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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:mia.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings mia_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/mia.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* 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 ‘mia/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mia’ 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 ‘mia’ 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 R 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown package ‘https’ in Rd xrefs
* 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 ... NOTE
  Note: found 101 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘mia-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculateDMN
> ### Title: Dirichlet-Multinomial Mixture Model: Machine Learning for
> ###   Microbiome Data
> ### Aliases: calculateDMN calculateDMN,ANY-method
> ###   calculateDMN,SummarizedExperiment-method runDMN getDMN
> ###   getDMN,SummarizedExperiment-method bestDMNFit
> ###   bestDMNFit,SummarizedExperiment-method getBestDMNFit
> ###   getBestDMNFit,SummarizedExperiment-method calculateDMNgroup
> ###   calculateDMNgroup,ANY-method
> ###   calculateDMNgroup,SummarizedExperiment-method performDMNgroupCV
> ###   performDMNgroupCV,ANY-method
> ###   performDMNgroupCV,SummarizedExperiment-method
> 
> ### ** Examples
> 
> fl <- system.file(package="DirichletMultinomial", "extdata", "Twins.csv")
> counts <- as.matrix(read.csv(fl, row.names=1))
> fl <- system.file(package="DirichletMultinomial", "extdata", "TwinStudy.t")
> pheno0 <- scan(fl)
Read 278 items
> lvls <- c("Lean", "Obese", "Overwt")
> pheno <- factor(lvls[pheno0 + 1], levels=lvls)
> colData <- DataFrame(pheno = pheno)
> 
> tse <- TreeSummarizedExperiment(assays = list(counts = counts),
+                                 colData = colData)
> 
> library(bluster)
> 
> # Compute DMM algorithm and store result in metadata
> tse <- cluster(tse, name = "DMM", DmmParam(k = 1:3, type = "laplace"),
+                MARGIN = "samples", full = TRUE)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 1508929 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  Loading required package: SingleCellExperiment
  Loading required package: TreeSummarizedExperiment
  Loading required package: Biostrings
  Loading required package: XVector
  
  Attaching package: 'Biostrings'
  
  The following object is masked from 'package:base':
  
      strsplit
  
  Loading required package: MultiAssayExperiment
  > 
  > test_check("mia")
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/mia.Rcheck/00check.log’
for details.