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This page was generated on 2023-10-16 11:35:30 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1176/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagenomeSeq 1.42.0  (landing page)
Joseph N. Paulson
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/metagenomeSeq
git_branch: RELEASE_3_17
git_last_commit: 5ecb4dd
git_last_commit_date: 2023-04-25 10:26:39 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for metagenomeSeq on nebbiolo1


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: 1.42.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings metagenomeSeq_1.42.0.tar.gz
StartedAt: 2023-10-15 22:38:34 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 22:42:53 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 259.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: metagenomeSeq.Rcheck
Warnings: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:metagenomeSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings metagenomeSeq_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/metagenomeSeq.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.42.0’
* 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 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  13.283  0.228  13.510
MRfulltable  0.907  0.057   5.634
* 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:
  Loaded glmnet 4.1-8
  Loading required package: RColorBrewer
  [ FAIL 2 | WARN 6 | SKIP 0 | PASS 13 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-norm.R:28:3'): `cumNormStat` returns the correct value ───────
  cumNormStat(lungData) not equal to 0.7014946.
  names for target but not for current
  ── Failure ('test-norm.R:34:3'): `cumNormStatFast` returns the correct value ───
  cumNormStatFast(lungData) not equal to 0.7014946.
  names for target but not for current
  
  [ FAIL 2 | WARN 6 | SKIP 0 | PASS 13 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘fitTimeSeries.Rnw’... OK
  ‘metagenomeSeq.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/metagenomeSeq.Rcheck/00check.log’
for details.


Installation output

metagenomeSeq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL metagenomeSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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] '1.42.0'
> # 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, 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 4.1-8
Loading required package: RColorBrewer
[ FAIL 2 | WARN 6 | SKIP 0 | PASS 13 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-norm.R:28:3'): `cumNormStat` returns the correct value ───────
cumNormStat(lungData) not equal to 0.7014946.
names for target but not for current
── Failure ('test-norm.R:34:3'): `cumNormStatFast` returns the correct value ───
cumNormStatFast(lungData) not equal to 0.7014946.
names for target but not for current

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

Example timings

metagenomeSeq.Rcheck/metagenomeSeq-Ex.timings

nameusersystemelapsed
MRcoefs1.0910.1081.198
MRcounts0.4580.0170.473
MRexperiment-class000
MRfulltable0.9070.0575.634
MRtable1.0130.2911.305
aggregateBySample0.1380.0210.159
aggregateByTaxonomy0.1570.0200.177
biom2MRexperiment0.2290.0000.228
calcNormFactors0.4560.0310.488
correctIndices0.1030.0150.119
correlationTest0.2130.0240.237
cumNorm0.6350.0440.679
cumNormMat0.4520.0200.471
cumNormStat0.4600.0120.471
cumNormStatFast0.3120.0200.332
expSummary0.1020.0070.111
exportMat1.1972.9614.157
exportStats0.5910.0070.598
extractMR0.6841.3282.011
filterData0.1450.0090.152
fitDO0.3620.0022.851
fitFeatureModel1.0070.0121.019
fitLogNormal1.7990.0271.827
fitMultipleTimeSeries1.6230.0041.627
fitPA0.6370.0152.992
fitSSTimeSeries0.3820.0640.445
fitTimeSeries0.3890.0080.398
fitZig1.8230.0321.855
libSize-set0.3000.0160.316
libSize0.3110.0000.310
loadBiom0.0360.0000.036
loadMeta0.0170.0000.018
loadMetaQ000
loadPhenoData0.0070.0000.008
makeLabels0.0000.0000.001
mergeMRexperiments1.2580.1471.405
newMRexperiment0.0260.0000.026
normFactors-set0.3090.0080.315
normFactors0.2740.0040.278
plotBubble0.2550.0172.621
plotClassTimeSeries0.9780.0000.978
plotCorr0.4160.0160.432
plotFeature0.1380.0080.147
plotGenus0.1120.0160.127
plotMRheatmap1.8190.0561.875
plotOTU0.1280.0040.133
plotOrd0.1970.0040.201
plotRare0.1070.0160.123
plotTimeSeries0.9320.0160.947
posteriorProbs1.5760.0571.632
returnAppropriateObj0.2770.0130.291
ssFit000
ssIntervalCandidate000
ssPerm000
ssPermAnalysis000
trapz0.0000.0000.001
ts2MRexperiment1.5300.0341.563
uniqueFeatures0.1040.0140.117
wrenchNorm13.283 0.22813.510
zigControl000