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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: fitModels
> ### Title: fitModels
> ### Aliases: fitModels
> 
> ### ** 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 
  0.478   0.087   0.598 
After right optimization = -1207.77070452653
After orthogonalization = -1207.77070452653
   user  system elapsed 
  0.050   0.000   0.072 
After left optimization = -1204.98391365776
After orthogonalization = -1204.98391365776
Iteration 2
penalized log-likelihood = -1204.98391365776
After dispersion optimization = -1204.98391365776
   user  system elapsed 
  0.298   0.211   1.022 
After right optimization = -1203.06043616196
After orthogonalization = -1203.06043616196
   user  system elapsed 
  0.042   0.000   0.085 
After left optimization = -1202.94616837058
After orthogonalization = -1202.94616837058
Iteration 3
penalized log-likelihood = -1202.94616837058
After dispersion optimization = -1202.94616837058
   user  system elapsed 
  0.303   0.030   0.401 
After right optimization = -1202.91343811246
After orthogonalization = -1202.91343811246
   user  system elapsed 
  0.034   0.004   0.038 
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-1724.23283617012"
[1] "Iteration 4 Newton's update, log-likelihood-1653.33066927551"
[1] "Iteration 5 Newton's update, log-likelihood-1534.25649332615"
[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
createTIEC        5.412 10.569  55.403
createConcordance 7.943  0.431  15.585
areaCAT           6.369  0.481   8.342
DA_ALDEx2         4.966  0.148   5.124
createPositives   1.682  0.046   5.183
* 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-3.22-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-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)
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 2 | SKIP 0 | PASS 334 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 334 ]
> 
> proc.time()
    user   system  elapsed 
 100.374  275.684 1030.547