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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_1.14.3.tar.gz
###
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* 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 ‘1.14.3’
* 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: 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

Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
norm_DESeq2         1.032 32.810 101.324
createConcordance   7.642  0.028  10.187
areaCAT             6.709  0.024  10.804
DA_ALDEx2           5.703  0.107   5.834
createTIEC          4.124  0.023   7.270
fitModels           3.828  0.035   5.341
getDA               0.263  2.445  17.436
get_counts_metadata 0.232  0.948   5.692
* 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.

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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-devel_2025-02-19/site-library’
* installing *source* package ‘benchdamic’ ...
** this is package ‘benchdamic’ version ‘1.14.3’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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)
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'spam'
> 
> test_check("benchdamic")
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 334 ]
> 
> proc.time()
   user  system elapsed 
 99.246  43.594 334.618