Back to Multiple platform build/check report for BioC 3.22:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-10-18 12:03 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 164/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.15.4  (landing page)
Matteo Calgaro
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 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    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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for benchdamic on nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings benchdamic_1.15.4.tar.gz
StartedAt: 2025-10-17 21:22:22 -0400 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 21:54:22 -0400 (Fri, 17 Oct 2025)
EllapsedTime: 1919.9 seconds
RetCode: 0
Status:   OK  
CheckDir: benchdamic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings benchdamic_1.15.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/benchdamic.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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
plotFPR        7.663  0.073   9.431
plotFDR        7.083  0.012  10.288
plotEnrichment 4.912  0.143   7.304
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/benchdamic.Rcheck/00check.log’
for details.


Installation output

benchdamic.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL benchdamic
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 67.680   3.369  79.658 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
CAT0.0040.0000.004
DA_ALDEx23.8150.3014.117
DA_ANCOM0.7400.0250.764
DA_DESeq22.7010.0942.794
DA_MAST1.2160.0421.235
DA_Maaslin20.2620.0080.271
DA_NOISeq1.3550.0911.446
DA_Seurat2.0830.0112.098
DA_ZicoSeq0.6130.0030.616
DA_basic0.0280.0000.029
DA_corncob0.6030.0060.611
DA_dearseq0.0520.0000.052
DA_edgeR0.1660.0020.168
DA_limma0.0660.0010.067
DA_linda0.0430.0000.043
DA_maaslin30.4600.0040.466
DA_metagenomeSeq0.2210.0020.224
DA_mixMC0.6100.0280.639
RMSE0.0000.0000.001
addKnowledge0.1510.0000.151
areaCAT3.6870.0433.730
checkNormalization000
createColors0.0040.0000.004
createConcordance4.3740.0444.417
createEnrichment0.2220.0030.225
createMocks0.0020.0000.002
createPositives0.9250.0060.931
createSplits0.0290.0000.029
createTIEC2.8210.0482.873
enrichmentTest0.1450.0020.147
extractDA0.1640.0000.163
extractStatistics0.1610.0000.161
fitDM0.0260.0010.028
fitHURDLE0.5870.0050.592
fitModels2.1020.0582.161
fitNB0.0420.0000.042
fitZIG0.0480.0000.049
fitZINB0.4080.0110.419
getDA0.0680.0030.072
getPositives0.0710.0010.072
getStatistics0.0620.0000.063
get_counts_metadata0.1030.0010.105
iterative_ordering0.0080.0000.008
meanDifferences0.0000.0010.002
norm_CSS0.0660.0000.066
norm_DESeq20.4220.0020.423
norm_TSS0.0290.0000.030
norm_edgeR0.0330.0000.034
plotConcordance4.6500.1024.752
plotContingency1.3170.0031.320
plotEnrichment4.9120.1437.304
plotFDR 7.083 0.01210.288
plotFPR7.6630.0739.431
plotKS3.7630.0523.832
plotLogP2.9220.0162.950
plotMD3.7380.0373.806
plotMutualFindings1.3270.0421.368
plotPositives0.7840.0020.786
plotQQ2.3460.0052.352
plotRMSE2.6690.0532.722
prepareObserved0.0010.0000.001
runDA0.4460.0010.447
runMocks0.6710.0010.671
runNormalizations0.4090.0000.409
runSplits3.2890.0723.361
setNormalizations0.0000.0000.001
set_ALDEx20.0060.0000.006
set_ANCOM0.0070.0000.007
set_DESeq20.0070.0000.007
set_MAST0.0030.0000.003
set_Maaslin20.0040.0000.005
set_NOISeq0.0030.0000.003
set_Seurat0.0050.0000.005
set_ZicoSeq0.0060.0000.006
set_basic0.0010.0000.001
set_corncob0.0030.0000.003
set_dearseq0.0010.0000.001
set_edgeR0.010.000.01
set_limma0.0060.0010.008
set_linda0.0050.0000.005
set_maaslin30.0060.0000.006
set_metagenomeSeq0.0050.0000.005
set_mixMC0.0030.0000.003
weights_ZINB0.3820.0000.382