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This page was generated on 2025-09-01 12:04 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 162/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.15.3  (landing page)
Matteo Calgaro
Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 Aug 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    ERROR  
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: 2025-08-31 19:18:48 -0400 (Sun, 31 Aug 2025)
EndedAt: 2025-08-31 19:32:35 -0400 (Sun, 31 Aug 2025)
EllapsedTime: 827.3 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 (2025-06-13)
* 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   7.940  0.093  13.645
DA_ALDEx2         4.780  1.014   5.862
createConcordance 5.181  0.086   5.293
* 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 (2025-06-13) -- "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_ALDEx24.7801.0145.862
DA_ANCOM0.8830.0600.955
DA_DESeq23.2460.0373.312
DA_MAST1.4620.0331.509
DA_Maaslin20.2400.0430.314
DA_NOISeq1.4490.0121.469
DA_Seurat2.1290.0632.213
DA_ZicoSeq0.5880.0210.611
DA_basic0.0320.0010.034
DA_corncob0.6560.0570.748
DA_dearseq0.0580.0020.062
DA_edgeR0.1760.0060.183
DA_limma0.0720.0030.075
DA_linda0.0410.0020.044
DA_maaslin30.5030.0170.525
DA_metagenomeSeq0.2660.0070.277
DA_mixMC0.7470.0120.765
RMSE0.0010.0000.001
addKnowledge0.1900.0070.197
areaCAT4.3920.0774.492
checkNormalization0.0010.0010.001
createColors0.0040.0000.004
createConcordance5.1810.0865.293
createEnrichment0.2620.0050.269
createMocks0.0010.0010.003
createPositives0.9350.0120.952
createSplits0.0370.0010.038
createTIEC2.7370.0402.794
enrichmentTest0.1080.0040.111
extractDA0.1720.0040.177
extractStatistics0.1570.0030.160
fitDM0.0280.0010.030
fitHURDLE0.6280.0110.640
fitModels2.3430.0422.404
fitNB0.0560.0000.056
fitZIG0.0690.0010.070
fitZINB0.5850.0090.604
getDA0.0960.0100.107
getPositives0.0990.0040.105
getStatistics0.0910.0060.098
get_counts_metadata0.1460.0030.150
iterative_ordering0.0110.0010.012
meanDifferences0.0020.0010.003
norm_CSS0.0910.0030.100
norm_DESeq20.5680.0060.666
norm_TSS0.0510.0010.091
norm_edgeR0.0570.0010.099
plotConcordance 7.940 0.09313.645
plotContingency1.9190.0473.325
plotEnrichment1.5290.0382.478
plotFDR2.7840.0393.042
plotFPR2.9360.0464.392
plotKS1.7570.0362.143
plotLogP2.1530.0423.209
plotMD3.1800.0463.731
plotMutualFindings0.8860.0161.083
plotPositives0.7090.0140.871
plotQQ2.9930.0414.241
plotRMSE2.6460.0213.179
prepareObserved0.0010.0000.002
runDA0.4560.0030.475
runMocks0.6270.0080.728
runNormalizations0.3350.0010.345
runSplits3.2390.0514.484
setNormalizations0.0000.0000.001
set_ALDEx20.0070.0000.007
set_ANCOM0.0070.0010.009
set_DESeq20.0060.0010.006
set_MAST0.0030.0000.006
set_Maaslin20.0040.0010.004
set_NOISeq0.0040.0000.004
set_Seurat0.0050.0000.006
set_ZicoSeq0.0060.0000.008
set_basic0.0010.0010.002
set_corncob0.0030.0000.004
set_dearseq0.0010.0000.002
set_edgeR0.0080.0010.010
set_limma0.0050.0010.006
set_linda0.0050.0010.006
set_maaslin30.0060.0010.022
set_metagenomeSeq0.0050.0010.005
set_mixMC0.0020.0010.002
weights_ZINB0.3740.0060.516