##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:atacInferCnv.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings atacInferCnv_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/atacInferCnv.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* 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: 2026-04-29 00:05:01 UTC
* using option ‘--no-vignettes’
* checking for file ‘atacInferCnv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘atacInferCnv’ version ‘1.0.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘atacInferCnv’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.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 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
plotCnvBlocks: no visible binding for global variable ‘x’
plotCnvBlocks: no visible binding for global variable ‘value’
Undefined global functions or variables:
  value x
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
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
plotCnvBlocks            21.149  0.434  21.635
runAtacInferCnv          17.271  0.175  17.479
prepareAtacInferCnvInput  7.004  0.203   7.248
* 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/atacInferCnv.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘atacInferCnv’ ...
** this is package ‘atacInferCnv’ version ‘1.0.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c aggregate_bins.cpp -o aggregate_bins.o
In file included from aggregate_bins.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from aggregate_bins.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from aggregate_bins.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from aggregate_bins.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o atacInferCnv.so RcppExports.o aggregate_bins.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-atacInferCnv/00new/atacInferCnv/libs
** R
** 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
** 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 (atacInferCnv)

R version 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(atacInferCnv)
> 
> test_check("atacInferCnv")
Loading input...
Loading input...
Loading input...
Input is a file, assuming peaks matrix...
Loading input...
Input is a file, assuming peaks matrix...
Loading input...
Input is a file, assuming peaks matrix...
Using target annotation column: cnvBlock
    C1     C2 Normal    167    116     17 
Loading input...
Using existing input object
Loading input...
Input is a file, assuming peaks matrix...
Using target annotation column: cnvBlock
Using external control (assigned as ExtControl)
Loading input...
Input is a file, assuming peaks matrix...
Using target annotation column: cnvBlock
    C1     C2 Normal     16     10      4 
Creating result directory: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKf4v16/file15c66189cd02a
Prepare input data...
Adjust for custom annotation
Save signal...
Write configuration...
Loading input...
    C1     C2 Normal     16     10      4 
Creating result directory: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKf4v16/file15c667fd84fa3
Save signal...
Write configuration...
Prepared input.
Loading InferCNV configuration from: infercnv_config.yml
Processing sample_infercnv
Input: sample_raw_counts.txt.gz
Annotation: sample_cnv_ann.txt
Normal clusters: Normal
Cut off: 0.1
Num tumor clusters: 1
Assign custom reference: sample_cnv_ref.txt
INFO [2026-04-28 20:08:16] Parsing matrix: sample_raw_counts.txt.gz
INFO [2026-04-28 20:08:16] Parsing gene order file: sample_cnv_ref.txt
INFO [2026-04-28 20:08:16] Parsing cell annotations file: sample_cnv_ann.txt
INFO [2026-04-28 20:08:16] ::order_reduce:Start.
INFO [2026-04-28 20:08:16] .order_reduce(): expr and order match.
INFO [2026-04-28 20:08:16] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 80677,30 Total=241851 Min=0 Max=90.
INFO [2026-04-28 20:08:16] num genes removed taking into account provided gene ordering list: 41 = 0.050819936289153% removed.
INFO [2026-04-28 20:08:16] -filtering out cells < 100 or > Inf, removing 0 % of cells
WARN [2026-04-28 20:08:16] Please use "options(scipen = 100)" before running infercnv if you are using the analysis_mode="subclusters" option or you may encounter an error while the hclust is being generated.
INFO [2026-04-28 20:08:16] validating infercnv_obj
INFO [2026-04-28 20:08:16] ::process_data:Start
INFO [2026-04-28 20:08:16] Creating output path sample_infercnv
INFO [2026-04-28 20:08:16] Checking for saved results.
INFO [2026-04-28 20:08:16] 

	STEP 1: incoming data

INFO [2026-04-28 20:08:17] 

	STEP 02: Removing lowly expressed genes

INFO [2026-04-28 20:08:17] ::above_min_mean_expr_cutoff:Start
INFO [2026-04-28 20:08:17] Removing 58582 genes from matrix as below mean expr threshold: 0.1
INFO [2026-04-28 20:08:17] validating infercnv_obj
INFO [2026-04-28 20:08:17] There are 22054 genes and 30 cells remaining in the expr matrix.
INFO [2026-04-28 20:08:17] Removed 9102 genes having fewer than 3 min cells per gene = 41.2714 % genes removed here
INFO [2026-04-28 20:08:17] validating infercnv_obj
INFO [2026-04-28 20:08:17] 

