############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings benchdamic_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/benchdamic.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (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 ‘1.10.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * 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 ... OK * 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 ... NOTE checkRd: (-1) DA_Seurat.Rd:29-31: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:33-36: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:42-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:45-46: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:47-56: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:57-58: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:59-61: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:62-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:64-67: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:68-70: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:71-73: Lost braces in \itemize; meant \describe ? checkRd: (-1) areaCAT.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) areaCAT.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) areaCAT.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) areaCAT.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) areaCAT.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) areaCAT.Rd:24-28: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) areaCAT.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) areaCAT.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createConcordance.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createConcordance.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createConcordance.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createConcordance.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createConcordance.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createConcordance.Rd:36-40: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createEnrichment.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createEnrichment.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createEnrichment.Rd:83-84: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createEnrichment.Rd:85-86: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createTIEC.Rd:17-19: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createTIEC.Rd:20-23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createTIEC.Rd:24-27: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createTIEC.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createTIEC.Rd:31-34: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) enrichmentTest.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) enrichmentTest.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) enrichmentTest.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) enrichmentTest.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extractDA.Rd:62-63: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extractDA.Rd:64-66: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extractDA.Rd:67-70: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getDA.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getDA.Rd:60-62: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getDA.Rd:63-66: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) get_counts_metadata.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) get_counts_metadata.Rd:34-35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) get_counts_metadata.Rd:36-37: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotConcordance.Rd:21-23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotConcordance.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) set_Seurat.Rd:26-28: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:29-30: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:31-40: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:41-42: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:43-45: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:46-47: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:48-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:52-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:55-57: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:64-66: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:68-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:72: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... OK * 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: plotConcordance > ### Title: plotConcordance > ### Aliases: plotConcordance > > ### ** 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 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 - Comparison6 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 - Comparison7 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 - Comparison8 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 - Comparison9 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 - Comparison10 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 - Subset2 - 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 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 - Comparison6 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 - Comparison7 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 - Comparison8 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 - Comparison9 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 - Comparison10 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 > > # Concordance for p-values > concordance_pvalues <- createConcordance( + object = results, slot = "pValMat", colName = "rawP", type = "pvalue" + ) * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’/home/biocbuild/R/R-beta-2024-04-15_r86425/bin/BATCH: line 60: 1271526 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(benchdamic) * 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 ERRORs, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/benchdamic.Rcheck/00check.log’ for details.