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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DEFormats.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings DEFormats_1.27.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DEFormats.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘DEFormats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DEFormats’ version ‘1.27.0’
* 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 ‘DEFormats’ 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 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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'DGEList':
DGEList
  Code: function(counts, ...)
  Docs: function(counts = matrix(0, 0, 0), lib.size = colSums(counts),
                 norm.factors = rep(1, ncol(counts)), samples = NULL,
                 group = NULL, genes = NULL, remove.zeros = FALSE)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    lib.size norm.factors samples group genes remove.zeros
  Mismatches in argument names:
    Position: 2 Code: ... Docs: lib.size
  Mismatches in argument default values:
    Name: 'counts' Code:  Docs: matrix(0, 0, 0)

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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:
  ── Error ('test-DGEList.R:10:3'): the returned value is of class DGEList ───────
  Error in `as.matrix(counts)`: argument "counts" is missing, with no default
  Backtrace:
      ▆
   1. ├─testthat::expect_is(DGEList(), "DGEList") at test-DGEList.R:10:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─edgeR::DGEList()
   5. ├─edgeR::DGEList()
   6. └─edgeR::DGEList.default()
   7.   └─base::as.matrix(counts)
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 38 ]
  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 ...
  ‘DEFormats.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/DEFormats.Rcheck/00check.log’
for details.