	STEP 03: normalization by sequencing depth

INFO [2026-04-28 20:08:17] normalizing counts matrix by depth
INFO [2026-04-28 20:08:17] Computed total sum normalization factor as median libsize: 3623.500000
INFO [2026-04-28 20:08:17] 

	STEP 04: log transformation of data

INFO [2026-04-28 20:08:17] transforming log2xplus1()
INFO [2026-04-28 20:08:17] 

	STEP 08: removing average of reference data (before smoothing)

INFO [2026-04-28 20:08:17] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2026-04-28 20:08:17] subtracting mean(normal) per gene per cell across all data
INFO [2026-04-28 20:08:19] -subtracting expr per gene, use_bounds=TRUE
INFO [2026-04-28 20:08:19] 

	STEP 09: apply max centered expression threshold: 3

INFO [2026-04-28 20:08:19] ::process_data:setting max centered expr, threshold set to: +/-:  3
INFO [2026-04-28 20:08:20] 

	STEP 10: Smoothing data per cell by chromosome

INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 1
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 2
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 3
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 4
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 5
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 6
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 7
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 8
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 9
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 10
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 11
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 12
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 13
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 14
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 15
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 16
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 17
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 18
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 19
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 20
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 21
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: 22
INFO [2026-04-28 20:08:20] smooth_by_chromosome: chr: X
INFO [2026-04-28 20:08:21] 

	STEP 11: re-centering data across chromosome after smoothing

INFO [2026-04-28 20:08:21] ::center_smooth across chromosomes per cell
INFO [2026-04-28 20:08:21] 

	STEP 12: removing average of reference data (after smoothing)

INFO [2026-04-28 20:08:21] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2026-04-28 20:08:21] subtracting mean(normal) per gene per cell across all data
INFO [2026-04-28 20:08:23] -subtracting expr per gene, use_bounds=TRUE
INFO [2026-04-28 20:08:23] 

	STEP 14: invert log2(FC) to FC

INFO [2026-04-28 20:08:23] invert_log2(), computing 2^x
INFO [2026-04-28 20:08:24] 

	STEP 15: computing tumor subclusters via leiden

INFO [2026-04-28 20:08:24] define_signif_tumor_subclusters(p_val=0.1
INFO [2026-04-28 20:08:24] define_signif_tumor_subclusters(), tumor: C1
INFO [2026-04-28 20:08:24] Less cells in group C1 than k_nn setting. Keeping as a single subcluster.
INFO [2026-04-28 20:08:24] define_signif_tumor_subclusters(), tumor: C2
INFO [2026-04-28 20:08:24] Less cells in group C2 than k_nn setting. Keeping as a single subcluster.
INFO [2026-04-28 20:08:24] define_signif_tumor_subclusters(), tumor: Normal
INFO [2026-04-28 20:08:24] Less cells in group Normal than k_nn setting. Keeping as a single subcluster.
INFO [2026-04-28 20:08:25] ::plot_cnv:Start
INFO [2026-04-28 20:08:25] ::plot_cnv:Current data dimensions (r,c)=12952,30 Total=389496.51366287 Min=0.790258757829601 Max=1.61478114475046.
INFO [2026-04-28 20:08:25] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2026-04-28 20:08:25] plot_cnv(): auto thresholding at: (0.861114 , 1.143707)
INFO [2026-04-28 20:08:25] plot_cnv_observation:Start
INFO [2026-04-28 20:08:25] Observation data size: Cells= 26 Genes= 12952
INFO [2026-04-28 20:08:25] clustering observations via method: ward.D
INFO [2026-04-28 20:08:25] Number of cells in group(1) is 16
INFO [2026-04-28 20:08:25] group size being clustered:  16,12952
INFO [2026-04-28 20:08:25] Number of cells in group(2) is 10
INFO [2026-04-28 20:08:25] group size being clustered:  10,12952
INFO [2026-04-28 20:08:25] plot_cnv_observation:Writing observation groupings/color.
INFO [2026-04-28 20:08:25] plot_cnv_observation:Done writing observation groupings/color.
INFO [2026-04-28 20:08:25] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2026-04-28 20:08:25] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2026-04-28 20:08:25] Colors for breaks:  #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2026-04-28 20:08:25] Quantiles of plotted data range: 0.86111376099084,0.96527385916358,0.998865481750607,1.03584507397658,1.14370667169843
INFO [2026-04-28 20:08:25] plot_cnv_references:Start
INFO [2026-04-28 20:08:25] Reference data size: Cells= 4 Genes= 12952
INFO [2026-04-28 20:08:25] plot_cnv_references:Number reference groups= 1
INFO [2026-04-28 20:08:25] plot_cnv_references:Plotting heatmap.
INFO [2026-04-28 20:08:25] Colors for breaks:  #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2026-04-28 20:08:25] Quantiles of plotted data range: 0.872622511719713,0.978122386705928,0.998865481750801,1.02033117977316,1.14370667169843
INFO [2026-04-28 20:08:26] ::plot_cnv:Start
INFO [2026-04-28 20:08:26] ::plot_cnv:Current data dimensions (r,c)=12952,30 Total=389496.51366287 Min=0.790258757829601 Max=1.61478114475046.
INFO [2026-04-28 20:08:26] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2026-04-28 20:08:26] plot_cnv(): auto thresholding at: (0.861114 , 1.143707)
INFO [2026-04-28 20:08:26] plot_cnv_observation:Start
INFO [2026-04-28 20:08:26] Observation data size: Cells= 26 Genes= 12952
INFO [2026-04-28 20:08:26] plot_cnv_observation:Writing observation groupings/color.
INFO [2026-04-28 20:08:26] plot_cnv_observation:Done writing observation groupings/color.
INFO [2026-04-28 20:08:26] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2026-04-28 20:08:26] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2026-04-28 20:08:26] Colors for breaks:  #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2026-04-28 20:08:26] Quantiles of plotted data range: 0.86111376099084,0.96527385916358,0.998865481750607,1.03584507397658,1.14370667169843
INFO [2026-04-28 20:08:26] plot_cnv_references:Start
INFO [2026-04-28 20:08:26] Reference data size: Cells= 4 Genes= 12952
INFO [2026-04-28 20:08:26] plot_cnv_references:Number reference groups= 1
INFO [2026-04-28 20:08:26] plot_cnv_references:Plotting heatmap.
INFO [2026-04-28 20:08:26] Colors for breaks:  #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2026-04-28 20:08:26] Quantiles of plotted data range: 0.872622511719713,0.978122386705928,0.998865481750801,1.02033117977316,1.14370667169843
INFO [2026-04-28 20:08:26] 

