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This page was generated on 2025-08-18 12:04 -0400 (Mon, 18 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4538
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 161/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.15.3  (landing page)
Matteo Calgaro
Snapshot Date: 2025-08-17 13:45 -0400 (Sun, 17 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    OK  NO, package depends on 'MAST' which is not available
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    ERROR  


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: 2025-08-17 19:15:43 -0400 (Sun, 17 Aug 2025)
EndedAt: 2025-08-17 19:29:05 -0400 (Sun, 17 Aug 2025)
EllapsedTime: 801.8 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_1.15.3.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
DA_ALDEx2         5.875  1.105   8.823
plotConcordance   5.556  0.189  10.104
createConcordance 5.372  0.105   9.609
DA_DESeq2         4.930  0.044   8.201
areaCAT           3.957  0.109   9.540
plotMD            2.860  0.127   8.321
* 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-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


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 0 | WARN 2 | SKIP 0 | PASS 334 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 334 ]
> 
> proc.time()
   user  system elapsed 
 75.915   5.935 148.287 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
CAT0.0050.0010.006
DA_ALDEx25.8751.1058.823
DA_ANCOM1.2710.0662.263
DA_DESeq24.9300.0448.201
DA_MAST2.2790.0413.835
DA_Maaslin20.3460.0620.701
DA_NOISeq1.5700.0231.767
DA_Seurat2.5020.0573.232
DA_ZicoSeq0.8740.0321.547
DA_basic0.0470.0020.082
DA_corncob0.8500.0731.394
DA_dearseq0.0650.0030.076
DA_edgeR0.1930.0090.289
DA_limma0.0710.0030.170
DA_linda0.0430.0040.055
DA_maaslin30.5980.0200.880
DA_metagenomeSeq0.3180.0120.579
DA_mixMC0.9750.0231.548
RMSE0.0010.0000.001
addKnowledge0.2090.0090.501
areaCAT3.9570.1099.540
checkNormalization0.0010.0000.000
createColors0.0050.0000.006
createConcordance5.3720.1059.609
createEnrichment0.2320.0070.348
createMocks0.0020.0010.003
createPositives0.8650.0171.103
createSplits0.0260.0020.029
createTIEC2.3100.0863.737
enrichmentTest0.1130.0050.189
extractDA0.1650.0050.199
extractStatistics0.1490.0050.208
fitDM0.0340.0060.115
fitHURDLE0.9200.0491.528
fitModels2.2040.1463.297
fitNB0.0340.0010.035
fitZIG0.0400.0000.041
fitZINB0.3650.0040.397
getDA0.0630.0080.107
getPositives0.0720.0030.078
getStatistics0.0750.0060.120
get_counts_metadata0.1130.0060.178
iterative_ordering0.0070.0020.011
meanDifferences0.0020.0000.002
norm_CSS0.0600.0030.078
norm_DESeq20.3740.0100.631
norm_TSS0.0240.0010.025
norm_edgeR0.0280.0010.029
plotConcordance 5.556 0.18910.104
plotContingency0.7880.0131.071
plotEnrichment1.1860.0302.480
plotFDR2.7900.0713.757
plotFPR2.1540.0653.661
plotKS2.4030.0473.961
plotLogP2.6320.0484.389
plotMD2.8600.1278.321
plotMutualFindings0.7560.0101.000
plotPositives0.5950.0120.876
plotQQ2.2960.0402.750
plotRMSE2.7810.0653.281
prepareObserved0.0010.0000.001
runDA0.4490.0140.692
runMocks0.8150.0140.858
runNormalizations0.5550.0040.564
runSplits3.4740.0684.467
setNormalizations0.0010.0010.000
set_ALDEx20.0060.0010.007
set_ANCOM0.0080.0020.033
set_DESeq20.0070.0000.008
set_MAST0.0030.0000.004
set_Maaslin20.0040.0000.005
set_NOISeq0.0030.0010.004
set_Seurat0.0050.0010.005
set_ZicoSeq0.0050.0010.006
set_basic0.0010.0000.003
set_corncob0.0030.0000.003
set_dearseq0.0020.0000.002
set_edgeR0.0090.0010.010
set_limma0.0070.0010.007
set_linda0.0050.0000.006
set_maaslin30.0060.0020.033
set_metagenomeSeq0.0050.0000.005
set_mixMC0.0020.0010.003
weights_ZINB0.3370.0030.344