##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MutSeqR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MutSeqR_0.99.11.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/MutSeqR.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-25 01:07:28 UTC
* using option ‘--no-vignettes’
* checking for file ‘MutSeqR/DESCRIPTION’ ... OK
* this is package ‘MutSeqR’ version ‘0.99.11’
* 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 ‘MutSeqR’ 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 whether startup messages can be suppressed ... 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
  ‘[magrittr:pipe]{%>%}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/MutSeqR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MutSeqR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘MutSeqR’ ...
** this is package ‘MutSeqR’ version ‘0.99.11’
** using staged installation
** R
** inst
** 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 (MutSeqR)

R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(MutSeqR)
                                                         
  @                                  %                   
  @&  @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@                   
  %@@. *@@@@@@@@@@@@@@@@@@@@@@@@@@@@@&                   
   &@@@.                         @@@@                    
     @@@@@.  /@@@@@@@@@@@@@@@@@@@@@.                     
       @@@@@@%            #@@@@@@.                       
         .@@@@@@@@,     @@@@@@,                          
             &@@@@@@@@%   ,                              
             ,  .@@@@@@@@@                              
         *@@@@@@    (@@@@@@@@                          
       @@@@@@@@        *@@@@@@@@            .@@/       
     @@@@@@@    ,%%%%%%%%%@@@@@@@@         %@@@@@.     
    @@@@@@    *@@@@@@@@@@@@@@@@@@@@      .@@&          
   @@@@@@                    @@@@@@@     #              
  @@@@@@    ,@@@@@@@@@@@@@@@@@(              ./&@@@@@@@, 
  @@@@@@    *%%%%%%%%%%%%%%%%&@@@&@@@.        .(@@@@@@@, 
  &@@@@@@                    @@@@@@@    #,             
   @@@@@@     @@@@@@@@@@@@@@@@@@@@@@       @@@*         
    &@@@@@@                @@@@@@@@         (@@@@@*     
      @@@@@@@           ,@@@@@@@@             @@.       
        (@@@@@@@      @@@@@@@@@                         
            @@@@@@@@@&   %@@@                            
               /@@@@@@@@@                               
           @@@@&    @@@@@@@@@                            
        @@@@@@@)        *@@@@@@@                         
     ,@@@@@@@@@@@@@@@@@@@   ,@@@@@/                      
    @@@@,                      .@@@@.                    
  .@@@                            &@@*                   
  @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@(  @@                   
  @                                  @                   
                                                           
  __  __       _   ____             ____  
 |  \/  |_   _| |_/ ___|  ___  __ _|  _ \ 
 | |\/| | | | | __\___ \ / _ \/ _` | |_) |
 | |  | | |_| | |_ ___) |  __/ (_| |  _ < 
 |_|  |_|\__,_|\__|____/ \___|\__, |_| \_\
                                 |_|      
> 
> test_check("MutSeqR")
Performing internal depth correction to prevent double-counting
Internal depth correction complete.
Joining with `by = join_by(sample)`
Performing internal depth correction to prevent double-counting
Internal depth correction complete.
Joining with `by = join_by(sample)`
Performing internal depth correction to prevent double-counting
Internal depth correction complete.
Joining with `by = join_by(sample, normalized_ref)`
Joining with `by = join_by(sample)`
Joining with `by = join_by(sample, normalized_ref)`
Performing internal depth correction to prevent double-counting
Internal depth correction complete.
Joining with `by = join_by(sample)`
Performing internal depth correction to prevent double-counting
Internal depth correction complete.
Joining with `by = join_by(sample)`
Flagging germline mutations...
Found 15 germline mutations.
Filtering complete.
Flagging germline mutations...
Found 15 germline mutations.
Flagging SNVs overlapping with germline MNVs...
Found 1 SNVs overlapping with germline MNVs.
Removing filtered mutations from the total_depth...
Filtering complete.
Removing rows with abnormal VAF...
Removed 5 rows with abnormal VAF.
Filtering complete.
Returning a list: mutation_data and filtered_rows.
Applying custom filter...
Flagged 11 rows with values in <sd_metadata> column that matched C
Filtering complete.
Applying custom filter...
Removed 25 rows with values in <sd_metadata> that contained AB from mutation_data
Filtering complete.
Returning a list: mutation_data and filtered_rows.
Applying region filter...
Removed 1 rows based on regions.
Filtering complete.
Applying region filter...
Removed 0 rows based on regions.
Filtering complete.
Applying region filter...
Removed 35 rows based on regions.
Filtering complete.
Loading reference genome: BSgenome.Mmusculus.UCSC.mm10.

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


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname


Attaching package: 'Biostrings'

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

    strsplit

Sample metadata successfully joined to mutation data

Regions metadata successfully joined to mutation data

Expected 'alt' but found 'alt.value', renaming it.
Expected 'alt_depth' but found 'VD', renaming it.
Loading reference genome: BSgenome.Mmusculus.UCSC.mm10.
Retrieving context sequences from BSgenome
Expected 'alt' but found 'alt.value', renaming it.
Expected 'alt_depth' but found 'VD', renaming it.
Loading reference genome: BSgenome.Hsapiens.UCSC.hg38.
Retrieving context sequences from BSgenome
Expected 'alt' but found 'alt.value', renaming it.
Expected 'alt_depth' but found 'VD', renaming it.
Reference level for factor dose: 25
Fitting GLM: glm(cbind(sum_min, group_depth) ~ dose, family = quasibinomial)
Max absolute residual: 2.86407416439137e-15 (Row 8)
Warning: we have recently become aware that large mutation counts
    can lead to inflated G2 statistics and false positives. We are actively
    investigating this issue and will update the function accordingly. In the
    meantime, we recommend using this function with caution, especially for
    comparisons involving large mutation counts (> 10 mutations per sample).
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 119 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 119 ]
> 
> proc.time()
   user  system elapsed 
  8.134   0.671   8.904