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###
### Running command:
###
###   /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_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/midasHLA.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* 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 ‘midasHLA/DESCRIPTION’ ... OK
* this is package ‘midasHLA’ version ‘1.18.0’
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MiDAS-class.Rd: MultiAssayExperiment
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
* 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         13.075  0.208  22.089
omnibusTest       7.118  0.155  12.345
getAAFrequencies  6.748  0.160  13.180
kableResults      6.049  0.074  11.276
hlaToAAVariation  3.990  0.681   9.175
* 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:
  > test_check("midasHLA")
  Saving _problems/test_utils-176.R
  [ FAIL 1 | WARN 20 | SKIP 0 | PASS 308 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_utils.R:166:3'): LRTest ──────────────────────────────────────
  Expected `lrt_res` to equal `data.frame(...)`.
  Differences:
  Component "logLik": Mean relative difference: 0.01460859
  Component "statistic": Mean relative difference: 0.01460859
  
  [ 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-3.22-bioc/meat/midasHLA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL midasHLA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘midasHLA’ ...
** this is package ‘midasHLA’ version ‘1.18.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (midasHLA)

R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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(midasHLA)
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("midasHLA")
Saving _problems/test_utils-176.R
[ FAIL 1 | WARN 20 | SKIP 0 | PASS 308 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_utils.R:166:3'): LRTest ──────────────────────────────────────
Expected `lrt_res` to equal `data.frame(...)`.
Differences:
Component "logLik": Mean relative difference: 0.01460859
Component "statistic": Mean relative difference: 0.01460859

[ FAIL 1 | WARN 20 | SKIP 0 | PASS 308 ]
Error:
! Test failures.
Execution halted