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This page was generated on 2025-10-14 12:05 -0400 (Tue, 14 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4610
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 163/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.15.4  (landing page)
Matteo Calgaro
Snapshot Date: 2025-10-13 13:45 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/benchdamic
git_branch: devel
git_last_commit: 7c5727b
git_last_commit_date: 2025-10-09 09:40:05 -0400 (Thu, 09 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    TIMEOUT  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'MAST' which is not available
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'MAST' which is not available
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  


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: 1.15.4
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_1.15.4.tar.gz
StartedAt: 2025-10-13 18:22:33 -0400 (Mon, 13 Oct 2025)
EndedAt: 2025-10-13 18:26:30 -0400 (Mon, 13 Oct 2025)
EllapsedTime: 236.4 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_1.15.4.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 ‘1.15.4’
* 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
* 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 ‘1.15.4’
** 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 (2025-09-10 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 2 | SKIP 0 | PASS 334 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 334 ]
> 
> proc.time()
   user  system elapsed 
 24.873   1.294  30.917 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
CAT0.0010.0000.002
DA_ALDEx21.3700.2361.610
DA_ANCOM0.2430.0030.251
DA_DESeq20.9020.0060.907
DA_MAST0.3710.0070.377
DA_Maaslin20.0920.0100.108
DA_NOISeq0.6540.0020.659
DA_Seurat0.9310.0120.944
DA_ZicoSeq0.2210.0180.241
DA_basic0.0100.0000.011
DA_corncob0.2150.0230.251
DA_dearseq0.0210.0010.023
DA_edgeR0.0680.0020.071
DA_limma0.0250.0010.026
DA_linda0.0150.0010.015
DA_maaslin30.1670.0040.174
DA_metagenomeSeq0.0750.0020.077
DA_mixMC0.1850.0030.189
RMSE0.0010.0000.001
addKnowledge0.0550.0030.058
areaCAT1.2460.0281.275
checkNormalization000
createColors0.0020.0000.002
createConcordance1.4660.0401.505
createEnrichment0.0760.0030.081
createMocks0.0000.0010.001
createPositives0.3100.0060.493
createSplits0.0120.0000.019
createTIEC1.1800.0201.885
enrichmentTest0.0390.0020.058
extractDA0.0710.0020.128
extractStatistics0.0610.0020.094
fitDM0.0110.0010.013
fitHURDLE0.2350.0030.382
fitModels0.8960.0221.499
fitNB0.0170.0000.031
fitZIG0.0180.0010.039
fitZINB0.1650.0020.264
getDA0.0250.0020.037
getPositives0.0380.0030.066
getStatistics0.0250.0030.051
get_counts_metadata0.0460.0010.066
iterative_ordering0.0030.0010.004
meanDifferences0.0010.0000.001
norm_CSS0.0280.0010.051
norm_DESeq20.1680.0010.258
norm_TSS0.0140.0010.015
norm_edgeR0.0130.0000.037
plotConcordance1.6840.0252.428
plotContingency0.5370.0080.839
plotEnrichment0.5670.0070.906
plotFDR1.0500.0151.704
plotFPR0.9600.0131.331
plotKS0.9090.0131.487
plotLogP1.0320.0121.632
plotMD1.4910.0142.451
plotMutualFindings0.4890.0070.566
plotPositives0.2600.0040.387
plotQQ0.9920.0141.669
plotRMSE1.1230.0091.889
prepareObserved0.0010.0000.001
runDA0.2040.0010.350
runMocks0.3440.0060.609
runNormalizations0.2020.0010.364
runSplits1.4210.0402.235
setNormalizations0.0010.0000.001
set_ALDEx20.0020.0010.002
set_ANCOM0.0030.0000.006
set_DESeq20.0020.0000.002
set_MAST0.0010.0000.002
set_Maaslin20.0020.0000.002
set_NOISeq0.0010.0000.001
set_Seurat0.0020.0000.007
set_ZicoSeq0.0020.0000.003
set_basic0.0010.0000.001
set_corncob0.0010.0000.001
set_dearseq0.0010.0010.001
set_edgeR0.0040.0000.009
set_limma0.0020.0000.002
set_linda0.0010.0000.001
set_maaslin30.0030.0000.002
set_metagenomeSeq0.0010.0000.003
set_mixMC0.0010.0000.001
weights_ZINB0.1330.0010.226