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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NanoMethViz_3.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/NanoMethViz.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* 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: 2026-05-22 00:47:39 UTC
* using option ‘--no-vignettes’
* checking for file ‘NanoMethViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NanoMethViz’ version ‘3.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 31 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 ‘NanoMethViz’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking C++ specification ... INFO
  specified C++20
* checking installed package size ... INFO
  installed size is 13.5Mb
* 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 ... NOTE
reformat_modkit: no visible binding for global variable ‘ref_position’
Undefined global functions or variables:
  ref_position
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'assert_valid_genomic_coords.Rd':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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
get_exons              27.031  0.890  28.042
get_exons_homo_sapiens 11.989  0.152  12.184
filter_methy            7.816  0.516   8.335
get_exons_mus_musculus  5.208  0.060   5.278
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.24-bioc/meat/NanoMethViz.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NanoMethViz
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘NanoMethViz’ ...
** this is package ‘NanoMethViz’ version ‘3.9.0’
** using staged installation
** libs
specified C++20
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++20
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/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
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/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o
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/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c count_cg.cpp -o count_cg.o
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/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c genome.cpp -o genome.o
genome.cpp:43:21: warning: unused variable 'chrom_view' [-Wunused-variable]
   43 |         string_view chrom_view = this->bases_at(chrom, motif_start, motif_end);
      |                     ^~~~~~~~~~
1 warning 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/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c modbam.cpp -o modbam.o
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/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c utils.cpp -o utils.o
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 NanoMethViz.so RcppExports.o convert_methy_to_dss.o count_cg.o genome.o modbam.o utils.o -lz -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-NanoMethViz/00new/NanoMethViz/libs
** 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
** 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 (NanoMethViz)

R version 4.6.0 Patched (2026-05-01 r89994) -- "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.

> library(testthat)
> library(NanoMethViz)
Loading required package: ggplot2
> 
> test_check("NanoMethViz")
Starting 2 test processes.
> test-ModBamResults.R: Successfully created ModBamResult with 1 matched samples.
> test-ModBamResults.R: Successfully created ModBamResult with 1 matched samples.
> test-NanoMethResults.R: Successfully matched 6 samples between data and annotation.
> test-bsseq_to_edger.R: Successfully matched 6 samples between data and annotation.
> test-bsseq_to_edger.R: [2026-05-21 20:51:09] creating intermediate files...
> test-bsseq_to_edger.R: [2026-05-21 20:51:09] parsing chr11...
> test-NanoMethResults.R: Successfully matched 6 samples between data and annotation.
> test-bsseq_to_edger.R: [2026-05-21 20:51:09] parsing chr12...
> test-bsseq_to_edger.R: [2026-05-21 20:51:09] parsing chr18...
> test-bsseq_to_edger.R: [2026-05-21 20:51:09] parsing chr5...
> test-bsseq_to_edger.R: [2026-05-21 20:51:09] parsing chr7...
> test-bsseq_to_edger.R: [2026-05-21 20:51:09] parsing chrX...
> test-cluster_reads.R: Successfully created ModBamResult with 1 matched samples.
> test-bsseq_to_edger.R: [2026-05-21 20:51:09] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 
> test-bsseq_to_edger.R: [2026-05-21 20:51:09] creating bsseq object...
> test-bsseq_to_edger.R: [2026-05-21 20:51:09] reading in parsed data...
> test-bsseq_to_edger.R: [2026-05-21 20:51:09] constructing matrices...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] done
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] creating intermediate files...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] parsing chr11...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] parsing chr12...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] parsing chr18...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] parsing chr5...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] parsing chr7...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] parsing chrX...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] creating bsseq object...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] reading in parsed data...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] constructing matrices...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] done
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] creating intermediate files...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] parsing chr11...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] parsing chr12...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] parsing chr18...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] parsing chr5...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] parsing chr7...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] parsing chrX...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] creating bsseq object...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] reading in parsed data...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] constructing matrices...
> test-bsseq_to_edger.R: [2026-05-21 20:51:10] done
> test-cluster_regions.R: Successfully matched 6 samples between data and annotation.
> test-filter_methy.R: Successfully matched 6 samples between data and annotation.
> test-methy_to_bsseq.R: Successfully matched 6 samples between data and annotation.
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] creating intermediate files...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chr11...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chr12...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chr18...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chr5...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chr7...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chrX...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] creating bsseq object...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] reading in parsed data...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] constructing matrices...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] done
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] creating intermediate files...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chr11...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chr12...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chr18...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chr5...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chr7...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chrX...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] creating bsseq object...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] reading in parsed data...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] constructing matrices...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] done
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] creating intermediate files...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chr11...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chr12...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chr18...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chr5...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chr7...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] parsing chrX...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] creating bsseq object...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] reading in parsed data...
> test-methy_to_bsseq.R: [2026-05-21 20:51:13] constructing matrices...
> test-methy_to_bsseq.R: [2026-05-21 20:51:14] done
> test-methy_to_bsseq.R: Successfully matched 6 samples between data and annotation.
> test-methy_to_bsseq.R: [2026-05-21 20:51:14] creating intermediate files...
