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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:biomformat.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings biomformat_1.40.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/biomformat.Rcheck’
* using R version 4.6.0 RC (2026-04-22 r89945)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-07 18:06:08 UTC
* checking for file ‘biomformat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biomformat’ version ‘1.40.0’
* 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 ‘biomformat’ 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  biom-methods.Rd: fromJSON
  biom_data-methods.Rd: Matrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘biomformat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: biom_to_SummarizedExperiment
> ### Title: Convert a biom object to a SummarizedExperiment
> ### Aliases: biom_to_SummarizedExperiment
> 
> ### ** Examples
> 
> biom_file <- system.file("extdata", "rich_sparse_otu_table.biom",
+                          package = "biomformat")
> x <- read_biom(biom_file)
> if (requireNamespace("SummarizedExperiment", quietly = TRUE)) {
+   se <- biom_to_SummarizedExperiment(x)
+   se
+   # S4 coercion syntax also works:
+   se2 <- as(x, "SummarizedExperiment")
+   identical(SummarizedExperiment::assay(se), SummarizedExperiment::assay(se2))
+ }
Error in as(x, "SummarizedExperiment") : 
  no method or default for coercing “biom” to “SummarizedExperiment”
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-biomformat.R’
 ERROR
Running the tests in ‘tests/testthat-biomformat.R’ failed.
Last 13 lines of output:
  Loading required package: biomformat
  Saving _problems/test-SE-63.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 279 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-SE.R:63:3'): as(x, 'SummarizedExperiment') coercion gives the same result ──
  Error in `as(x_rich, "SummarizedExperiment")`: no method or default for coercing "biom" to "SummarizedExperiment"
  Backtrace:
      ▆
   1. └─methods::as(x_rich, "SummarizedExperiment") at test-SE.R:63:3
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 279 ]
  Error:
  ! Test failures.
  Execution halted
* 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 ‘biomformat.Rmd’ using rmarkdown
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/biomformat.Rcheck/vign_test/biomformat/vignettes/biomformat_files/figure-html/plot-1.png" but not available.
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/biomformat.Rcheck/vign_test/biomformat/vignettes/biomformat_files/figure-html/plot-2.png" but not available.
The magick package is required to crop "/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/biomformat.Rcheck/vign_test/biomformat/vignettes/biomformat_files/figure-html/plot-3.png" but not available.

Quitting from biomformat.Rmd:324-327 [se-as-coercion]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `as()`:
! no method or default for coercing "biom" to "SummarizedExperiment"
---
Backtrace:
    ▆
 1. └─methods::as(x4, "SummarizedExperiment")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'biomformat.Rmd' failed with diagnostics:
no method or default for coercing "biom" to "SummarizedExperiment"
--- failed re-building ‘biomformat.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 1 NOTE
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/biomformat.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL biomformat
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘biomformat’ ...
** this is package ‘biomformat’ version ‘1.40.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘biomformat’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘biomformat’
Creating a generic function for ‘rownames’ from package ‘base’ in package ‘biomformat’
Creating a generic function for ‘colnames’ from package ‘base’ in package ‘biomformat’
** help
*** 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 (biomformat)

R version 4.6.0 RC (2026-04-22 r89945) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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")
> # As suggested for opt-out option on testing by users, recommended by CRAN
> # http://adv-r.had.co.nz/Testing.html
> # Previously, best practice was to put all test files in inst/tests and ensure that R CMD check ran them by putting the following code in tests/test-all.R:  
> # library(testthat)
> # library(yourpackage)
> # test_package("yourpackage")
> # Now, recommended practice is to put your tests in tests/testthat, and ensure R CMD check runs them by putting the following code in tests/test-all.R:
> # library(testthat)
> # test_check("yourpackage")
> # The advantage of this new structure is that the user has control over whether or not tests are installed using the –install-tests parameter to R CMD install, or INSTALL_opts = c(“–install-tests”) argument to install.packages(). I’m not sure why you wouldn’t want to install the tests, but now you have the flexibility as requested by CRAN maintainers.
> test_check("biomformat")
Loading required package: biomformat
Saving _problems/test-SE-63.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 279 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-SE.R:63:3'): as(x, 'SummarizedExperiment') coercion gives the same result ──
Error in `as(x_rich, "SummarizedExperiment")`: no method or default for coercing "biom" to "SummarizedExperiment"
Backtrace:
    ▆
 1. └─methods::as(x_rich, "SummarizedExperiment") at test-SE.R:63:3

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 279 ]
Error:
! Test failures.
Execution halted