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This page was generated on 2025-09-20 12:04 -0400 (Sat, 20 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: 2025-09-19 13:45 -0400 (Fri, 19 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 lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings benchdamic_1.15.3.tar.gz
StartedAt: 2025-09-19 19:27:24 -0400 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 19:42:32 -0400 (Fri, 19 Sep 2025)
EllapsedTime: 908.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: benchdamic.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings benchdamic_1.15.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/benchdamic.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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   7.659  0.098  11.679
DA_ALDEx2         4.961  1.067   6.098
createConcordance 5.574  0.101   5.712
runSplits         4.305  0.270   6.247
fitModels         3.801  0.063   6.659
plotRMSE          3.549  0.075   5.333
plotMD            3.478  0.083   5.531
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/benchdamic.Rcheck/00check.log’
for details.


Installation output

benchdamic.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL benchdamic
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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
CAT0.0030.0000.003
DA_ALDEx24.9611.0676.098
DA_ANCOM0.9680.0221.004
DA_DESeq23.4980.0403.568
DA_MAST1.4720.0301.520
DA_Maaslin20.3060.0510.378
DA_NOISeq1.4650.0131.494
DA_Seurat2.2940.0432.368
DA_ZicoSeq0.7010.0720.780
DA_basic0.0350.0040.040
DA_corncob0.7220.1140.866
DA_dearseq0.0550.0030.060
DA_edgeR0.1890.0070.198
DA_limma0.0830.0030.087
DA_linda0.0520.0020.055
DA_maaslin30.5650.0190.592
DA_metagenomeSeq0.3030.0090.316
DA_mixMC0.7320.0150.753
RMSE0.0010.0010.001
addKnowledge0.1710.0100.181
areaCAT4.6840.1014.810
checkNormalization0.0000.0000.001
createColors0.0030.0010.003
createConcordance5.5740.1015.712
createEnrichment0.2530.0060.260
createMocks0.0030.0010.004
createPositives1.0120.0131.030
createSplits0.0290.0020.032
createTIEC3.6390.0563.733
enrichmentTest0.1560.0050.163
extractDA0.2370.0030.242
extractStatistics0.2450.0060.258
fitDM0.0400.0020.044
fitHURDLE0.9330.0101.028
fitModels3.8010.0636.659
fitNB0.0860.0010.160
fitZIG0.0960.0010.171
fitZINB0.6430.0051.149
getDA0.1170.0100.202
getPositives0.1160.0050.206
getStatistics0.1030.0060.182
get_counts_metadata0.1830.0030.316
iterative_ordering0.0130.0010.027
meanDifferences0.0020.0000.003
norm_CSS0.1050.0020.180
norm_DESeq20.6800.0031.145
norm_TSS0.0540.0010.098
norm_edgeR0.0660.0010.115
plotConcordance 7.659 0.09811.679
plotContingency1.9290.0331.993
plotEnrichment1.6730.0182.513
plotFDR2.3780.0403.200
plotFPR2.3590.0312.746
plotKS2.0100.0342.359
plotLogP3.2550.0414.562
plotMD3.4780.0835.531
plotMutualFindings1.9090.0232.466
plotPositives1.0030.0281.328
plotQQ2.2970.0503.303
plotRMSE3.5490.0755.333
prepareObserved0.0010.0010.002
runDA0.3830.0110.825
runMocks0.9650.0191.367
runNormalizations0.5860.0050.660
runSplits4.3050.2706.247
setNormalizations000
set_ALDEx20.0050.0000.006
set_ANCOM0.0070.0050.035
set_DESeq20.0100.0010.012
set_MAST0.0040.0010.004
set_Maaslin20.0060.0000.006
set_NOISeq0.0060.0010.006
set_Seurat0.0060.0010.010
set_ZicoSeq0.0090.0010.010
set_basic0.0020.0010.003
set_corncob0.0030.0010.004
set_dearseq0.0020.0000.001
set_edgeR0.0090.0010.010
set_limma0.0070.0010.007
set_linda0.0050.0010.004
set_maaslin30.0070.0020.012
set_metagenomeSeq0.0060.0000.017
set_mixMC0.0030.0010.003
weights_ZINB0.4960.0050.506