| Back to Build/check report for BioC 3.22: simplified long |
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This page was generated on 2026-02-26 11:57 -0500 (Thu, 26 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4891 |
| 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 1.16.0 (landing page) Matteo Calgaro
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| See other builds for benchdamic in R Universe. | ||||||||||||||
|
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: 1.16.0 |
| 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_1.16.0.tar.gz |
| StartedAt: 2026-02-25 21:58:15 -0500 (Wed, 25 Feb 2026) |
| EndedAt: 2026-02-25 22:31:40 -0500 (Wed, 25 Feb 2026) |
| EllapsedTime: 2005.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: benchdamic.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.16.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/benchdamic.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.16.0’
* 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 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
createConcordance 8.065 0.176 9.532
areaCAT 7.085 0.206 8.015
plotConcordance 6.281 0.071 6.575
* 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.
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 ‘1.16.0’ ** 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)
benchdamic.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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 0 | SKIP 0 | PASS 334 ]
>
> proc.time()
user system elapsed
68.782 4.452 81.547
benchdamic.Rcheck/benchdamic-Ex.timings
| name | user | system | elapsed | |
| CAT | 0.003 | 0.000 | 0.003 | |
| DA_ALDEx2 | 3.703 | 0.225 | 3.928 | |
| DA_ANCOM | 0.725 | 0.023 | 0.748 | |
| DA_DESeq2 | 2.669 | 0.042 | 2.711 | |
| DA_MAST | 1.196 | 0.010 | 1.179 | |
| DA_Maaslin2 | 0.252 | 0.010 | 0.263 | |
| DA_NOISeq | 1.358 | 0.101 | 1.459 | |
| DA_Seurat | 2.155 | 0.015 | 2.171 | |
| DA_ZicoSeq | 0.660 | 0.015 | 0.675 | |
| DA_basic | 0.037 | 0.000 | 0.036 | |
| DA_corncob | 0.683 | 0.013 | 0.701 | |
| DA_dearseq | 0.089 | 0.000 | 0.098 | |
| DA_edgeR | 0.345 | 0.001 | 0.477 | |
| DA_limma | 0.119 | 0.000 | 0.119 | |
| DA_linda | 0.085 | 0.002 | 0.088 | |
| DA_maaslin3 | 0.959 | 0.030 | 1.121 | |
| DA_metagenomeSeq | 0.447 | 0.005 | 0.452 | |
| DA_mixMC | 1.194 | 0.024 | 1.298 | |
| RMSE | 0.001 | 0.000 | 0.002 | |
| addKnowledge | 0.443 | 0.015 | 0.458 | |
| areaCAT | 7.085 | 0.206 | 8.015 | |
| checkNormalization | 0 | 0 | 0 | |
| createColors | 0.006 | 0.001 | 0.007 | |
| createConcordance | 8.065 | 0.176 | 9.532 | |
| createEnrichment | 0.430 | 0.003 | 0.433 | |
| createMocks | 0.004 | 0.000 | 0.004 | |
| createPositives | 1.569 | 0.033 | 1.626 | |
| createSplits | 0.058 | 0.000 | 0.058 | |
| createTIEC | 4.691 | 0.027 | 4.722 | |
| enrichmentTest | 0.206 | 0.000 | 0.206 | |
| extractDA | 0.331 | 0.001 | 0.332 | |
| extractStatistics | 0.195 | 0.001 | 0.196 | |
| fitDM | 0.032 | 0.000 | 0.032 | |
| fitHURDLE | 0.779 | 0.005 | 0.784 | |
| fitModels | 2.709 | 0.039 | 2.749 | |
| fitNB | 0.044 | 0.000 | 0.044 | |
| fitZIG | 0.054 | 0.000 | 0.054 | |
| fitZINB | 0.522 | 0.002 | 0.523 | |
| getDA | 0.083 | 0.000 | 0.083 | |
| getPositives | 0.08 | 0.00 | 0.08 | |
| getStatistics | 0.081 | 0.002 | 0.082 | |
| get_counts_metadata | 0.110 | 0.003 | 0.113 | |
| iterative_ordering | 0.008 | 0.000 | 0.009 | |
| meanDifferences | 0.002 | 0.000 | 0.002 | |
| norm_CSS | 0.07 | 0.00 | 0.07 | |
| norm_DESeq2 | 0.438 | 0.001 | 0.439 | |
| norm_TSS | 0.035 | 0.000 | 0.034 | |
| norm_edgeR | 0.037 | 0.000 | 0.036 | |
| plotConcordance | 6.281 | 0.071 | 6.575 | |
| plotContingency | 1.397 | 0.001 | 1.399 | |
| plotEnrichment | 2.661 | 0.139 | 2.800 | |
| plotFDR | 2.403 | 0.034 | 2.438 | |
| plotFPR | 2.390 | 0.003 | 2.394 | |
| plotKS | 2.549 | 0.042 | 2.591 | |
| plotLogP | 2.483 | 0.023 | 2.507 | |
| plotMD | 3.428 | 0.025 | 3.454 | |
| plotMutualFindings | 1.346 | 0.039 | 1.385 | |
| plotPositives | 0.778 | 0.008 | 0.786 | |
| plotQQ | 2.445 | 0.007 | 2.453 | |
| plotRMSE | 2.599 | 0.022 | 2.622 | |
| prepareObserved | 0.001 | 0.000 | 0.002 | |
| runDA | 0.458 | 0.003 | 0.462 | |
| runMocks | 0.652 | 0.015 | 0.667 | |
| runNormalizations | 0.461 | 0.000 | 0.461 | |
| runSplits | 3.346 | 0.030 | 3.376 | |
| setNormalizations | 0.001 | 0.000 | 0.000 | |
| set_ALDEx2 | 0.006 | 0.000 | 0.006 | |
| set_ANCOM | 0.005 | 0.001 | 0.007 | |
| set_DESeq2 | 0.006 | 0.000 | 0.006 | |
| set_MAST | 0.003 | 0.000 | 0.003 | |
| set_Maaslin2 | 0.004 | 0.000 | 0.004 | |
| set_NOISeq | 0.003 | 0.000 | 0.003 | |
| set_Seurat | 0.006 | 0.000 | 0.006 | |
| set_ZicoSeq | 0.006 | 0.000 | 0.006 | |
| set_basic | 0.002 | 0.000 | 0.001 | |
| set_corncob | 0.003 | 0.000 | 0.003 | |
| set_dearseq | 0.002 | 0.000 | 0.002 | |
| set_edgeR | 0.01 | 0.00 | 0.01 | |
| set_limma | 0.007 | 0.000 | 0.007 | |
| set_linda | 0.005 | 0.000 | 0.005 | |
| set_maaslin3 | 0.008 | 0.000 | 0.008 | |
| set_metagenomeSeq | 0.005 | 0.000 | 0.005 | |
| set_mixMC | 0.002 | 0.000 | 0.002 | |
| weights_ZINB | 0.387 | 0.001 | 0.388 | |