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This page was generated on 2026-05-07 11:36 -0400 (Thu, 07 May 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4990
kjohnson3macOS 13.7.7 Venturaarm644.6.0 Patched (2026-04-24 r89963) -- "Because it was There" 4723
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1474/2418HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoMethViz 3.8.0  (landing page)
Shian Su
Snapshot Date: 2026-05-06 13:40 -0400 (Wed, 06 May 2026)
git_url: https://git.bioconductor.org/packages/NanoMethViz
git_branch: RELEASE_3_23
git_last_commit: 4193d2c
git_last_commit_date: 2026-04-28 08:54:18 -0400 (Tue, 28 Apr 2026)
nebbiolo1Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
See other builds for NanoMethViz in R Universe.

CHECK results for NanoMethViz on kjohnson3

To the developers/maintainers of the NanoMethViz package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NanoMethViz.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: NanoMethViz
Version: 3.8.0
Command: /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_3.8.0.tar.gz
StartedAt: 2026-05-06 21:31:38 -0400 (Wed, 06 May 2026)
EndedAt: 2026-05-06 21:35:55 -0400 (Wed, 06 May 2026)
EllapsedTime: 256.4 seconds
RetCode: 0
Status:   OK  
CheckDir: NanoMethViz.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /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_3.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/NanoMethViz.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: 2026-05-07 01:31:38 UTC
* using option ‘--no-vignettes’
* checking for file ‘NanoMethViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NanoMethViz’ version ‘3.8.0’
* 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              27.369  1.181  28.703
get_exons_homo_sapiens 12.587  0.201  12.808
filter_methy            7.925  0.528   8.461
* 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-3.23-bioc/meat/NanoMethViz.Rcheck/00check.log’
for details.

Installation output

NanoMethViz.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘NanoMethViz’ ...
** this is package ‘NanoMethViz’ version ‘3.8.0’
** 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)

Tests output

NanoMethViz.Rcheck/tests/testthat.Rout


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.

