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This page was generated on 2025-01-02 12:05 -0500 (Thu, 02 Jan 2025).

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: 2024-12-30 13:00 -0500 (Mon, 30 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 palomino8

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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metagenomeSeq.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings metagenomeSeq_1.48.0.tar.gz
StartedAt: 2024-12-31 03:06:20 -0500 (Tue, 31 Dec 2024)
EndedAt: 2024-12-31 03:11:02 -0500 (Tue, 31 Dec 2024)
EllapsedTime: 282.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: metagenomeSeq.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metagenomeSeq.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings metagenomeSeq_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/metagenomeSeq.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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  18.09   0.78   18.89
MRfulltable  1.23   0.15    6.45
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/metagenomeSeq.Rcheck/00check.log'
for details.


Installation output

metagenomeSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL metagenomeSeq
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-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.fail


R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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
MRcoefs1.290.161.45
MRcounts0.580.130.70
MRexperiment-class000
MRfulltable1.230.156.45
MRtable1.230.131.36
aggregateBySample0.110.010.12
aggregateByTaxonomy0.180.020.19
biom2MRexperiment0.230.030.27
calcNormFactors0.760.110.89
correctIndices0.160.010.17
correlationTest0.230.070.30
cumNorm0.520.090.61
cumNormMat0.720.090.81
cumNormStat0.840.100.94
cumNormStatFast0.480.000.48
expSummary0.140.020.16
exportMat1.941.773.83
exportStats0.500.090.60
extractMR1.900.912.81
filterData0.220.040.27
fitDO0.440.113.39
fitFeatureModel1.230.191.45
fitLogNormal2.350.392.74
fitMultipleTimeSeries2.220.412.62
fitPA0.500.123.25
fitSSTimeSeries0.480.090.58
fitTimeSeries0.600.070.64
fitZig2.500.432.94
libSize-set0.340.100.44
libSize0.330.140.46
loadBiom0.040.000.05
loadMeta0.050.000.05
loadMetaQ000
loadPhenoData0.020.000.01
makeLabels000
mergeMRexperiments1.810.422.25
newMRexperiment0.030.000.03
normFactors-set0.390.120.52
normFactors0.300.100.39
plotBubble0.300.033.21
plotClassTimeSeries1.170.281.45
plotCorr0.690.030.72
plotFeature0.180.010.21
plotGenus0.190.040.21
plotMRheatmap2.470.202.68
plotOTU0.250.030.28
plotOrd0.390.030.42
plotRare0.090.050.14
plotTimeSeries1.140.391.53
posteriorProbs2.290.342.63
returnAppropriateObj0.390.140.53
ssFit000
ssIntervalCandidate000
ssPerm000
ssPermAnalysis000
trapz000
ts2MRexperiment2.020.392.41
uniqueFeatures0.090.100.19
wrenchNorm18.09 0.7818.89
zigControl000