Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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: 2024-11-19 13:40 -0500 (Tue, 19 Nov 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)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  


CHECK results for metagenomeSeq on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: metagenomeSeq
Version: 1.48.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings metagenomeSeq_1.48.0.tar.gz
StartedAt: 2024-11-20 09:38:27 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 09:43:05 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 278.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: metagenomeSeq.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings metagenomeSeq_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/metagenomeSeq.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 loading without being on the library search path ... 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  17.706  0.192  17.925
MRfulltable  1.386  0.024   6.680
* 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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/metagenomeSeq.Rcheck/00check.log’
for details.


Installation output

metagenomeSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL metagenomeSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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
MRcoefs1.5470.0641.613
MRcounts0.5330.0000.535
MRexperiment-class000
MRfulltable1.3860.0246.680
MRtable1.3770.0561.436
aggregateBySample0.1740.0040.178
aggregateByTaxonomy0.1900.0080.198
biom2MRexperiment0.2690.0120.283
calcNormFactors0.8800.0440.925
correctIndices0.1170.0040.122
correlationTest0.2470.0080.256
cumNorm0.6600.0040.665
cumNormMat0.6960.0080.705
cumNormStat0.9810.0281.010
cumNormStatFast0.3880.0040.393
expSummary0.1040.0040.108
exportMat1.0820.4991.584
exportStats0.5050.0120.518
extractMR0.5780.2110.791
filterData0.2540.0030.259
fitDO0.5060.0013.558
fitFeatureModel1.4640.0561.523
fitLogNormal2.6720.0722.749
fitMultipleTimeSeries2.4140.0752.494
fitPA0.5180.0083.415
fitSSTimeSeries0.5230.0200.545
fitTimeSeries0.5440.0040.549
fitZig2.2220.0322.258
libSize-set0.3160.0120.328
libSize0.2950.0000.296
loadBiom0.0450.0040.049
loadMeta0.0240.0000.025
loadMetaQ000
loadPhenoData0.0120.0000.012
makeLabels000
mergeMRexperiments2.0510.0602.113
newMRexperiment0.0360.0000.036
normFactors-set0.3120.0000.312
normFactors0.2750.0040.280
plotBubble0.3340.0073.183
plotClassTimeSeries1.1980.0271.228
plotCorr0.8300.0080.840
plotFeature0.1530.0120.166
plotGenus0.1530.0040.158
plotMRheatmap2.7110.0202.735
plotOTU0.1710.0000.171
plotOrd0.3180.0000.312
plotRare0.2520.0040.177
plotTimeSeries1.1560.0081.166
posteriorProbs2.4810.0522.538
returnAppropriateObj0.3000.0080.308
ssFit0.0010.0000.000
ssIntervalCandidate000
ssPerm000
ssPermAnalysis000
trapz000
ts2MRexperiment2.1090.0142.126
uniqueFeatures0.1210.0010.122
wrenchNorm17.706 0.19217.925
zigControl000