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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 162/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.14.4  (landing page)
Matteo Calgaro
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/benchdamic
git_branch: RELEASE_3_21
git_last_commit: 822521d
git_last_commit_date: 2025-10-09 09:36:33 -0400 (Thu, 09 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    TIMEOUT  skippedskipped
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for benchdamic on kjohnson1

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: 1.14.4
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_1.14.4.tar.gz
StartedAt: 2025-10-14 13:52:08 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 14:04:46 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 758.1 seconds
RetCode: 0
Status:   OK  
CheckDir: benchdamic.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.14.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/benchdamic.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘benchdamic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘benchdamic’ version ‘1.14.4’
* 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   5.505  0.098   6.237
createConcordance 5.274  0.161   5.500
DA_ALDEx2         4.608  0.683   5.380
runSplits         4.562  0.082   8.399
plotRMSE          3.446  0.041   6.405
plotQQ            3.139  0.056   5.853
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-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-arm64/Resources/library’
* installing *source* package ‘benchdamic’ ...
** this is package ‘benchdamic’ version ‘1.14.4’
** 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


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 0 | WARN 2 | SKIP 0 | PASS 334 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 334 ]
> 
> proc.time()
   user  system elapsed 
 78.959   5.519 127.008 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
CAT0.0050.0010.005
DA_ALDEx24.6080.6835.380
DA_ANCOM0.8100.0160.838
DA_DESeq23.3360.0363.405
DA_MAST1.3270.0271.365
DA_Maaslin20.2710.0400.327
DA_NOISeq1.9100.0131.943
DA_Seurat2.9730.0433.061
DA_ZicoSeq0.6860.0650.757
DA_basic0.0330.0040.038
DA_corncob0.7400.0960.866
DA_dearseq0.0680.0030.075
DA_edgeR0.2130.0070.220
DA_limma0.0870.0040.093
DA_linda0.0490.0020.052
DA_maaslin30.5490.0230.585
DA_metagenomeSeq0.2780.0190.305
DA_mixMC0.6250.0400.675
RMSE0.0010.0000.001
addKnowledge0.1990.0200.220
areaCAT4.4400.1314.627
checkNormalization0.0000.0000.001
createColors0.0050.0000.005
createConcordance5.2740.1615.500
createEnrichment0.2570.0090.268
createMocks0.0030.0010.004
createPositives0.9530.0190.982
createSplits0.0360.0020.038
createTIEC3.2020.0673.311
enrichmentTest0.1180.0050.123
extractDA0.1790.0060.188
extractStatistics0.1800.0080.188
fitDM0.0310.0020.033
fitHURDLE0.6770.0080.690
fitModels2.4810.0732.742
fitNB0.0490.0010.053
fitZIG0.0600.0020.072
fitZINB0.4600.0060.554
getDA0.0830.0090.092
getPositives0.0810.0060.087
getStatistics0.0720.0070.079
get_counts_metadata0.1260.0030.132
iterative_ordering0.0090.0010.011
meanDifferences0.0020.0000.002
norm_CSS0.0720.0010.076
norm_DESeq20.4930.0050.525
norm_TSS0.0330.0020.035
norm_edgeR0.0390.0040.043
plotConcordance5.5050.0986.237
plotContingency1.6070.0251.802
plotEnrichment1.5640.0211.738
plotFDR2.7500.0342.823
plotFPR2.7740.0442.845
plotKS2.7490.0322.805
plotLogP2.7600.0332.829
plotMD3.3010.0453.532
plotMutualFindings1.6750.0223.193
plotPositives1.0100.0161.996
plotQQ3.1390.0565.853
plotRMSE3.4460.0416.405
prepareObserved0.0010.0000.003
runDA0.6310.0061.152
runMocks0.9230.0181.843
runNormalizations0.5680.0051.027
runSplits4.5620.0828.399
setNormalizations0.0010.0000.001
set_ALDEx20.0080.0010.017
set_ANCOM0.0110.0010.023
set_DESeq20.0110.0010.020
set_MAST0.0040.0000.004
set_Maaslin20.0060.0000.010
set_NOISeq0.0040.0000.006
set_Seurat0.0110.0010.011
set_ZicoSeq0.0110.0000.024
set_basic0.0030.0000.004
set_corncob0.0070.0000.007
set_dearseq0.0030.0010.008
set_edgeR0.0170.0010.043
set_limma0.0120.0010.020
set_linda0.0060.0000.008
set_maaslin30.0090.0010.009
set_metagenomeSeq0.0080.0010.023
set_mixMC0.0030.0010.003
weights_ZINB0.4750.0050.862