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This page was generated on 2025-09-22 12:03 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 162/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.15.3  (landing page)
Matteo Calgaro
Snapshot Date: 2025-09-21 13:45 -0400 (Sun, 21 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: 2025-09-21 21:14:37 -0400 (Sun, 21 Sep 2025)
EndedAt: 2025-09-21 21:54:37 -0400 (Sun, 21 Sep 2025)
EllapsedTime: 2400.8 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
plotConcordance   7.585  0.117   8.865
createConcordance 5.958  0.054   6.073
areaCAT           5.573  0.135   5.841
DA_ALDEx2         5.116  0.214   5.667
plotMD            4.999  0.081   6.155
fitModels         3.690  0.097   5.133
* 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
CAT0.0050.0000.005
DA_ALDEx25.1160.2145.667
DA_ANCOM1.2010.0351.492
DA_DESeq23.6640.0753.934
DA_MAST1.5380.0341.624
DA_Maaslin20.3420.0220.419
DA_NOISeq1.6330.1862.003
DA_Seurat2.8000.0843.196
DA_ZicoSeq1.0060.0021.145
DA_basic0.0420.0000.042
DA_corncob0.7780.0390.952
DA_dearseq0.0640.0050.095
DA_edgeR0.2120.0020.219
DA_limma0.0850.0000.109
DA_linda0.0540.0000.054
DA_maaslin30.6350.0140.673
DA_metagenomeSeq0.2710.0140.284
DA_mixMC0.7860.0080.796
RMSE0.0010.0000.000
addKnowledge0.2070.0150.221
areaCAT5.5730.1355.841
checkNormalization000
createColors0.0060.0000.005
createConcordance5.9580.0546.073
createEnrichment0.2950.0060.327
createMocks0.0020.0000.003
createPositives1.3750.0121.419
createSplits0.0510.0010.052
createTIEC4.7770.0784.915
enrichmentTest0.1810.0040.327
extractDA0.2950.0160.524
extractStatistics0.2170.0170.409
fitDM0.0380.0010.068
fitHURDLE1.0410.0091.524
fitModels3.6900.0975.133
fitNB0.0600.0010.147
fitZIG0.0680.0000.103
fitZINB0.5670.0090.928
getDA0.1240.0020.170
getPositives0.1120.0040.126
getStatistics0.0800.0050.179
get_counts_metadata0.1420.0060.349
iterative_ordering0.0100.0010.029
meanDifferences0.0020.0000.006
norm_CSS0.0860.0030.179
norm_DESeq20.5120.0250.815
norm_TSS0.0390.0020.056
norm_edgeR0.0500.0070.146
plotConcordance7.5850.1178.865
plotContingency2.1670.0302.609
plotEnrichment2.0380.0052.077
plotFDR3.7560.0234.264
plotFPR3.4720.0144.707
plotKS3.8520.0443.943
plotLogP3.0600.0034.321
plotMD4.9990.0816.155
plotMutualFindings2.0820.0012.305
plotPositives0.9550.0240.989
plotQQ3.1120.0423.581
plotRMSE4.0310.0614.198
prepareObserved0.0020.0000.002
runDA0.7200.0020.766
runMocks1.0290.0291.077
runNormalizations0.7080.0000.712
runSplits4.7600.0884.956
setNormalizations0.0010.0000.000
set_ALDEx20.0080.0020.010
set_ANCOM0.0120.0000.011
set_DESeq20.0100.0010.011
set_MAST0.0050.0000.005
set_Maaslin20.0070.0000.008
set_NOISeq0.0050.0000.006
set_Seurat0.0090.0000.009
set_ZicoSeq0.0110.0000.011
set_basic0.0030.0000.002
set_corncob0.0060.0000.006
set_dearseq0.0030.0000.002
set_edgeR0.0190.0000.019
set_limma0.0120.0000.013
set_linda0.0090.0000.009
set_maaslin30.0080.0020.010
set_metagenomeSeq0.0070.0010.008
set_mixMC0.0040.0000.004
weights_ZINB0.5930.0030.597