Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-11 12:06 -0400 (Sat, 11 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
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 163/2346 | 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 | TIMEOUT | |||||||||
lconway | macOS 12.7.1 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 | OK | TIMEOUT | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: benchdamic |
Version: 1.15.4 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings benchdamic_1.15.4.tar.gz |
StartedAt: 2025-10-10 05:49:04 -0000 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 06:33:00 -0000 (Fri, 10 Oct 2025) |
EllapsedTime: 2636.1 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: benchdamic.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings benchdamic_1.15.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/benchdamic.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * 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 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 ... ERROR Running examples in ‘benchdamic-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: fitModels > ### Title: fitModels > ### Aliases: fitModels > > ### ** Examples > > # Generate some random counts > counts <- matrix(rnbinom(n = 600, size = 3, prob = 0.5), + nrow = 100, ncol = 6) > # Estimate the counts assuming several distributions > GOF <- fitModels( + object = counts, models = c( + "NB", "ZINB", + "DM", "ZIG", "HURDLE" + ), scale_HURDLE = c("median", "default") + ) Model: Negative Binomial Estimating dispersions Using classic mode. Examples with CPU (user + system) or elapsed time > 5s user system elapsed createConcordance 7.640 0.139 8.614 areaCAT 6.186 0.061 6.506 DA_ALDEx2 5.084 0.212 5.310 createTIEC 4.798 0.112 6.103 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’
benchdamic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL benchdamic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/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)
benchdamic.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-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)
benchdamic.Rcheck/benchdamic-Ex.timings
name | user | system | elapsed | |
CAT | 0.004 | 0.000 | 0.004 | |
DA_ALDEx2 | 5.084 | 0.212 | 5.310 | |
DA_ANCOM | 1.130 | 0.060 | 1.193 | |
DA_DESeq2 | 3.858 | 0.067 | 3.936 | |
DA_MAST | 1.867 | 0.071 | 2.016 | |
DA_Maaslin2 | 0.399 | 0.040 | 0.634 | |
DA_NOISeq | 1.577 | 0.127 | 3.036 | |
DA_Seurat | 2.512 | 0.028 | 2.690 | |
DA_ZicoSeq | 1.033 | 0.043 | 1.386 | |
DA_basic | 0.042 | 0.007 | 0.053 | |
DA_corncob | 1.073 | 0.034 | 1.849 | |
DA_dearseq | 0.082 | 0.004 | 0.137 | |
DA_edgeR | 0.268 | 0.000 | 0.269 | |
DA_limma | 0.108 | 0.000 | 0.108 | |
DA_linda | 0.072 | 0.000 | 0.072 | |
DA_maaslin3 | 0.855 | 0.012 | 1.271 | |
DA_metagenomeSeq | 0.352 | 0.004 | 0.360 | |
DA_mixMC | 1.055 | 0.004 | 1.068 | |
RMSE | 0.001 | 0.000 | 0.001 | |
addKnowledge | 0.234 | 0.012 | 0.247 | |
areaCAT | 6.186 | 0.061 | 6.506 | |
checkNormalization | 0 | 0 | 0 | |
createColors | 0.006 | 0.000 | 0.005 | |
createConcordance | 7.640 | 0.139 | 8.614 | |
createEnrichment | 0.393 | 0.020 | 0.425 | |
createMocks | 0.003 | 0.000 | 0.003 | |
createPositives | 1.557 | 0.020 | 1.707 | |
createSplits | 0.048 | 0.000 | 0.057 | |
createTIEC | 4.798 | 0.112 | 6.103 | |
enrichmentTest | 0.198 | 0.001 | 0.393 | |
extractDA | 0.294 | 0.000 | 0.588 | |
extractStatistics | 0.262 | 0.000 | 0.357 | |
fitDM | 0.046 | 0.004 | 0.193 | |
fitHURDLE | 1.002 | 0.024 | 1.362 | |