> test-methy_to_bsseq.R: [2026-05-21 20:51:14] parsing chr11...
> test-methy_to_bsseq.R: [2026-05-21 20:51:14] parsing chr12...
> test-methy_to_bsseq.R: [2026-05-21 20:51:14] parsing chr18...
> test-methy_to_bsseq.R: [2026-05-21 20:51:14] parsing chr5...
> test-methy_to_bsseq.R: [2026-05-21 20:51:14] parsing chr7...
> test-methy_to_bsseq.R: [2026-05-21 20:51:14] parsing chrX...
> test-methy_to_bsseq.R: [2026-05-21 20:51:14] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 
> test-methy_to_bsseq.R: [2026-05-21 20:51:14] creating bsseq object...
> test-methy_to_bsseq.R: [2026-05-21 20:51:14] reading in parsed data...
> test-methy_to_bsseq.R: [2026-05-21 20:51:14] constructing matrices...
> test-methy_to_bsseq.R: [2026-05-21 20:51:14] done
> test-modbam_to_tabix.R: Successfully created ModBamResult with 1 matched samples.
> test-modbam_to_tabix.R: i Writing data to temporary file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl4000...
> test-modbam_to_tabix.R: v Writing data to temporary file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl4000...
> test-modbam_to_tabix.R: 
> test-modbam_to_tabix.R: i Converting data to TSV
> test-modbam_to_tabix.R: v Converting data to TSV [191ms]
> test-modbam_to_tabix.R: 
> test-modbam_to_tabix.R: i Sorting data
> test-modbam_to_tabix.R: v Sorting data [44ms]
> test-modbam_to_tabix.R: 
> test-modbam_to_tabix.R: i Compressing data
> test-modbam_to_tabix.R: i Moving data to final location: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9b4fD2/file726555978a36.tsv.bgz
> test-modbam_to_tabix.R: i Compressing data
> test-modbam_to_tabix.R: v Compressing data [18ms]
> test-modbam_to_tabix.R: 
> test-modbam_to_tabix.R: i Tabix file created: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9...
> test-modbam_to_tabix.R: v Tabix file created: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9...
> test-modbam_to_tabix.R: 
> test-modbam_to_tabix.R: Rows: 10371 Columns: 6
> test-modbam_to_tabix.R: -- Column specification --------------------------------------------------------
> test-modbam_to_tabix.R: Delimiter: "\t"
> test-modbam_to_tabix.R: chr (4): sample, chr, strand, read_name
> test-modbam_to_tabix.R: dbl (2): pos, statistic
> test-modbam_to_tabix.R: 
> test-modbam_to_tabix.R: i Use `spec()` to retrieve the full column specification for this data.
> test-modbam_to_tabix.R: i Specify the column types or set `show_col_types = FALSE` to quiet this message.
> test-modbam_to_tabix.R: Successfully created ModBamResult with 1 matched samples.
> test-plot_agg_genes.R: Successfully matched 6 samples between data and annotation.
> test-filter_methy.R: 21,798 of 224,267 (9.72%) entries kept after filtering
> test-filter_methy.R: results written to '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpYJgWh5/file726478202acf.tsv.bgz' along with index file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpYJgWh5/file726478202acf.tsv.bgz.tbi'
> test-plot_agg_regions.R: Successfully matched 6 samples between data and annotation.
> test-plot_agg_regions.R: Successfully created ModBamResult with 1 matched samples.
> test-filter_methy.R: 21,798 of 224,267 (9.72%) entries kept after filtering
> test-filter_methy.R: results written to '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpYJgWh5/file726478202acf.tsv.bgz' along with index file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpYJgWh5/file726478202acf.tsv.bgz.tbi'
> test-plot_agg_regions.R: Successfully matched 6 samples between data and annotation.
> test-plot_basic.R: Successfully matched 6 samples between data and annotation.
> test-plot_basic.R: Successfully created ModBamResult with 1 matched samples.
> test-plot_basic.R: Successfully created ModBamResult with 1 matched samples.
> test-filter_methy.R: 21,798 of 224,267 (9.72%) entries kept after filtering
> test-filter_methy.R: results written to '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpYJgWh5/file726478202acf.tsv.bgz' along with index file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpYJgWh5/file726478202acf.tsv.bgz.tbi'
> test-plot_gene_heatmap.R: Successfully matched 6 samples between data and annotation.
> test-plot_gene_heatmap.R: Successfully matched 6 samples between data and annotation.
> test-plot_gene_heatmap.R: Successfully matched 6 samples between data and annotation.
> test-plot_gene_heatmap.R: Successfully matched 6 samples between data and annotation.
> test-plot_mds.R: Successfully matched 6 samples between data and annotation.
> test-plot_mds.R: [2026-05-21 20:51:25] creating intermediate files...
> test-plot_mds.R: [2026-05-21 20:51:25] parsing chr11...
> test-plot_mds.R: [2026-05-21 20:51:25] parsing chr12...
> test-plot_mds.R: [2026-05-21 20:51:25] parsing chr18...
> test-plot_mds.R: [2026-05-21 20:51:25] parsing chr5...
> test-plot_mds.R: [2026-05-21 20:51:25] parsing chr7...
