##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MicrobiomeBenchmarkData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MicrobiomeBenchmarkData_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/MicrobiomeBenchmarkData.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MicrobiomeBenchmarkData/DESCRIPTION’ ... OK
* this is package ‘MicrobiomeBenchmarkData’ version ‘1.11.0’
* 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 ‘MicrobiomeBenchmarkData’ 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 ... NOTE
Documented arguments not in \usage in Rd file 'dot-assembleTreeSummarizedExperiment.Rd':
  ‘dat_name’ ‘dat_url’

Documented arguments not in \usage in Rd file 'dot-getResourcePath.Rd':
  ‘resource_name’ ‘resource_url’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘MicrobiomeBenchmarkData.Rmd’ using rmarkdown
1 HMP_2012_16S_gingival_V13
2 HMP_2012_16S_gingival_V35
3 HMP_2012_16S_gingival_V35_subset
4 HMP_2012_WMS_gingival
5 Stammler_2016_16S_spikein
6 Ravel_2011_16S_BV

Use vignette('datasets', package = 'MicrobiomeBenchmarkData') for a detailed description of the datasets.

Use getBenchmarkData(dryrun = FALSE) to import all of the datasets.

Quitting from MicrobiomeBenchmarkData.Rmd:108-111 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `BiocFileCache::bfcrpath()`:
! not all 'rnames' found or unique.
---
Backtrace:
    ▆
 1. └─MicrobiomeBenchmarkData::getBenchmarkData(dryrun = FALSE)
 2.   └─base::lapply(dataset_names, .assembleTreeSummarizedExperiment)
 3.     └─MicrobiomeBenchmarkData (local) FUN(X[[i]], ...)
 4.       ├─base::as.matrix(...)
 5.       ├─utils::read.table(...)
 6.       └─MicrobiomeBenchmarkData:::.getResourcePath(x, "_count_matrix")
 7.         ├─BiocFileCache::bfcrpath(...)
 8.         └─BiocFileCache::bfcrpath(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MicrobiomeBenchmarkData.Rmd' failed with diagnostics:
not all 'rnames' found or unique.
--- failed re-building ‘MicrobiomeBenchmarkData.Rmd’

--- re-building ‘datasets.Rmd’ using rmarkdown
--- finished re-building ‘datasets.Rmd’

--- re-building ‘recalibrare_spikein_data.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-data-experiment/meat/MicrobiomeBenchmarkData.Rcheck/vign_test/MicrobiomeBenchmarkData/vignettes/recalibrare_spikein_data_files/figure-html/unnamed-chunk-4-1.png" but not available.
--- finished re-building ‘recalibrare_spikein_data.Rmd’

SUMMARY: processing the following file failed:
  ‘MicrobiomeBenchmarkData.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/MicrobiomeBenchmarkData.Rcheck/00check.log’
for details.