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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scRepertoire_2.5.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/scRepertoire.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scRepertoire/DESCRIPTION’ ... OK
* this is package ‘scRepertoire’ version ‘2.5.3’
* 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 ‘scRepertoire’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION.cff
Most likely ‘inst/CITATION’ should be used instead.
* 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 ... NOTE
.calculatePairwiseIndices: no visible global function definition for
  ‘combn’
clonalSizeDistribution: no visible binding for global variable ‘y’
Undefined global functions or variables:
  combn y
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'StartracDiversity.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'alluvialClones.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalAbundance.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalBias.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalDiversity.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalHomeostasis.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalLength.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalNetwork.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalOccupy.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalOverlap.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalProportion.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalQuant.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalRarefaction.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalScatter.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalSizeDistribution.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'percentAA.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'percentGeneUsage.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'percentKmer.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'positionalEntropy.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'positionalProperty.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
      union
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 751 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-clonalScatter.R:76:3'): Plotting output has the correct components ──
  plot_output$labels$fill (`actual`) not equal to "class" (`expected`).
  
  `actual` is NULL
  `expected` is a character vector ('class')
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 751 ]
  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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/scRepertoire.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scRepertoire
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘scRepertoire’ ...
** this is package ‘scRepertoire’ version ‘2.5.3’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c constructConDfAndParseBCR.cpp -o constructConDfAndParseBCR.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c constructConDfAndparseTCR.cpp -o constructConDfAndparseTCR.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o scRepertoire.so RcppExports.o constructConDfAndParseBCR.o constructConDfAndparseTCR.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-scRepertoire/00new/scRepertoire/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to 'floor' 
Note: wrong number of arguments to 'floor' 
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scRepertoire)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.078   0.026   0.100 

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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(scRepertoire)
Loading required package: ggplot2
> 
> test_check("scRepertoire")

Attaching package: 'igraph'

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

    compare

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

    decompose, spectrum

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

    union

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 751 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-clonalScatter.R:76:3'): Plotting output has the correct components ──
plot_output$labels$fill (`actual`) not equal to "class" (`expected`).

`actual` is NULL
`expected` is a character vector ('class')

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 751 ]
Error: Test failures
Execution halted