenomeSeq.Rcheck/metagenomeSeq-Ex.timings

nameusersystemelapsed
MRcoefs2.1420.1162.284
MRcounts0.7040.0470.770
MRexperiment-class0.0000.0010.001
MRfulltable 1.833 0.05911.158
MRtable1.8100.0351.859
aggregateBySample0.2820.0200.305
aggregateByTaxonomy0.3330.0170.354
biom2MRexperiment0.4640.0210.525
calcNormFactors0.9780.1291.133
correctIndices0.1880.0160.205
correlationTest0.4040.0310.437
cumNorm0.7590.1130.892
cumNormMat0.8220.1380.980
cumNormStat0.9850.0621.060
cumNormStatFast0.5160.0330.554
expSummary0.1750.0140.192
exportMat 2.923 7.65710.843
exportStats0.6430.0330.682
extractMR2.1603.3265.566
filterData0.2980.0250.325
fitDO0.6330.0246.005
fitFeatureModel1.9860.0732.084
fitLogNormal2.4990.2032.752
fitMultipleTimeSeries2.7520.1962.984
fitPA0.6080.0315.858
fitSSTimeSeries0.6710.0320.710
fitTimeSeries0.6800.0520.740
fitZig2.5880.1812.777
libSize-set0.5160.0430.562
libSize0.4650.0280.496
loadBiom0.0800.0030.084
loadMeta0.0350.0030.038
loadMetaQ0.0000.0010.001
loadPhenoData0.0200.0020.022
makeLabels0.0000.0010.001
mergeMRexperiments2.1090.2532.369
newMRexperiment0.0640.0010.067
normFactors-set0.5140.0090.545
normFactors0.4620.0130.479
plotBubble0.4730.0465.617
plotClassTimeSeries1.6340.1451.796
plotCorr0.8710.0680.951
plotFeature0.2520.0240.281
plotGenus0.2460.0320.281
plotMRheatmap4.790.145.00
plotOTU0.2530.0150.271
plotOrd0.3790.0170.397
plotRare0.2260.0120.240
plotTimeSeries1.5940.1361.752
posteriorProbs2.5420.2882.880
returnAppropriateObj0.4670.0250.499
ssFit0.0000.0010.001
ssIntervalCandidate0.0010.0010.001
ssPerm0.0000.0000.001
ssPermAnalysis0.0000.0000.001
trapz0.0010.0010.002
ts2MRexperiment2.6240.1592.813
uniqueFeatures0.2280.0590.293
wrenchNorm29.171 1.79031.649
zigControl0.0000.0000.001