##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:miaTime.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings miaTime_0.99.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/miaTime.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 ‘miaTime/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miaTime’ version ‘0.99.9’
* 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 ‘miaTime’ 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 ... 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 ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘miaTime-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getBaselineDivergence
> ### Title: Beta diversity between the baseline and later time steps
> ### Aliases: getBaselineDivergence addBaselineDivergence
> ###   getBaselineDivergence,SummarizedExperiment-method
> ###   addBaselineDivergence,SummarizedExperiment-method
> 
> ### ** Examples
> 
> library(miaTime)
> 
> data(hitchip1006)
> tse <- transformAssay(hitchip1006, method = "relabundance")
Loading required namespace: GenomeInfoDb
Failed with error:  ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) : 
  unable to load required package ‘GenomeInfoDb’
Calls: transformAssay ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   16. │               ├─methods::callNextMethod()
   17. │               └─SummarizedExperiment (local) .nextMethod(object = object)
   18. │                 ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
   19. │                 └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
   20. │                   ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
   21. │                   └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
   22. │                     └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
   23. └─methods:::.extendsForS3(`<chr>`)
   24.   └─methods::extends(Class, maybe = FALSE)
   25.     └─methods::getClassDef(class1)
   26.       └─methods:::.requirePackage(package)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 176 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/miaTime.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL miaTime
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘miaTime’ ...
** this is package ‘miaTime’ version ‘0.99.9’
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (miaTime)

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(miaTime)
Loading required package: mia
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

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

This is mia version 1.17.9
- Online documentation and vignettes: https://microbiome.github.io/mia/
- Online book 'Orchestrating Microbiome Analysis (OMA)': https://microbiome.github.io/OMA/docs/devel/
> 
> test_check("miaTime")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 187 ]
> 
> proc.time()
   user  system elapsed 
 81.659   1.495  83.355 

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(miaTime)
Loading required package: mia
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

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

This is mia version 1.17.9
- Online documentation and vignettes: https://microbiome.github.io/mia/
- Online book 'Orchestrating Microbiome Analysis (OMA)': https://microbiome.github.io/OMA/docs/devel/
> 
> test_check("miaTime")
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
Failed with error:  'there is no package called 'GenomeInfoDb''
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 176 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-getBaselineDivergence.R:5:5'): addBaselineDivergence output ────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─tse[, !duplicated(colData(tse)[, c("time", "subject")])] at test-getBaselineDivergence.R:5:5
  2. ├─tse[, !duplicated(colData(tse)[, c("time", "subject")])]
  3. │ ├─BiocGenerics::updateObject(x)
  4. │ └─TreeSummarizedExperiment::updateObject(x)
  5. │   ├─methods::callNextMethod()
  6. │   └─SingleCellExperiment (local) .nextMethod(object = object)
  7. │     ├─methods::callNextMethod()
  8. │     └─SummarizedExperiment (local) .nextMethod(object = object)
  9. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 10. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 11. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 12. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 13. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 14. └─methods:::.extendsForS3(`<chr>`)
 15.   └─methods::extends(Class, maybe = FALSE)
 16.     └─methods::getClassDef(class1)
 17.       └─methods:::.requirePackage(package)
── Error ('test-getBaselineDivergence.R:32:5'): Divergence in baseline other than 0 ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'addBaselineDivergence': unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─miaTime::addBaselineDivergence(...) at test-getBaselineDivergence.R:32:5
  2. ├─tse[, inds]
  3. ├─tse[, inds]
  4. │ ├─BiocGenerics::updateObject(x)
  5. │ └─TreeSummarizedExperiment::updateObject(x)
  6. │   ├─methods::callNextMethod()
  7. │   └─SingleCellExperiment (local) .nextMethod(object = object)
  8. │     ├─methods::callNextMethod()
  9. │     └─SummarizedExperiment (local) .nextMethod(object = object)
 10. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 11. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 12. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 13. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 14. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 15. ├─methods:::.extendsForS3(`<chr>`)
 16. │ └─methods::extends(Class, maybe = FALSE)
 17. │   └─methods::getClassDef(class1)
 18. │     └─methods:::.requirePackage(package)
 19. │       └─base::stop(...)
 20. └─base::.handleSimpleError(...)
 21.   └─base (local) h(simpleError(msg, call))
── Error ('test-getBaselineDivergence.R:47:5'): addBaselineDivergence reference ──
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─tse[, tse[["subject"]] == "843"] at test-getBaselineDivergence.R:47:5
  2. ├─tse[, tse[["subject"]] == "843"]
  3. │ ├─BiocGenerics::updateObject(x)
  4. │ └─TreeSummarizedExperiment::updateObject(x)
  5. │   ├─methods::callNextMethod()
  6. │   └─SingleCellExperiment (local) .nextMethod(object = object)
  7. │     ├─methods::callNextMethod()
  8. │     └─SummarizedExperiment (local) .nextMethod(object = object)
  9. │       ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 10. │       └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 11. │         ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 12. │         └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 13. │           └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 14. └─methods:::.extendsForS3(`<chr>`)
 15.   └─methods::extends(Class, maybe = FALSE)
 16.     └─methods::getClassDef(class1)
 17.       └─methods:::.requirePackage(package)
── Error ('test-getBaselineDivergence.R:112:5'): Test altExp ───────────────────
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─mia::agglomerateByRank(tse, rank = "Family") at test-getBaselineDivergence.R:112:5
  2. ├─mia::agglomerateByRank(tse, rank = "Family")
  3. │ └─mia (local) .local(x, ...)
  4. │   ├─methods::callNextMethod(...)
  5. │   │ └─base::eval(call, callEnv)
  6. │   │   └─base::eval(call, callEnv)
  7. │   └─mia (local) .nextMethod(x, rank = rank, update.tree = update.tree, ...)
  8. │     └─mia (local) .local(x, ...)
  9. │       ├─SingleCellExperiment::`altExps<-`(`*tmp*`, value = `<NULL>`)
 10. │       └─SingleCellExperiment::`altExps<-`(`*tmp*`, value = `<NULL>`)
 11. │         └─SingleCellExperiment:::.set_internal_all(...)
 12. │           ├─BiocGenerics::updateObject(x)
 13. │           └─TreeSummarizedExperiment::updateObject(x)
 14. │             ├─methods::callNextMethod()
 15. │             └─SingleCellExperiment (local) .nextMethod(object = object)
 16. │               ├─methods::callNextMethod()
 17. │               └─SummarizedExperiment (local) .nextMethod(object = object)
 18. │                 ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 19. │                 └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 20. │                   ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 21. │                   └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 22. │                     └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 23. └─methods:::.extendsForS3(`<chr>`)
 24.   └─methods::extends(Class, maybe = FALSE)
 25.     └─methods::getClassDef(class1)
 26.       └─methods:::.requirePackage(package)

[ FAIL 4 | WARN 0 | SKIP 0 | PASS 176 ]
Error: Test failures
Execution halted