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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ANCOMBC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ANCOMBC_2.1.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ANCOMBC.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 ‘ANCOMBC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ANCOMBC’ version ‘2.1.2’
* 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 ‘ANCOMBC’ 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 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 ‘ANCOMBC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ancombc
> ### Title: Analysis of Compositions of Microbiomes with Bias Correction
> ###   (ANCOM-BC)
> ### Aliases: ancombc
> 
> ### ** Examples
> 
> #===========Build a TreeSummarizedExperiment Object from Scratch=============
> 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
> 
> # microbial count table
> otu_mat = matrix(sample(1:100, 100, replace = TRUE), nrow = 10, ncol = 10)
> rownames(otu_mat) = paste0("taxon", 1:nrow(otu_mat))
> colnames(otu_mat) = paste0("sample", 1:ncol(otu_mat))
> assays = SimpleList(counts = otu_mat)
> 
> # sample metadata
> smd = data.frame(group = sample(LETTERS[1:4], size = 10, replace = TRUE),
+                  row.names = paste0("sample", 1:ncol(otu_mat)),
+                  stringsAsFactors = FALSE)
> smd = DataFrame(smd)
> 
> # taxonomy table
> tax_tab = matrix(sample(letters, 70, replace = TRUE),
+                  nrow = nrow(otu_mat), ncol = 7)
> rownames(tax_tab) = rownames(otu_mat)
> colnames(tax_tab) = c("Kingdom", "Phylum", "Class", "Order",
+                       "Family", "Genus", "Species")
> tax_tab = DataFrame(tax_tab)
> 
> # create TSE
> tse = TreeSummarizedExperiment(assays = assays,
+                                colData = smd,
+                                rowData = tax_tab)
> 
> # convert TSE to phyloseq
> pseq = makePhyloseqFromTreeSummarizedExperiment(tse)
> 
> #========================Run ANCOMBC Using a Real Data=======================
> library(ANCOMBC)
> data(atlas1006)
> 
> # subset to baseline
> tse = atlas1006[, atlas1006$time == 0]
> 
> # run ancombc function
> set.seed(123)
> out = ancombc(data = tse, assay_name = "counts",
+               tax_level = "Family", phyloseq = NULL,
+               formula = "age + nationality + bmi_group",
+               p_adj_method = "holm", prv_cut = 0.10, lib_cut = 1000,
+               group = "bmi_group", struc_zero = TRUE, neg_lb = FALSE,
+               tol = 1e-5, max_iter = 100, conserve = TRUE,
+               alpha = 0.05, global = TRUE, n_cl = 1, verbose = TRUE)
'ancombc' is deprecated 
Use 'ancombc2' instead
Obtaining initial estimates ...
Estimating sample-specific biases ...
ANCOM-BC primary results ...
ANCOM-BC global test ...
Merge the information of structural zeros ... 
Note that taxa with structural zeros will have 0 p/q-values and SEs
> 
> res_prim = out$res
> res_global = out$res_global
> 
> # to run ancombc using the phyloseq object
> tse_alt = agglomerateByRank(tse, "Family")
> pseq = makePhyloseqFromTreeSummarizedExperiment(tse_alt)
> set.seed(123)
> out = ancombc(data = NULL, assay_name = NULL,
+               tax_level = "Family", phyloseq = pseq,
+               formula = "age + nationality + bmi_group",
+               p_adj_method = "holm", prv_cut = 0.10, lib_cut = 1000,
+               group = "bmi_group", struc_zero = TRUE, neg_lb = FALSE,
+               tol = 1e-5, max_iter = 100, conserve = TRUE,
+               alpha = 0.05, global = TRUE, n_cl = 1, verbose = TRUE)
'ancombc' is deprecated 
Use 'ancombc2' instead
Obtaining initial estimates ...
Estimating sample-specific biases ...
Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > packageVersion("ANCOMBC")
  [1] '2.1.2'
  > test_check("ANCOMBC")
  Loading required package: ANCOMBC
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ANCOM.Rmd’ using ‘UTF-8’... OK
  ‘ANCOMBC.Rmd’ using ‘UTF-8’... OK
  ‘ANCOMBC2.Rmd’ using ‘UTF-8’... OK
  ‘SECOM.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘ANCOM.Rmd’ using rmarkdown
Quitting from lines 109-137 (ANCOM.Rmd) 
Error: processing vignette 'ANCOM.Rmd' failed with diagnostics:
error reading from connection
--- failed re-building ‘ANCOM.Rmd’

--- re-building ‘ANCOMBC.Rmd’ using rmarkdown
Killed
--- re-building ‘ANCOMBC2.Rmd’ using rmarkdown
Killed
--- re-building ‘SECOM.Rmd’ using rmarkdown
Killed
SUMMARY: processing the following files failed:
  ‘ANCOM.Rmd’ ‘ANCOMBC.Rmd’ ‘ANCOMBC2.Rmd’ ‘SECOM.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/ANCOMBC.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ANCOMBC
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘ANCOMBC’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: ANCOMBC
*** installing help indices
** 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 (ANCOMBC)

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")
> packageVersion("ANCOMBC")
[1] '2.1.2'
> test_check("ANCOMBC")
Loading required package: ANCOMBC
Killed