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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MMUPHin.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MMUPHin_1.99.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/MMUPHin.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MMUPHin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MMUPHin’ version ‘1.99.0’
* 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 ‘MMUPHin’ 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘utils’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Maaslin3_wrapper: no visible global function definition for
  ‘capture.output’
Maaslin3_wrapper : restore_res: no visible binding for global variable
  ‘feature_rename’
diagnostic_adjust_batch: no visible binding for global variable
  ‘Adjustment’
diagnostic_adjust_batch: no visible binding for global variable ‘batch’
diagnostic_adjust_batch: no visible binding for global variable
  ‘mean_overall’
diagnostic_adjust_batch: no visible binding for global variable
  ‘mean_batch’
diagnostic_adjust_batch: no visible binding for global variable
  ‘Feature’
diagnostic_continuous_discover: no visible binding for global variable
  ‘community’
diagnostic_continuous_discover: no visible binding for global variable
  ‘correlation’
diagnostic_continuous_discover: no visible binding for global variable
  ‘batch’
diagnostic_discrete_discover: no visible binding for global variable
  ‘k’
rma_wrapper: no visible global function definition for ‘pdf’
rma_wrapper : <anonymous>: no visible global function definition for
  ‘qnorm’
rma_wrapper: no visible global function definition for ‘dev.off’
rma_wrapper: no visible global function definition for ‘p.adjust’
visualize_continuous_discover: no visible global function definition
  for ‘pdf’
visualize_continuous_discover: no visible global function definition
  for ‘dev.off’
Undefined global functions or variables:
  Adjustment Feature batch capture.output community correlation dev.off
  feature_rename k mean_batch mean_overall p.adjust pdf qnorm
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "p.adjust", "qnorm")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
* 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 ‘MMUPHin-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: maaslin_meta
> ### Title: maaslin3-based meta-analytical differential abundance testing
> ### Aliases: maaslin_meta
> 
> ### ** Examples
> 
> # Assuming CRC_abd and CRC_meta are available
> fit_meta <- maaslin_meta(feature_abd = CRC_abd,
+                          exposure = "study_condition",
+                          batch = "studyID",
+                          covariates = c("gender", "age"),
+                          data = CRC_meta)
Error: object 'CRC_abd' not found
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
continuous_discover 5.875  0.565   6.957
* 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:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-helpers.R:101:3'): shorten_name works ────────────────────────
  Expected `shorten_name(c("abc", "abcdefghi", "abcdefghijk"))` to equal `c("abc", "abc..ghi", "abc..ijk")`.
  Differences:
  2/3 mismatches
  x[2]: "abcdefghi"
  y[2]: "abc..ghi"
  
  x[3]: "abcdefghijk"
  y[3]: "abc..ijk"
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 40 ]
  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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/MMUPHin.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MMUPHin
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘MMUPHin’ ...
** this is package ‘MMUPHin’ version ‘1.99.0’
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (MMUPHin)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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)
> library(MMUPHin)
> 
> test_check("MMUPHin")
Saving _problems/test-helpers-104.R
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 40 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-helpers.R:101:3'): shorten_name works ────────────────────────
Expected `shorten_name(c("abc", "abcdefghi", "abcdefghijk"))` to equal `c("abc", "abc..ghi", "abc..ijk")`.
Differences:
2/3 mismatches
x[2]: "abcdefghi"
y[2]: "abc..ghi"

x[3]: "abcdefghijk"
y[3]: "abc..ijk"

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 40 ]
Error:
! Test failures.
Execution halted