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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:mia.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings mia_1.7.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/mia.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘mia/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mia’ version ‘1.7.4’
* 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 ... WARNING
Killed
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... 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: agglomerate-methods
> ### Title: Agglomerate data using taxonomic information
> ### Aliases: agglomerate-methods
> ###   agglomerateByRank,SummarizedExperiment-method agglomerateByRank
> ###   agglomerateByRank,SingleCellExperiment-method
> ###   agglomerateByRank,TreeSummarizedExperiment-method
> 
> ### ** Examples
> 
> data(GlobalPatterns)
> # print the available taxonomic ranks
> colnames(rowData(GlobalPatterns))
[1] "Kingdom" "Phylum"  "Class"   "Order"   "Family"  "Genus"   "Species"
> taxonomyRanks(GlobalPatterns)
[1] "Kingdom" "Phylum"  "Class"   "Order"   "Family"  "Genus"   "Species"
> 
> # agglomerate at the Family taxonomic rank
> x1 <- agglomerateByRank(GlobalPatterns, rank="Family")
> ## How many taxa before/after agglomeration?
> nrow(GlobalPatterns)
[1] 19216
> nrow(x1)
[1] 603
> 
> # with agglomeration of the tree
> x2 <- agglomerateByRank(GlobalPatterns, rank="Family",
+                        agglomerateTree = TRUE)
Warning in toTree(td) : The root is added with label 'ALL'
> nrow(x2) # same number of rows, but
[1] 603
> rowTree(x1) # ... different

Phylogenetic tree with 19216 tips and 19215 internal nodes.

Tip labels:
  549322, 522457, 951, 244423, 586076, 246140, ...
Node labels:
  , 0.858.4, 1.000.154, 0.764.3, 0.995.2, 1.000.2, ...

Rooted; includes branch lengths.
> rowTree(x2) # ... tree

Phylogenetic tree with 496 tips and 260 internal nodes.

Tip labels:
  Family:Cenarchaeaceae, Family:SAGMA-X, Family:Nitrososphaeraceae, Family:Sulfolobaceae, Family:Halobacteriaceae, Family:MSBL1, ...
Node labels:
  root:ALL, Kingdom:Archaea, Phylum:Crenarchaeota, Class:C2, Class:Sd-NA, Class:Thaumarchaeota, ...

Rooted; includes branch lengths.
> 
>  # If assay contains binary or negative values, summing might lead to meaningless
>  # values, and you will get a warning. In these cases, you might want to do 
>  # agglomeration again at chosen taxonomic level.
>  tse <- transformSamples(GlobalPatterns, method = "pa")
>  tse <- agglomerateByRank(tse, rank = "Genus")
Warning: 'pa' includes binary values.
Agglomeration of it might lead to meaningless values.
Check the assay, and consider doing transformation again manually with agglomerated data.
>  tse <- transformSamples(tse, method = "pa")
> 
> # removing empty labels by setting na.rm = TRUE
> sum(is.na(rowData(GlobalPatterns)$Family))
[1] 5603
> x3 <- agglomerateByRank(GlobalPatterns, rank="Family", na.rm = TRUE)
> nrow(x3) # different from x2
[1] 341
> 
> # Because all the rownames are from the same rank, rownames do not include 
> # prefixes, in this case "Family:". 
> print(rownames(x3[1:3,]))
[1] "Sulfolobaceae"  "SAGMA-X"        "Cenarchaeaceae"
> 
> # To add them, use getTaxonomyLabels function.
> rownames(x3) <- getTaxonomyLabels(x3, with_rank = TRUE)
> print(rownames(x3[1:3,]))
[1] "Family:Sulfolobaceae"  "Family:SAGMA-X"        "Family:Cenarchaeaceae"
> 
> # use 'remove_empty_ranks' to remove columns that include only NAs
> x4 <- agglomerateByRank(GlobalPatterns, rank="Phylum", remove_empty_ranks = TRUE)
> head(rowData(x4))
DataFrame with 6 rows and 2 columns
                          Kingdom         Phylum
                      <character>    <character>
Phylum:Crenarchaeota      Archaea  Crenarchaeota
Phylum:Euryarchaeota      Archaea  Euryarchaeota
Phylum:Actinobacteria    Bacteria Actinobacteria
Phylum:Spirochaetes      Bacteria   Spirochaetes
Phylum:MVP-15            Bacteria         MVP-15
Phylum:Proteobacteria    Bacteria Proteobacteria
> 
> # If assay contains NAs, you might want to consider replacing them since summing-up
> # NAs lead to NA
> x5 <- GlobalPatterns
> # Replace first value with NA
> assay(x5)[1,1] <- NA
> x6 <- agglomerateByRank(x5, "Kingdom")
Killed
* 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:
  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")
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘mia.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/mia.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL mia
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘mia’ ...
** using staged installation
** R
** data
** inst
** 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 (mia)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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(mia)
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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
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

Loading required package: MultiAssayExperiment
> 
> test_check("mia")
Killed