Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-14 12:06 -0400 (Tue, 14 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" | 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" | 4610 |
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: 2025-10-14 05:13:33 -0000 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 06:01:41 -0000 (Tue, 14 Oct 2025) |
EllapsedTime: 2887.6 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: plotEnrichment > ### Title: plotEnrichment > ### Aliases: plotEnrichment > > ### ** Examples > > data("ps_plaque_16S") > data("microbial_metabolism") > > # Extract genera from the phyloseq tax_table slot > genera <- phyloseq::tax_table(ps_plaque_16S)[, "GENUS"] > # Genera as rownames of microbial_metabolism data.frame > rownames(microbial_metabolism) <- microbial_metabolism$Genus > # Match OTUs to their metabolism > priorInfo <- data.frame(genera, + "Type" = microbial_metabolism[genera, "Type"]) > # Unmatched genera becomes "Unknown" > unknown_metabolism <- is.na(priorInfo$Type) > priorInfo[unknown_metabolism, "Type"] <- "Unknown" > priorInfo$Type <- factor(priorInfo$Type) > # Add a more informative names column > priorInfo[, "newNames"] <- paste0(rownames(priorInfo), priorInfo[, "GENUS"]) > > # Add some normalization/scaling factors to the phyloseq object > my_norm <- setNormalizations(fun = c("norm_edgeR", "norm_CSS"), + method = c("TMM", "CSS")) > ps_plaque_16S <- runNormalizations(normalization_list = my_norm, + object = ps_plaque_16S) + Running now:norm_edgeR Parameters:method=TMM NF.TMM column has been added. + Running now:norm_CSS Parameters:method=CSS Default value being used. NF.CSS column has been added. > > # Initialize some limma based methods > my_limma <- set_limma(design = ~ 1 + RSID + HMP_BODY_SUBSITE, + coef = "HMP_BODY_SUBSITESupragingival Plaque", + norm = c("TMM", "CSS")) Warning in set_limma(design = ~1 + RSID + HMP_BODY_SUBSITE, coef = "HMP_BODY_SUBSITESupragingival Plaque", : DA_limma One or more elements into 'norm' are not native to edgeR. > > # Make sure the subject ID variable is a factor > phyloseq::sample_data(ps_plaque_16S)[, "RSID"] <- as.factor( + phyloseq::sample_data(ps_plaque_16S)[["RSID"]]) > > # Perform DA analysis > Plaque_16S_DA <- runDA(method_list = my_limma, object = ps_plaque_16S) * Running now:DA_limma Parameters:assay_name=counts, pseudo_count=FALSE, design=~1 + RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", : DA_limma CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'. Automatically converting NF.CSS scaling/size factors to normalization factors. Differential abundance on CSS normalized data Estimating Differential Abundance without weighting Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient * Running now:DA_limma Parameters:assay_name=counts, pseudo_count=FALSE, design=~1 + RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE Differential abundance on TMM normalized data Estimating Differential Abundance without weighting Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient > > # Enrichment analysis > enrichment <- createEnrichment(object = Plaque_16S_DA, + priorKnowledge = priorInfo, enrichmentCol = "Type", namesCol = "GENUS", + slot = "pValMat", colName = "adjP", type = "pvalue", direction = "logFC", + threshold_pvalue = 0.1, threshold_logfc = 1, top = 10, verbose = TRUE) Method: limma.CSS * 'adjP' column, as pvalue type, of pValMat matrix. * 'logFC' column, as direction, of statInfo matrix. * DA: top 10 features, adjP<=0.1, |logFC|>=1 Method: limma.TMM * 'adjP' column, as pvalue type, of pValMat matrix. * 'logFC' column, as direction, of statInfo matrix. * DA: top 10 features, adjP<=0.1, |logFC|>=1 > > # Contingency tables > plotContingency(enrichment = enrichment, method = "limma.TMM") Using .id, direction, level as id variables > # Barplots > plotEnrichment(enrichment, enrichmentCol = "Type") > # Mutual findings > plotMutualFindings( + enrichment = enrichment, enrichmentCol = "Type", + n_methods = 1 + ) Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotConcordance 8.371 0.075 12.359 createConcordance 7.068 0.135 7.378 areaCAT 5.818 0.064 5.909 DA_ALDEx2 4.942 0.183 5.138 createTIEC 4.995 0.084 6.323 * 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 | 4.942 | 0.183 | 5.138 | |
DA_ANCOM | 1.161 | 0.028 | 1.192 | |
DA_DESeq2 | 3.868 | 0.064 | 3.943 | |
DA_MAST | 1.700 | 0.012 | 1.719 | |
DA_Maaslin2 | 0.361 | 0.012 | 0.383 | |
DA_NOISeq | 1.328 | 0.024 | 1.356 | |
DA_Seurat | 2.192 | 0.016 | 2.212 | |
DA_ZicoSeq | 0.976 | 0.008 | 0.987 | |
DA_basic | 0.043 | 0.000 | 0.043 | |
DA_corncob | 0.896 | 0.039 | 0.980 | |
DA_dearseq | 0.076 | 0.004 | 0.082 | |
DA_edgeR | 0.249 | 0.007 | 0.259 | |
DA_limma | 0.090 | 0.004 | 0.095 | |
DA_linda | 0.063 | 0.004 | 0.066 | |
DA_maaslin3 | 0.815 | 0.000 | 0.822 | |
DA_metagenomeSeq | 0.367 | 0.004 | 0.372 | |
DA_mixMC | 1.027 | 0.012 | 1.049 | |
RMSE | 0.001 | 0.000 | 0.001 | |
addKnowledge | 0.220 | 0.000 | 0.224 | |
areaCAT | 5.818 | 0.064 | 5.909 | |
checkNormalization | 0.001 | 0.000 | 0.001 | |
createColors | 0.005 | 0.000 | 0.005 | |
createConcordance | 7.068 | 0.135 | 7.378 | |
createEnrichment | 0.379 | 0.008 | 0.443 | |
createMocks | 0.003 | 0.000 | 0.003 | |
createPositives | 1.596 | 0.020 | 2.629 | |
createSplits | 0.051 | 0.000 | 0.099 | |
createTIEC | 4.995 | 0.084 | 6.323 | |
enrichmentTest | 0.178 | 0.000 | 0.180 | |
extractDA | 0.283 | 0.000 | 0.295 | |
extractStatistics | 0.278 | 0.000 | 0.279 | |
fitDM | 0.047 | 0.004 | 0.051 | |
fitHURDLE | 1.037 | 0.008 | 1.048 | |
fitModels | 3.614 | 0.035 | 4.093 | |
fitNB | 0.073 | 0.000 | 0.150 | |
fitZIG | 0.084 | 0.000 | 0.169 | |
fitZINB | 0.694 | 0.009 | 1.432 | |
getDA | 0.114 | 0.004 | 0.236 | |
getPositives | 0.122 | 0.000 | 0.249 | |
getStatistics | 0.112 | 0.000 | 0.225 | |
get_counts_metadata | 0.195 | 0.001 | 0.392 | |
iterative_ordering | 0.015 | 0.000 | 0.031 | |
meanDifferences | 0.003 | 0.000 | 0.009 | |
norm_CSS | 0.123 | 0.000 | 0.247 | |
norm_DESeq2 | 0.734 | 0.004 | 1.537 | |
norm_TSS | 0.060 | 0.000 | 0.121 | |
norm_edgeR | 0.139 | 0.000 | 0.277 | |
plotConcordance | 8.371 | 0.075 | 12.359 | |
plotContingency | 2.320 | 0.024 | 3.018 | |