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###
### 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_0.99.8.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/MutSeqR.Rcheck’
* using R Under development (unstable) (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 ‘MutSeqR/DESCRIPTION’ ... OK
* this is package ‘MutSeqR’ version ‘0.99.8’
* 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.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MutSeqR
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘MutSeqR’ ...
** this is package ‘MutSeqR’ version ‘0.99.8’
** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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.

> # 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

Joining with `by = join_by(sample)`
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
Reference level for factor dose: 25
Fitting GLM: glm(cbind(sum_min, group_depth) ~ dose, family = quasibinomial)
Max absolute residual: 5.72814832878274e-15 (Row 8)
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 110 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 110 ]
> 
> proc.time()
   user  system elapsed 
  8.144   0.584   9.178