| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-25 12:04 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 165/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| benchdamic 1.15.4 (landing page) Matteo Calgaro
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
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. |
| 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: 2025-10-24 19:41:57 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 19:55:05 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 788.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: benchdamic.Rcheck |
| Warnings: 0 |
##############################################################################
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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_1.15.4.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: 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 ‘1.15.4’
* 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 7.708 0.081 11.700
DA_ALDEx2 4.459 0.988 5.483
createConcordance 5.038 0.068 5.133
plotMD 4.720 0.062 6.929
fitModels 3.617 0.074 5.773
* 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.
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 ‘1.15.4’ ** 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)
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: 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
77.800 8.016 181.768
benchdamic.Rcheck/benchdamic-Ex.timings
| name | user | system | elapsed | |
| CAT | 0.004 | 0.001 | 0.005 | |
| DA_ALDEx2 | 4.459 | 0.988 | 5.483 | |
| DA_ANCOM | 0.764 | 0.013 | 0.780 | |
| DA_DESeq2 | 3.038 | 0.037 | 3.088 | |
| DA_MAST | 1.360 | 0.035 | 1.410 | |
| DA_Maaslin2 | 0.248 | 0.048 | 0.314 | |
| DA_NOISeq | 1.472 | 0.016 | 1.504 | |
| DA_Seurat | 2.235 | 0.063 | 2.320 | |
| DA_ZicoSeq | 0.665 | 0.028 | 0.697 | |
| DA_basic | 0.037 | 0.004 | 0.041 | |
| DA_corncob | 0.677 | 0.051 | 0.753 | |
| DA_dearseq | 0.058 | 0.002 | 0.061 | |
| DA_edgeR | 0.202 | 0.007 | 0.209 | |
| DA_limma | 0.076 | 0.003 | 0.080 | |
| DA_linda | 0.052 | 0.002 | 0.054 | |
| DA_maaslin3 | 0.626 | 0.020 | 0.655 | |
| DA_metagenomeSeq | 0.265 | 0.005 | 0.272 | |
| DA_mixMC | 0.621 | 0.008 | 0.633 | |
| RMSE | 0.001 | 0.000 | 0.001 | |
| addKnowledge | 0.162 | 0.006 | 0.168 | |
| areaCAT | 4.241 | 0.069 | 4.327 | |
| checkNormalization | 0 | 0 | 0 | |
| createColors | 0.003 | 0.000 | 0.003 | |
| createConcordance | 5.038 | 0.068 | 5.133 | |
| createEnrichment | 0.315 | 0.018 | 0.335 | |
| createMocks | 0.001 | 0.001 | 0.003 | |
| createPositives | 1.012 | 0.015 | 1.034 | |
| createSplits | 0.032 | 0.002 | 0.035 | |
| createTIEC | 3.177 | 0.045 | 3.247 | |
| enrichmentTest | 0.166 | 0.009 | 0.176 | |
| extractDA | 0.210 | 0.004 | 0.218 | |
| extractStatistics | 0.219 | 0.004 | 0.225 | |
| fitDM | 0.040 | 0.002 | 0.043 | |
| fitHURDLE | 0.841 | 0.009 | 0.861 | |
| fitModels | 3.617 | 0.074 | 5.773 | |
| fitNB | 0.063 | 0.001 | 0.105 | |
| fitZIG | 0.080 | 0.001 | 0.132 | |
| fitZINB | 0.735 | 0.006 | 1.197 | |
| getDA | 0.144 | 0.010 | 0.244 | |
| getPositives | 0.119 | 0.006 | 0.203 | |
| getStatistics | 0.292 | 0.012 | 0.513 | |
| get_counts_metadata | 0.176 | 0.004 | 0.307 | |
| iterative_ordering | 0.012 | 0.001 | 0.019 | |
| meanDifferences | 0.003 | 0.000 | 0.003 | |
| norm_CSS | 0.111 | 0.001 | 0.189 | |
| norm_DESeq2 | 0.660 | 0.004 | 1.107 | |
| norm_TSS | 0.051 | 0.001 | 0.092 | |
| norm_edgeR | 0.059 | 0.001 | 0.115 | |
| plotConcordance | 7.708 | 0.081 | 11.700 | |
| plotContingency | 2.056 | 0.023 | 2.672 | |
| plotEnrichment | 2.130 | 0.018 | 3.213 | |
| plotFDR | 3.070 | 0.042 | 4.399 | |
| plotFPR | 1.952 | 0.032 | 2.621 | |
| plotKS | 1.983 | 0.038 | 2.597 | |
| plotLogP | 2.300 | 0.048 | 2.672 | |
| plotMD | 4.720 | 0.062 | 6.929 | |
| plotMutualFindings | 1.386 | 0.015 | 1.502 | |
| plotPositives | 0.654 | 0.008 | 0.728 | |
| plotQQ | 2.809 | 0.032 | 3.126 | |
| plotRMSE | 2.301 | 0.035 | 2.718 | |
| prepareObserved | 0.001 | 0.001 | 0.001 | |
| runDA | 0.386 | 0.002 | 0.395 | |
| runMocks | 0.493 | 0.005 | 0.582 | |
| runNormalizations | 0.356 | 0.004 | 0.368 | |
| runSplits | 2.877 | 0.051 | 3.974 | |
| setNormalizations | 0.000 | 0.000 | 0.001 | |
| set_ALDEx2 | 0.006 | 0.001 | 0.009 | |
| set_ANCOM | 0.010 | 0.002 | 0.015 | |
| set_DESeq2 | 0.008 | 0.001 | 0.010 | |
| set_MAST | 0.004 | 0.000 | 0.005 | |
| set_Maaslin2 | 0.005 | 0.000 | 0.007 | |
| set_NOISeq | 0.004 | 0.001 | 0.005 | |
| set_Seurat | 0.006 | 0.001 | 0.007 | |
| set_ZicoSeq | 0.010 | 0.001 | 0.011 | |
| set_basic | 0.003 | 0.001 | 0.003 | |
| set_corncob | 0.004 | 0.001 | 0.008 | |
| set_dearseq | 0.004 | 0.001 | 0.006 | |
| set_edgeR | 0.018 | 0.002 | 0.032 | |
| set_limma | 0.012 | 0.002 | 0.014 | |
| set_linda | 0.009 | 0.001 | 0.009 | |
| set_maaslin3 | 0.011 | 0.003 | 0.029 | |
| set_metagenomeSeq | 0.010 | 0.001 | 0.011 | |
| set_mixMC | 0.004 | 0.001 | 0.005 | |
| weights_ZINB | 0.689 | 0.016 | 0.963 | |