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This page was generated on 2025-10-01 12:03 -0400 (Wed, 01 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4843
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4575
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 163/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.15.3  (landing page)
Matteo Calgaro
Snapshot Date: 2025-09-30 13:45 -0400 (Tue, 30 Sep 2025)
git_url: https://git.bioconductor.org/packages/benchdamic
git_branch: devel
git_last_commit: 9cef4f9
git_last_commit_date: 2025-07-29 12:29:48 -0400 (Tue, 29 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    TIMEOUT  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  


CHECK results for benchdamic on nebbiolo2

To the developers/maintainers of the benchdamic package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/benchdamic.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: benchdamic
Version: 1.15.3
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings benchdamic_1.15.3.tar.gz
StartedAt: 2025-09-30 21:19:35 -0400 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 21:59:35 -0400 (Tue, 30 Sep 2025)
EllapsedTime: 2400.6 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: benchdamic.Rcheck
Warnings: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings benchdamic_1.15.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/benchdamic.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘benchdamic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘benchdamic’ version ‘1.15.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘benchdamic’ 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 ... NOTE
Namespace in Imports field not imported from: ‘microbiome’
  All declared Imports should be used.
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'norm_DESeq2.Rd':
  ‘[DESeq2]{estimateSizeFactors}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 LazyData ... 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
createConcordance 10.440  0.422  17.416
areaCAT            7.514  0.358  18.375
plotConcordance    6.219  0.305   7.425
DA_ALDEx2          4.766  0.460   6.369
plotMD             4.757  0.047   6.147
runSplits          4.245  0.427   5.774
createTIEC         4.176  0.321   5.068
* 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:
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 333 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_getStatistics_getDA_extractDA.R:160:5'): Extract DA features from a list of methods: using threshold_pvalue
      and threshold_logfc ──
  length(unique(t1[[2]]$DA)) not equal to 3.
  1/1 mismatches
  [1] 2 - 3 == -1
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 333 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ...

Installation output

benchdamic.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL benchdamic
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘benchdamic’ ...
** this is package ‘benchdamic’ version ‘1.15.3’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
** testing if installed package can be loaded from final location
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
** testing if installed package keeps a record of temporary installation path
* DONE (benchdamic)

Tests output

benchdamic.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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)
> library(benchdamic)
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'spam'
> 
> test_check("benchdamic")
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 333 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_getStatistics_getDA_extractDA.R:160:5'): Extract DA features from a list of methods: using threshold_pvalue
    and threshold_logfc ──
length(unique(t1[[2]]$DA)) not equal to 3.
1/1 mismatches
[1] 2 - 3 == -1

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 333 ]
Error: Test failures
Execution halted

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
CAT0.0040.0010.006
DA_ALDEx24.7660.4606.369
DA_ANCOM0.9390.0611.074
DA_DESeq23.7410.2294.996
DA_MAST1.4670.0391.961
DA_Maaslin20.4020.0410.449
DA_NOISeq1.5210.2541.941
DA_Seurat2.3830.1013.128
DA_ZicoSeq0.8070.0020.921
DA_basic0.0350.0000.035
DA_corncob0.9670.0201.060
DA_dearseq0.0630.0050.072
DA_edgeR0.2060.0050.343
DA_limma0.0790.0000.125
DA_linda0.0500.0010.056
DA_maaslin30.5870.0060.652
DA_metagenomeSeq0.3600.0120.372
DA_mixMC1.0300.0181.157
RMSE0.0010.0000.001
addKnowledge0.2540.0030.256
areaCAT 7.514 0.35818.375
checkNormalization0.0000.0000.001
createColors0.0100.0000.029
createConcordance10.440 0.42217.416
createEnrichment0.3750.0100.837
createMocks0.0020.0020.004
createPositives1.1280.0251.251
createSplits0.0340.0010.035
createTIEC4.1760.3215.068
enrichmentTest0.1340.0020.162
extractDA0.1960.0000.208
extractStatistics0.1940.0110.205
fitDM0.0370.0020.039
fitHURDLE0.7640.0420.809
fitModels2.8090.1963.042
fitNB0.0600.0020.062
fitZIG0.0670.0010.072
fitZINB0.4880.0030.490
getDA0.0880.0010.089
getPositives0.0840.0010.085
getStatistics0.0770.0020.079
get_counts_metadata0.1250.0080.133
iterative_ordering0.010.000.01
meanDifferences0.0020.0000.002
norm_CSS0.0790.0010.080
norm_DESeq20.6140.0100.656
norm_TSS0.0480.0000.049
norm_edgeR0.0570.0010.067
plotConcordance6.2190.3057.425
plotContingency2.2480.0302.291
plotEnrichment2.1770.0082.547
plotFDR3.6240.0674.629
plotFPR3.1430.0833.485
plotKS3.2420.0743.638
plotLogP3.5610.0744.581
plotMD4.7570.0476.147
plotMutualFindings1.6010.0031.846
plotPositives1.0930.0031.403
plotQQ3.4120.0284.405
plotRMSE3.5760.2873.864
prepareObserved0.0020.0010.001
runDA0.6000.0650.806
runMocks0.8390.0631.156
runNormalizations0.7230.0700.808
runSplits4.2450.4275.774
setNormalizations0.0000.0000.001
set_ALDEx20.0050.0030.009
set_ANCOM0.0100.0000.016
set_DESeq20.0080.0020.022
set_MAST0.0050.0000.010
set_Maaslin20.0060.0020.016
set_NOISeq0.0050.0000.013
set_Seurat0.0050.0030.015
set_ZicoSeq0.0090.0040.013
set_basic0.0030.0000.002
set_corncob0.0050.0000.004
set_dearseq0.0010.0010.002
set_edgeR0.0150.0000.015
set_limma0.0100.0000.011
set_linda0.0060.0000.007
set_maaslin30.0060.0020.012
set_metagenomeSeq0.0060.0010.007
set_mixMC0.0030.0000.004
weights_ZINB0.5220.0220.583