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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_2.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/scRepertoire.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scRepertoire/DESCRIPTION’ ... OK
* this is package ‘scRepertoire’ version ‘2.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.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 ... 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 '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 'percentGenes.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 'percentVJ.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}’

Non-topic package-anchored link(s) in Rd file 'vizGenes.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
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
clonalSizeDistribution 34.389  3.429  38.092
StartracDiversity       6.638  0.368   7.055
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-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-x86_64/Resources/library’
* installing *source* package ‘scRepertoire’ ...
** this is package ‘scRepertoire’ version ‘2.4.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c aaKmers.cpp -o aaKmers.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c constructConDfAndParseBCR.cpp -o constructConDfAndParseBCR.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c constructConDfAndparseTCR.cpp -o constructConDfAndparseTCR.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c lvCompare.cpp -o lvCompare.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ntKmers.cpp -o ntKmers.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o scRepertoire.so RcppExports.o aaKmers.o constructConDfAndParseBCR.o constructConDfAndparseTCR.o lvCompare.o ntKmers.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-scRepertoire/00new/scRepertoire/libs
** R
** data
*** moving datasets to lazyload DB
** 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
** 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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)
NULL
> 
> proc.time()
   user  system elapsed 
  0.227   0.083   0.305 

R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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")
Meta data contains an 'ident' column and will likely result
                  in errors downstream.
[ FAIL 0 | WARN 0 | SKIP 23 | PASS 98 ]

══ Skipped tests (23) ══════════════════════════════════════════════════════════
• On CRAN (23): 'test-StartractDiversity.R:10:3', 'test-alluvialClones.R:10:3',
  'test-clonalAbundance.R:4:3', 'test-clonalCompare.R:7:3',
  'test-clonalDiversity.R:8:3', 'test-clonalHomeostasis.R:7:3',
  'test-clonalLength.R:4:3', 'test-clonalNetwork.R:9:3',
  'test-clonalOccupy.R:8:3', 'test-clonalOverlap.R:7:3',
  'test-clonalOverlay.R:10:3', 'test-clonalProportion.R:7:3',
  'test-clonalQuant.R:10:2', 'test-clonalRarefaction.R:9:3',
  'test-clonalScatter.R:5:3', 'test-clonalSizeDistribution.R:7:3',
  'test-percentAA.R:8:3', 'test-percentGenes.R:8:3', 'test-percentKmer.R:26:3',
  'test-percentVJ.R:8:3', 'test-positionalEntropy.R:6:3',
  'test-positionalProperty.R:6:3', 'test-vizGenes.R:7:3'

[ FAIL 0 | WARN 0 | SKIP 23 | PASS 98 ]
Deleting unused snapshots:
• alluvialClones/alluvialclones-alpha-plot.svg
• alluvialClones/alluvialclones-alphapluscolor-plot.svg
• alluvialClones/alluvialclones-facet-plot.svg
• alluvialClones/alluvialclones-nocolor-plot.svg
• alluvialClones/alluvialclones-trb-plot.svg
• clonalAbundance/clonalabundance-group-plot.svg
• clonalAbundance/clonalabundance-order-plot.svg
• clonalAbundance/clonalabundance-scaled-plot.svg
• clonalCompare/clonalcompare-alluvial-order-plot.svg
• clonalCompare/clonalcompare-area-plot.svg
• clonalCompare/clonalcompare-highlight-relabel-plot.svg
• clonalHomeostasis/clonalhomeostasis-order-plot.svg
• clonalLength/clonallength-both-chain-order-plot.svg
• clonalLength/clonallength-groupby-plot.svg
• clonalLength/clonallength-scaled-plot.svg
• clonalLength/clonallength-tra-plot.svg
• clonalLength/clonallength-trb-plot.svg
• clonalNetwork/clonalnetwork-filterclones-1-plot.svg
• clonalOccupy/clonaloccupy-proportion-plot.svg
• clonalOverlap/clonaloverlap-cosine-plot.svg
• clonalOverlap/clonaloverlap-coverlap-plot.svg
• clonalOverlap/clonaloverlap-jaccard-plot.svg
• clonalOverlap/clonaloverlap-morisita-plot.svg
• clonalOverlap/clonaloverlap-order-plot.svg
• clonalOverlap/clonaloverlap-reorder-plot.svg
• clonalOverlay/clonaloverlay-clonalproportion-plot.svg
• clonalProportion/clonalproportion-order-plot.svg
• clonalQuant/clonalquant-order-plot.svg
• clonalQuant/clonalquant-unscaled-plot.svg
• clonalRarefaction/clonalclonalrarefaction-h1-p2-plot.svg
• clonalRarefaction/clonalclonalrarefaction-h2-p3-plot.svg
• clonalScatter/clonalscatter-raw-plot.svg
• percentAA/percentaa-plot.svg
• percentGenes/percentgenes-order-plot.svg
• percentKmer/percentkmer-group-motif2-order-plot.svg
• percentVJ/percentvj-order-plot.svg
• positionalEntropy/positionalentropy-tra-plot.svg
• positionalEntropy/positionalentropy-trb-order-plot.svg
• positionalProperty/positionalentropy-kidera-plot.svg
• positionalProperty/positionalentropy-stscales-plot.svg
• positionalProperty/positionalentropy-tra-plot.svg
• positionalProperty/positionalentropy-trb-order-plot.svg
• positionalProperty/positionalentropy-tscales-plot.svg
• positionalProperty/positionalentropy-vhse-plot.svg
• vizGenes/vizgenes-heatmap-vignette-plot.svg
> 
> proc.time()
   user  system elapsed 
155.791   5.981 164.829