> library(testthat)
> library(NanoMethViz)
Loading required package: ggplot2
> 
> test_check("NanoMethViz")
Starting 2 test processes.
> test-NanoMethResults.R: Successfully matched 6 samples between data and annotation.
> 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: [2026-05-06 21:35:12] creating intermediate files...
> test-bsseq_to_edger.R: [2026-05-06 21:35:12] parsing chr11...
> test-bsseq_to_edger.R: [2026-05-06 21:35:12] parsing chr12...
> test-cluster_reads.R: Successfully created ModBamResult with 1 matched samples.
> test-bsseq_to_edger.R: [2026-05-06 21:35:12] parsing chr18...
> test-bsseq_to_edger.R: [2026-05-06 21:35:12] parsing chr5...
> test-bsseq_to_edger.R: [2026-05-06 21:35:12] parsing chr7...
> test-bsseq_to_edger.R: [2026-05-06 21:35:12] parsing chrX...
> test-bsseq_to_edger.R: [2026-05-06 21:35:12] 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: [2026-05-06 21:35:12] creating bsseq object...
> test-bsseq_to_edger.R: [2026-05-06 21:35:12] reading in parsed data...
> test-bsseq_to_edger.R: [2026-05-06 21:35:12] constructing matrices...
> test-bsseq_to_edger.R: [2026-05-06 21:35:12] done
> test-bsseq_to_edger.R: [2026-05-06 21:35:12] creating intermediate files...
> test-bsseq_to_edger.R: [2026-05-06 21:35:12] parsing chr11...
> test-bsseq_to_edger.R: [2026-05-06 21:35:12] parsing chr12...
> test-bsseq_to_edger.R: [2026-05-06 21:35:12] parsing chr18...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] parsing chr5...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] parsing chr7...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] parsing chrX...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] 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-bsseq_to_edger.R: [2026-05-06 21:35:13] creating bsseq object...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] reading in parsed data...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] constructing matrices...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] done
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] creating intermediate files...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] parsing chr11...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] parsing chr12...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] parsing chr18...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] parsing chr5...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] parsing chr7...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] parsing chrX...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] 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-bsseq_to_edger.R: [2026-05-06 21:35:13] creating bsseq object...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] reading in parsed data...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] constructing matrices...
> test-bsseq_to_edger.R: [2026-05-06 21:35:13] 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: [2026-05-06 21:35:15] creating intermediate files...
> test-methy_to_bsseq.R: [2026-05-06 21:35:15] parsing chr11...
> test-methy_to_bsseq.R: [2026-05-06 21:35:15] parsing chr12...
> test-methy_to_bsseq.R: [2026-05-06 21:35:15] parsing chr18...
> test-methy_to_bsseq.R: [2026-05-06 21:35:15] parsing chr5...
> test-methy_to_bsseq.R: [2026-05-06 21:35:15] parsing chr7...
> test-methy_to_bsseq.R: [2026-05-06 21:35:15] parsing chrX...
> test-methy_to_bsseq.R: [2026-05-06 21:35:15] 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: [2026-05-06 21:35:15] creating bsseq object...
> test-methy_to_bsseq.R: [2026-05-06 21:35:15] reading in parsed data...
> test-methy_to_bsseq.R: [2026-05-06 21:35:15] constructing matrices...
> test-methy_to_bsseq.R: [2026-05-06 21:35:15] done
> test-methy_to_bsseq.R: [2026-05-06 21:35:15] creating intermediate files...
> test-methy_to_bsseq.R: [2026-05-06 21:35:15] parsing chr11...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] parsing chr12...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] parsing chr18...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] parsing chr5...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] parsing chr7...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] parsing chrX...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] 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: [2026-05-06 21:35:16] creating bsseq object...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] reading in parsed data...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] constructing matrices...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] done
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] creating intermediate files...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] parsing chr11...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] parsing chr12...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] parsing chr18...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] parsing chr5...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] parsing chr7...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] parsing chrX...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] 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: [2026-05-06 21:35:16] creating bsseq object...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] reading in parsed data...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] constructing matrices...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] done
> test-methy_to_bsseq.R: Successfully matched 6 samples between data and annotation.
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] creating intermediate files...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] parsing chr11...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] parsing chr12...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] parsing chr18...
> test-methy_to_bsseq.R: [2026-05-06 21:35:16] parsing chr5...
> test-methy_to_bsseq.R: [2026-05-06 21:35:17] parsing chr7...
> test-methy_to_bsseq.R: [2026-05-06 21:35:17] parsing chrX...
> test-methy_to_bsseq.R: [2026-05-06 21:35:17] 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: [2026-05-06 21:35:17] creating bsseq object...
> test-methy_to_bsseq.R: [2026-05-06 21:35:17] reading in parsed data...
> test-methy_to_bsseq.R: [2026-05-06 21:35:17] constructing matrices...
> test-methy_to_bsseq.R: [2026-05-06 21:35:17] 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 [235ms]
> test-modbam_to_tabix.R: 
> test-modbam_to_tabix.R: i Sorting data
> test-modbam_to_tabix.R: v Sorting data [55ms]
> 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//RtmpOqowDM/file10b55eccae02.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//RtmpO...
> test-modbam_to_tabix.R: v Tabix file created: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpO...
> 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-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//Rtmpurc4z4/file10b5952a3c6dd.tsv.bgz' along with index file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpurc4z4/file10b5952a3c6dd.tsv.bgz.tbi'
> test-plot_agg_genes.R: Successfully matched 6 samples between data and annotation.
> 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//Rtmpurc4z4/file10b5952a3c6dd.tsv.bgz' along with index file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpurc4z4/file10b5952a3c6dd.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//Rtmpurc4z4/file10b5952a3c6dd.tsv.bgz' along with index file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpurc4z4/file10b5952a3c6dd.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: [2026-05-06 21:35:27] creating intermediate files...
> test-plot_mds.R: [2026-05-06 21:35:27] parsing chr11...
> test-plot_mds.R: [2026-05-06 21:35:27] parsing chr12...
> test-plot_mds.R: [2026-05-06 21:35:27] parsing chr18...
> test-plot_mds.R: [2026-05-06 21:35:27] parsing chr5...
> test-plot_mds.R: [2026-05-06 21:35:27] parsing chr7...
> test-plot_mds.R: [2026-05-06 21:35:28] parsing chrX...
> test-plot_mds.R: [2026-05-06 21:35:28] 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: [2026-05-06 21:35:28] creating bsseq object...
> test-plot_mds.R: [2026-05-06 21:35:28] reading in parsed data...
> test-plot_mds.R: [2026-05-06 21:35:28] constructing matrices...
> test-plot_mds.R: [2026-05-06 21:35:28] 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: [2026-05-06 21:35:29] creating intermediate files...
> test-plot_pca.R: [2026-05-06 21:35:29] parsing chr11...
> test-plot_pca.R: [2026-05-06 21:35:29] parsing chr12...
> test-plot_pca.R: [2026-05-06 21:35:29] parsing chr18...
> test-plot_pca.R: [2026-05-06 21:35:29] parsing chr5...
> test-plot_pca.R: [2026-05-06 21:35:29] parsing chr7...
> test-plot_pca.R: [2026-05-06 21:35:29] parsing chrX...
> test-plot_pca.R: [2026-05-06 21:35:29] 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: [2026-05-06 21:35:29] creating bsseq object...
> test-plot_pca.R: [2026-05-06 21:35:29] reading in parsed data...
> test-plot_pca.R: [2026-05-06 21:35:29] constructing matrices...
> test-plot_pca.R: [2026-05-06 21:35:29] 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: [2026-05-06 21:35:35] sorting methylation table
> test-tabix_utils.R: [2026-05-06 21:35:35] compressing methylation table to tabix with index
> test-tabix_utils.R: [2026-05-06 21:35:35] creating intermediate files...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr1...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr2...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr3...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr4...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr5...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr6...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr7...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr8...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr9...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr10...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr11...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr12...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr13...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr14...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr15...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr16...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr17...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr18...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chr19...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chrM...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chrX...
> test-tabix_utils.R: [2026-05-06 21:35:35] parsing chrY...
> test-tabix_utils.R: [2026-05-06 21:35:35] 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: [2026-05-06 21:35:35] creating bsseq object...
> test-tabix_utils.R: [2026-05-06 21:35:35] reading in parsed data...
> test-tabix_utils.R: [2026-05-06 21:35:35] constructing matrices...
> test-tabix_utils.R: [2026-05-06 21:35:35] 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: [2026-05-06 21:35:35] sorting methylation table
> test-tabix_utils.R: [2026-05-06 21:35:35] 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 
 81.680   4.130  53.217

