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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_1.14.4.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 ‘1.14.4’
* 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: plotMD
> ### Title: plotMD
> ### Aliases: plotMD
> 
> ### ** Examples
> 
> # Generate some random counts
> counts = matrix(rnbinom(n = 600, size = 3, prob = 0.5), nrow = 100, ncol = 6)
> 
> # Estimate the counts assuming several distributions
> GOF <- fitModels(
+     object = counts, models = c(
+         "NB", "ZINB",
+         "DM", "ZIG", "HURDLE"
+     ), scale_HURDLE = c("median", "default")
+ )
Model: Negative Binomial
Estimating dispersions
Using classic mode.
Model: Zero-Inflated Negative Binomial
Create model:
ok
Initialize parameters:
ok
Optimize parameters:
Iteration 1
penalized log-likelihood = -1347.76278210063
After dispersion optimization = -1244.63583478121
   user  system elapsed 
  0.374   0.020   0.400 
After right optimization = -1207.77070452653
After orthogonalization = -1207.77070452653
   user  system elapsed 
  0.036   0.004   0.041 
After left optimization = -1204.98391365776
After orthogonalization = -1204.98391365776
Iteration 2
penalized log-likelihood = -1204.98391365776
After dispersion optimization = -1204.98391365776
   user  system elapsed 
  0.344   0.044   0.391 
After right optimization = -1203.06043616196
After orthogonalization = -1203.06043616196
   user  system elapsed 
  0.041   0.008   0.049 
After left optimization = -1202.94616837058
After orthogonalization = -1202.94616837058
Iteration 3
penalized log-likelihood = -1202.94616837058
After dispersion optimization = -1202.94616837058
   user  system elapsed 
  0.297   0.031   0.335 
After right optimization = -1202.91343811246
After orthogonalization = -1202.91343811246
   user  system elapsed 
  0.045   0.004   0.073 
After left optimization = -1202.90041668469
After orthogonalization = -1202.90041668469
Iteration 4
penalized log-likelihood = -1202.90041668469
ok
Model: Dirichlet Multinomial
Warning in MGLM::MGLMreg.fit(Y = data, X = X, dist = "DM", display = verbose) :
  Sample size is smaller than the number of parameters.

[1] "Iteration 2 Newton's update, log-likelihood-1981.72940248219"
[1] "Iteration 3 Newton's update, log-likelihood-1724.23283617011"
[1] "Iteration 4 Newton's update, log-likelihood-1653.33066927543"
[1] "Iteration 5 Newton's update, log-likelihood-1534.25649332612"
[1] "Iteration 6 Newton's update, log-likelihood-1286.79535867652"
[1] "Iteration 7 Newton's update, log-likelihood-1230.06023319365"
[1] "Iteration 8 Newton's update, log-likelihood-1208.93424429382"
[1] "Iteration 9 Newton's update, log-likelihood-1208.3955918424"
[1] "Iteration 10 Newton's update, log-likelihood-1208.39188601233"
Model: Zero-Inflated Gaussian
Default value being used.
it= 0, nll=10.71, log10(eps+1)=Inf, stillActive=100
it= 1, nll=11.26, log10(eps+1)=0.12, stillActive=15
it= 2, nll=11.36, log10(eps+1)=0.01, stillActive=0
Model: Truncated Gaussian Hurdle
The counts provided have been rescaled and log2 transformed.
Making a SingleCellExperiment:
No dimnames in `exprsArray`, assuming `fData` and `cData` are sorted according to `exprsArray`
Assuming data assay in position 1, with name et is log-transformed.
Model: Truncated Gaussian Hurdle
The counts provided have been rescaled and log2 transformed.
Making a SingleCellExperiment:
No dimnames in `exprsArray`, assuming `fData` and `cData` are sorted according to `exprsArray`
Assuming data assay in position 1, with name et is log-transformed.
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plotConcordance   7.076  0.096   7.242
createConcordance 6.992  0.040   7.060
areaCAT           5.747  0.119   5.915
plotLogP          4.260  1.560  15.928
plotKS            4.213  0.035   9.047
plotContingency   3.980  0.124   7.583
plotFDR           3.978  0.036   8.163
plotFPR           3.899  0.056   5.950
plotEnrichment    2.242  0.020   5.047
* 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 ‘1.14.4’
** 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 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 
102.455 159.577 697.370