	STEP 22: Denoising

INFO [2026-04-28 20:08:26] ::process_data:Remove noise, noise threshold defined via ref mean sd_amplifier:  1.5
INFO [2026-04-28 20:08:26] denoising using mean(normal) +- sd_amplifier * sd(normal) per gene per cell across all data
INFO [2026-04-28 20:08:26] :: **** clear_noise_via_ref_quantiles **** : removing noise between bounds:  0.949958858030604 - 1.05119143943608
INFO [2026-04-28 20:08:27] ::plot_cnv:Start
INFO [2026-04-28 20:08:27] ::plot_cnv:Current data dimensions (r,c)=12952,30 Total=390011.121721246 Min=0.790258757829601 Max=1.61478114475046.
INFO [2026-04-28 20:08:27] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2026-04-28 20:08:27] plot_cnv(): auto thresholding at: (0.856293 , 1.143707)
INFO [2026-04-28 20:08:27] plot_cnv_observation:Start
INFO [2026-04-28 20:08:27] Observation data size: Cells= 26 Genes= 12952
INFO [2026-04-28 20:08:27] plot_cnv_observation:Writing observation groupings/color.
INFO [2026-04-28 20:08:27] plot_cnv_observation:Done writing observation groupings/color.
INFO [2026-04-28 20:08:27] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2026-04-28 20:08:27] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2026-04-28 20:08:27] Colors for breaks:  #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2026-04-28 20:08:27] Quantiles of plotted data range: 0.856293328301567,1.00057514873334,1.00057514873334,1.00057514873334,1.14370667169843
INFO [2026-04-28 20:08:27] plot_cnv_references:Start
INFO [2026-04-28 20:08:27] Reference data size: Cells= 4 Genes= 12952
INFO [2026-04-28 20:08:27] plot_cnv_references:Number reference groups= 1
INFO [2026-04-28 20:08:27] plot_cnv_references:Plotting heatmap.
INFO [2026-04-28 20:08:27] Colors for breaks:  #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2026-04-28 20:08:27] Quantiles of plotted data range: 0.872622511719713,1.00057514873334,1.00057514873334,1.00057514873334,1.14370667169843
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
 46.278   1.157  47.869