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This page was generated on 2025-10-02 12:04 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4844
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" 4576
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: 2025-10-01 13:45 -0400 (Wed, 01 Oct 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: 2025-10-01 19:45:03 -0400 (Wed, 01 Oct 2025)
EndedAt: 2025-10-01 20:00:04 -0400 (Wed, 01 Oct 2025)
EllapsedTime: 900.8 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
DA_ALDEx2         5.681  1.152   7.486
createConcordance 4.958  0.217  13.456
plotConcordance   4.948  0.167   6.891
areaCAT           4.781  0.179  16.417
DA_DESeq2         4.831  0.034   8.474
runSplits         4.254  0.476   9.408
plotMD            4.352  0.187   7.972
createTIEC        2.938  0.178   8.000
plotRMSE          2.929  0.093   6.689
createPositives   1.053  0.123   5.408
* 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
CAT0.0040.0010.004
DA_ALDEx25.6811.1527.486
DA_ANCOM1.2990.0262.459
DA_DESeq24.8310.0348.474
DA_MAST2.0110.0433.258
DA_Maaslin20.4370.0720.961
DA_NOISeq1.7490.0192.249
DA_Seurat2.0680.0642.971
DA_ZicoSeq0.7840.1013.071
DA_basic0.0400.0060.047
DA_corncob0.7580.1291.059
DA_dearseq0.0540.0020.058
DA_edgeR0.1780.0070.188
DA_limma0.0770.0040.085
DA_linda0.0540.0030.060
DA_maaslin30.5320.0301.496
DA_metagenomeSeq0.2390.0131.267
DA_mixMC0.6510.0241.934
RMSE0.0020.0010.002
addKnowledge0.2330.0190.424
areaCAT 4.781 0.17916.417
checkNormalization0.0010.0000.000
createColors0.0040.0010.019
createConcordance 4.958 0.21713.456
createEnrichment0.2260.0090.449
createMocks0.0020.0020.004
createPositives1.0530.1235.408
createSplits0.0270.0030.030
createTIEC2.9380.1788.000
enrichmentTest0.1740.0090.272
extractDA0.2260.0080.356
extractStatistics0.2420.0120.314
fitDM0.0430.0090.103
fitHURDLE0.7800.1271.825
fitModels2.1470.0963.664
fitNB0.0370.0000.047
fitZIG0.0430.0010.045
fitZINB0.3250.0050.333
getDA0.0600.0070.114
getPositives0.0690.0040.110
getStatistics0.0540.0050.106
get_counts_metadata0.0980.0080.187
iterative_ordering0.0070.0020.032
meanDifferences0.0020.0010.002
norm_CSS0.0600.0040.080
norm_DESeq20.4950.0210.562
norm_TSS0.0290.0010.030
norm_edgeR0.0340.0020.038
plotConcordance4.9480.1676.891
plotContingency1.2350.0261.373
plotEnrichment1.8140.0312.217
plotFDR2.3460.0433.239
plotFPR2.0900.0523.179
plotKS2.3880.0463.390
plotLogP2.1780.0372.983
plotMD4.3520.1877.972
plotMutualFindings2.3770.0403.733
plotPositives0.8970.0221.223
plotQQ3.0780.0974.973
plotRMSE2.9290.0936.689
prepareObserved0.0020.0000.002
runDA0.7930.0150.931
runMocks0.8120.0210.947
runNormalizations0.4340.0070.457
runSplits4.2540.4769.408
setNormalizations0.0000.0000.001
set_ALDEx20.0050.0000.007
set_ANCOM0.0070.0030.080
set_DESeq20.0080.0010.041
set_MAST0.0040.0010.004
set_Maaslin20.0040.0000.005
set_NOISeq0.0040.0010.016
set_Seurat0.0090.0010.046
set_ZicoSeq0.0080.0010.012
set_basic0.0020.0000.003
set_corncob0.0050.0000.007
set_dearseq0.0030.0000.002
set_edgeR0.0130.0010.024
set_limma0.0080.0000.008
set_linda0.0060.0000.008
set_maaslin30.0060.0030.039
set_metagenomeSeq0.0040.0010.005
set_mixMC0.0020.0000.004
weights_ZINB0.3380.0020.367