############################################################################## ############################################################################## ### ### 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_1.14.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/benchdamic.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * 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-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘benchdamic/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘benchdamic’ version ‘1.14.2’ * 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: createConcordance > ### Title: createConcordance > ### Aliases: createConcordance > > ### ** Examples > > data(ps_plaque_16S) > > # Balanced design > my_splits <- createSplits( + object = ps_plaque_16S, varName = "HMP_BODY_SUBSITE", balanced = TRUE, + paired = "RSID", N = 10 # N = 100 suggested + ) Warning in createSplits(object = ps_plaque_16S, varName = "HMP_BODY_SUBSITE", : The variable HMP_BODY_SUBSITE is not a factor. Coercing to factor. Working on 30 paired samples. 2 repeated measures for each RSID ID. > > # 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"]]) > > # Initialize some limma based methods > my_limma <- set_limma(design = ~ RSID + HMP_BODY_SUBSITE, + coef = "HMP_BODY_SUBSITESupragingival Plaque", + norm = c("TMM", "CSS")) Warning in set_limma(design = ~RSID + HMP_BODY_SUBSITE, coef = "HMP_BODY_SUBSITESupragingival Plaque", : DA_limma One or more elements into 'norm' are not native to edgeR. > > # Set the normalization methods according to the DA methods > my_norm <- setNormalizations(fun = c("norm_edgeR", "norm_CSS"), + method = c("TMM", "CSS")) > > # Run methods on split datasets > results <- runSplits(split_list = my_splits, method_list = my_limma, + normalization_list = my_norm, object = ps_plaque_16S) - Subset1 - Comparison1 Splitting the samples... Keeping taxa with more than 0 counts in more than 0 samples. Computing normalizations... + 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. Differential abundance: * Running now:DA_limma Parameters:assay_name=counts, pseudo_count=FALSE, design=~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=~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 - Comparison2 Splitting the samples... Keeping taxa with more than 0 counts in more than 0 samples. Computing normalizations... + 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. Differential abundance: * Running now:DA_limma Parameters:assay_name=counts, pseudo_count=FALSE, design=~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=~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 - Comparison3 Splitting the samples... Keeping taxa with more than 0 counts in more than 0 samples. Computing normalizations... + 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. Differential abundance: * Running now:DA_limma Parameters:assay_name=counts, pseudo_count=FALSE, design=~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=~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 - Comparison4 Splitting the samples... Keeping taxa with more than 0 counts in more than 0 samples. Computing normalizations... + 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. Differential abundance: * Running now:DA_limma Parameters:assay_name=counts, pseudo_count=FALSE, design=~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=~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 - Comparison5 Splitting the samples... Keeping taxa with more than 0 counts in more than 0 samples. Computing normalizations... + Running now:norm_edgeR Parameters:method=TMM NF.TMM column has been added. + Running now:norm_CSS Parameters:method=CSS Examples with CPU (user + system) or elapsed time > 5s user system elapsed areaCAT 6.562 5.485 36.115 DA_ALDEx2 5.773 0.187 7.521 DA_DESeq2 4.646 0.116 9.543 DA_mixMC 1.033 1.159 9.915 * 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: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/benchdamic.Rcheck/00check.log’ for details.