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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:midasHLA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings midasHLA_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/midasHLA.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-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 Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘midasHLA/DESCRIPTION’ ... OK
* this is package ‘midasHLA’ version ‘1.13.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘midasHLA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) omnibusTest.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) omnibusTest.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) omnibusTest.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) omnibusTest.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) omnibusTest.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) omnibusTest.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) omnibusTest.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) runMiDAS.Rd:151-154: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runMiDAS.Rd:155-158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runMiDAS.Rd:159-163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runMiDAS.Rd:164-168: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'kableResults.Rd':
kableResults
  Code: function(results, colnames = NULL, header = "MiDAS analysis
                 results", pvalue_cutoff = NULL, format = "html",
                 scroll_box_height = "400px")
  Docs: function(results, colnames = NULL, header = "MiDAS analysis
                 results", pvalue_cutoff = NULL, format =
                 getOption("knitr.table.format"), scroll_box_height =
                 "400px")
  Mismatches in argument default values:
    Name: 'format' Code: "html" Docs: getOption("knitr.table.format")

* 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 1180 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
runMiDAS         11.602  0.264  11.914
omnibusTest       6.866  0.158   7.069
getAAFrequencies  5.412  0.160   5.627
kableResults      5.095  0.092   5.187
* 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:
      anyMissing, rowMedians
  
  > 
  > test_check("midasHLA")
  [ FAIL 1 | WARN 20 | SKIP 0 | PASS 308 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_utils.R:166:3'): LRTest ──────────────────────────────────────
  `lrt_res` not equal to data.frame(...).
  Component "logLik": Mean relative difference: 0.005254902
  Component "statistic": Mean relative difference: 0.005254902
  
  [ FAIL 1 | WARN 20 | SKIP 0 | PASS 308 ]
  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: 1 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/midasHLA.Rcheck/00check.log’
for details.