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### 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
###
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* 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’

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL benchdamic
###
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* 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)

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)