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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lefser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lefser_1.15.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/lefser.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lefser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lefser’ version ‘1.15.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘lefser’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
lefserPlot: no visible binding for global variable ‘.’
Undefined global functions or variables:
  .
* 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 ... NOTE
  Note: found 1 marked UTF-8 string
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘lefser-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lefser
> ### Title: R implementation of the LEfSe method
> ### Aliases: lefser
> 
> ### ** Examples
> 
>     
>     data(zeller14)
>     zeller14 <- zeller14[, zeller14$study_condition != "adenoma"]
>     tn <- get_terminal_nodes(rownames(zeller14ra))
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'zeller14ra' not found
Calls: get_terminal_nodes -> logical -> rownames -> .handleSimpleError -> h
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:
  15/15 mismatches (average diff: 0.704)
  [1] -3.34 - -3.80 ==  0.459
  [2] -3.26 - -3.70 ==  0.438
  [3] -3.13 - -3.52 ==  0.388
  [4] -2.92 - -3.36 ==  0.440
  [5] -2.79 - -3.13 ==  0.339
  [6] -2.63 - -3.08 ==  0.453
  [7] -2.51 - -3.07 ==  0.560
  [8] -2.14 -  2.14 == -4.283
  [9]  3.08 -  2.49 ==  0.590
  ...
  
  [ FAIL 3 | WARN 0 | SKIP 1 | PASS 16 ]
  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-3.20-bioc/meat/lefser.Rcheck/00check.log’
for details.