> test-plot_mds.R: [2026-05-21 20:51:25] parsing chrX...
> test-plot_mds.R: [2026-05-21 20:51:25] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 
> test-plot_mds.R: [2026-05-21 20:51:25] creating bsseq object...
> test-plot_mds.R: [2026-05-21 20:51:25] reading in parsed data...
> test-plot_mds.R: [2026-05-21 20:51:25] constructing matrices...
> test-plot_mds.R: [2026-05-21 20:51:25] done
> test-plot_methylation.R: Successfully matched 6 samples between data and annotation.
> test-plot_pca.R: Successfully matched 6 samples between data and annotation.
> test-plot_pca.R: [2026-05-21 20:51:26] creating intermediate files...
> test-plot_pca.R: [2026-05-21 20:51:26] parsing chr11...
> test-plot_pca.R: [2026-05-21 20:51:26] parsing chr12...
> test-plot_pca.R: [2026-05-21 20:51:26] parsing chr18...
> test-plot_pca.R: [2026-05-21 20:51:26] parsing chr5...
> test-plot_pca.R: [2026-05-21 20:51:26] parsing chr7...
> test-plot_pca.R: [2026-05-21 20:51:26] parsing chrX...
> test-plot_pca.R: [2026-05-21 20:51:26] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 
> test-plot_pca.R: [2026-05-21 20:51:26] creating bsseq object...
> test-plot_pca.R: [2026-05-21 20:51:26] reading in parsed data...
> test-plot_pca.R: [2026-05-21 20:51:26] constructing matrices...
> test-plot_pca.R: [2026-05-21 20:51:26] done
> test-plot_region_heatmap.R: Successfully matched 6 samples between data and annotation.
> test-plot_region_heatmap.R: Successfully matched 6 samples between data and annotation.
> test-plot_region_heatmap.R: Successfully matched 6 samples between data and annotation.
> test-plot_region_heatmap.R: Successfully matched 6 samples between data and annotation.
> test-plot_region_heatmap.R: Successfully matched 6 samples between data and annotation.
> test-query_exons.R: Successfully matched 6 samples between data and annotation.
> test-query_exons.R: Successfully matched 6 samples between data and annotation.
> test-query_exons.R: Successfully matched 6 samples between data and annotation.
> test-query_exons.R: Successfully matched 6 samples between data and annotation.
> test-query_exons.R: Successfully matched 6 samples between data and annotation.
> test-query_exons.R: Successfully matched 6 samples between data and annotation.
> test-query_exons.R: Successfully matched 6 samples between data and annotation.
> test-query_exons.R: Successfully matched 6 samples between data and annotation.
> test-query_methy.R: Successfully matched 6 samples between data and annotation.
> test-query_methy.R: Successfully created ModBamResult with 1 matched samples.
> test-region_methy_stats.R: Successfully matched 6 samples between data and annotation.
> test-stack_interval.R: Successfully matched 6 samples between data and annotation.
> test-tabix_utils.R: processing /Library/Frameworks/R.framework/Versions/4.6/Resources/library/NanoMethViz/sample1_nanopolish.tsv.gz...
> test-tabix_utils.R: guessing file is produced by nanopolish...
> test-tabix_utils.R: processing /Library/Frameworks/R.framework/Versions/4.6/Resources/library/NanoMethViz/sample2_nanopolish.tsv.gz...
> test-tabix_utils.R: guessing file is produced by nanopolish...
> test-tabix_utils.R: [2026-05-21 20:51:32] sorting methylation table
> test-tabix_utils.R: [2026-05-21 20:51:32] compressing methylation table to tabix with index
> test-tabix_utils.R: [2026-05-21 20:51:32] creating intermediate files...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr1...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr2...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr3...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr4...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr5...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr6...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr7...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr8...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr9...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr10...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr11...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr12...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr13...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr14...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr15...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr16...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr17...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr18...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chr19...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chrM...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chrX...
> test-tabix_utils.R: [2026-05-21 20:51:32] parsing chrY...
> test-tabix_utils.R: [2026-05-21 20:51:32] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 sample1_nanopolish.tsv sample2_nanopolish.tsv 
> test-tabix_utils.R: [2026-05-21 20:51:32] creating bsseq object...
> test-tabix_utils.R: [2026-05-21 20:51:32] reading in parsed data...
> test-tabix_utils.R: [2026-05-21 20:51:32] constructing matrices...
> test-tabix_utils.R: [2026-05-21 20:51:32] done
> test-tabix_utils.R: processing /Library/Frameworks/R.framework/Versions/4.6/Resources/library/NanoMethViz/megalodon_calls.txt.gz...
> test-tabix_utils.R: guessing file is produced by megalodon...
> test-tabix_utils.R: [2026-05-21 20:51:32] sorting methylation table
> test-tabix_utils.R: [2026-05-21 20:51:32] compressing methylation table to tabix with index
[ FAIL 0 | WARN 83 | SKIP 0 | PASS 719 ]

[ FAIL 0 | WARN 83 | SKIP 0 | PASS 719 ]
> 
> proc.time()
   user  system elapsed 
 80.996   3.838  52.973