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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Macarron.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Macarron_1.4.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/Macarron.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Macarron/DESCRIPTION' ... OK
* this is package 'Macarron' version '1.4.0'
* 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 whether package 'Macarron' 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 ... NOTE
calQval: no visible binding for global variable 'metadata'
calQval: no visible binding for global variable 'value'
calQval: no visible binding for global variable 'pval'
Undefined global functions or variables:
  metadata pval value
* 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 files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'Macarron-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: decorateID
> ### Title: Create a chemical taxonomy table for annotated metabolic
> ###   features.
> ### Aliases: decorateID
> 
> ### ** Examples
> 
> prism_annotations = system.file("extdata", "demo_annotations.csv", package="Macarron")
> annotations_df = read.csv(file = prism_annotations, row.names = 1)
> input_taxonomy <- decorateID(annotations_df)
Error in `colnames<-`(`*tmp*`, value = c(names(input_annotations)[1],  : 
  attempt to set 'colnames' on an object with less than two dimensions
Calls: decorateID -> colnames<-
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:
  2023-10-16 03:39:42.55757 INFO::Writing heatmap of significant results to file: maaslin2_output/heatmap.pdf
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 17 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-decorateID.R:10:1'): (code run outside of `test_that()`) ───────
  Error in ``colnames<-`(`*tmp*`, value = c(names(input_annotations)[1], 
      "Sub_Class", "Class"))`: attempt to set 'colnames' on an object with less than two dimensions
  Backtrace:
      ▆
   1. └─Macarron::decorateID(annotations_df) at test-decorateID.R:10:0
   2.   └─base::`colnames<-`(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 17 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc/meat/Macarron.Rcheck/00check.log'
for details.