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This page was generated on 2025-11-01 12:04 -0400 (Sat, 01 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
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 165/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.16.0  (landing page)
Matteo Calgaro
Snapshot Date: 2025-10-31 13:45 -0400 (Fri, 31 Oct 2025)
git_url: https://git.bioconductor.org/packages/benchdamic
git_branch: RELEASE_3_22
git_last_commit: fcdab2a
git_last_commit_date: 2025-10-29 11:13:16 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  NO, package depends on 'Maaslin2' which is not available
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'Maaslin2' which is not available
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'Maaslin2' which is not available


CHECK results for benchdamic on kjohnson3

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: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2025-10-31 18:41:46 -0400 (Fri, 31 Oct 2025)
EndedAt: 2025-10-31 18:45:50 -0400 (Fri, 31 Oct 2025)
EllapsedTime: 243.9 seconds
RetCode: 0
Status:   OK  
CheckDir: benchdamic.Rcheck
Warnings: 0

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_1.16.0.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: 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘benchdamic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘benchdamic’ version ‘1.16.0’
* 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
* 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-3.22-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-arm64/Resources/library’
* installing *source* package ‘benchdamic’ ...
** this is package ‘benchdamic’ version ‘1.16.0’
** 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 (2025-09-10 r88807) -- "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 0 | SKIP 0 | PASS 334 ]
> 
> proc.time()
   user  system elapsed 
 24.974   1.360  29.821 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
CAT0.0020.0000.001
DA_ALDEx21.4020.2671.697
DA_ANCOM0.2290.0060.237
DA_DESeq20.9200.0130.934
DA_MAST0.3940.0090.404
DA_Maaslin20.0820.0120.105
DA_NOISeq0.6670.0050.684
DA_Seurat0.8190.0150.837
DA_ZicoSeq0.2190.0080.230
DA_basic0.0100.0020.011
DA_corncob0.2080.0160.244
DA_dearseq0.0220.0010.024
DA_edgeR0.0640.0030.068
DA_limma0.0260.0020.028
DA_linda0.0160.0010.017
DA_maaslin30.1710.0060.184
DA_metagenomeSeq0.0980.0040.105
DA_mixMC0.1790.0020.181
RMSE0.0010.0000.000
addKnowledge0.0560.0030.059
areaCAT1.3590.0381.934
checkNormalization0.0010.0000.000
createColors0.0020.0000.002
createConcordance1.8590.0363.045
createEnrichment0.1050.0040.174
createMocks0.0020.0010.017
createPositives0.4360.0120.728
createSplits0.0130.0010.025
createTIEC1.1220.0171.475
enrichmentTest0.0390.0030.110
extractDA0.0730.0030.129
extractStatistics0.0560.0020.097
fitDM0.0110.0010.012
fitHURDLE0.2220.0010.401
fitModels0.7850.0121.254
fitNB0.0190.0000.026
fitZIG0.0160.0010.022
fitZINB0.1590.0010.267
getDA0.0310.0020.051
getPositives0.0270.0020.043
getStatistics0.0250.0040.042
get_counts_metadata0.1490.0030.268
iterative_ordering0.0060.0010.011
meanDifferences0.0000.0000.001
norm_CSS0.0280.0000.044
norm_DESeq20.1670.0000.287
norm_TSS0.010.000.02
norm_edgeR0.0180.0000.024
plotConcordance2.0310.0313.248
plotContingency0.4660.0060.678
plotEnrichment0.5010.0060.813
plotFDR1.0490.0111.682
plotFPR1.0520.0141.714
plotKS1.1750.0161.839
plotLogP0.9250.0121.388
plotMD1.4250.0122.302
plotMutualFindings0.6020.0070.989
plotPositives0.3100.0040.519
plotQQ1.0890.0141.630
plotRMSE1.0030.0141.416
prepareObserved0.0000.0000.001
runDA0.1840.0020.307
runMocks0.2450.0030.440
runNormalizations0.2190.0020.370
runSplits1.4490.0212.304
setNormalizations0.0010.0010.001
set_ALDEx20.0050.0010.006
set_ANCOM0.0040.0000.011
set_DESeq20.0020.0000.002
set_MAST0.0010.0000.001
set_Maaslin20.0020.0000.002
set_NOISeq0.0010.0010.008
set_Seurat0.0050.0000.007
set_ZicoSeq0.0030.0000.005
set_basic0.0000.0000.001
set_corncob0.0020.0010.001
set_dearseq0.0000.0000.001
set_edgeR0.0040.0000.004
set_limma0.0030.0000.003
set_linda0.0030.0000.004
set_maaslin30.0050.0010.018
set_metagenomeSeq0.0010.0000.002
set_mixMC0.0000.0000.001
weights_ZINB0.2030.0020.319