Example timings

NanoMethViz.Rcheck/NanoMethViz-Ex.timings

nameusersystemelapsed
NanoMethResult-class1.6100.4102.047
bsseq_to_edger0.3440.0120.360
bsseq_to_log_methy_ratio0.8230.0140.839
cluster_regions1.2190.0271.247
create_tabix_file0.4770.0580.537
exons_to_genes0.1150.0030.119
filter_methy7.9250.5288.461
get_example_exons_mus_musculus0.0880.0020.090
get_exons27.369 1.18128.703
get_exons_homo_sapiens12.587 0.20112.808
get_exons_mus_musculus4.4310.0844.525
load_example_modbamresult0.0890.0020.091
load_example_nanomethresult0.0880.0020.089
methy0.0010.0000.001
methy_col_names000
methy_to_bsseq0.3740.0080.382
methy_to_edger0.4590.0100.469
modbam_to_tabix0.1920.1080.216
plot_agg_genes1.6600.0191.692
plot_agg_regions1.9260.0201.952
plot_gene2.7370.0312.775
plot_gene_heatmap2.3520.0142.367
plot_grange2.0930.0122.110
plot_grange_heatmap1.5460.0101.559
plot_mds0.5970.0100.607
plot_pca0.5400.0080.549
plot_region1.9580.0131.987
plot_region_heatmap1.5870.0261.612
plot_violin0.9510.0120.967
query_methy0.1310.0020.133
region_methy_stats0.3650.0040.368