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### Running command:
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###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Macarron.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings Macarron_1.13.2.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/Macarron.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* 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 '1.13.2'
* 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 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 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 dependencies in R code ... WARNING
'::' or ':::' import not declared from: 'stringr'
Namespaces in Imports field not imported from:
  'methods' 'utils'
  All declared Imports should be used.
Package in Depends field not imported from: 'SummarizedExperiment'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Macarron: no visible global function definition for 'write.csv'
calAVA : find.anchor: no visible global function definition for 'tail'
calQval: no visible binding for global variable 'metadata'
calQval: no visible binding for global variable 'value'
calQval: no visible binding for global variable 'pval'
findMacMod: no visible global function definition for 'hclust'
findMacMod: no visible global function definition for 'as.dist'
findMacMod: no visible global function definition for 'quantile'
makeDisMat : .getCorMat: no visible global function definition for 'as'
showBest : digest.each : analyze.module: no visible global function
  definition for 'head'
showBest : digest.each: no visible global function definition for
  'head'
showBest : digest.each: no visible global function definition for
  'tail'
showBest : digest.each: no visible global function definition for
  'complete.cases'
Undefined global functions or variables:
  as as.dist complete.cases hclust head metadata pval quantile tail
  value write.csv
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "as.dist", "complete.cases", "hclust", "quantile")
  importFrom("utils", "head", "tail", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Macarron 320.24   6.56  328.54
calQval   10.36   0.33   10.70
calES      9.84   0.20   10.10
calAVA     6.74   0.16    6.89
* 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:
  2025-07-24 03:51:37.617905 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): maaslin2_output/significant_results.tsv
  [ FAIL 1 | WARN 109 | 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:10:1
   2.   └─base::`colnames<-`(...)
  
  [ FAIL 1 | WARN 109 | SKIP 0 | PASS 17 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.22-bioc/meat/Macarron.Rcheck/00check.log'
for details.