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This page was generated on 2025-11-18 11:40 -0500 (Tue, 18 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4826
lconwaymacOS 12.7.6 Montereyx86_64R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" 4561
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4562
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Package 1420/2325HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoMethViz 3.7.0  (landing page)
Shian Su
Snapshot Date: 2025-11-17 13:40 -0500 (Mon, 17 Nov 2025)
git_url: https://git.bioconductor.org/packages/NanoMethViz
git_branch: devel
git_last_commit: 4349b36
git_last_commit_date: 2025-10-29 11:04:08 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'BiocSingular' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'BiocSingular' which is only available as a source package that needs compilation

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: 3.7.0
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_3.7.0.tar.gz
StartedAt: 2025-11-17 22:18:27 -0500 (Mon, 17 Nov 2025)
EndedAt: 2025-11-17 22:23:27 -0500 (Mon, 17 Nov 2025)
EllapsedTime: 299.2 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_3.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/NanoMethViz.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NanoMethViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NanoMethViz’ version ‘3.7.0’
* 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 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking C++ specification ... OK
  Not all R platforms support 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 ... OK
* 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              31.536  1.713  34.349
get_exons_homo_sapiens 14.772  0.851  16.123
filter_methy            9.521  0.684  10.361
get_exons_mus_musculus  5.116  0.359   5.583
* 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/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-arm64/Resources/library’
* installing *source* package ‘NanoMethViz’ ...
** this is package ‘NanoMethViz’ version ‘3.7.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++20
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/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-arm64/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-arm64/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]
        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-arm64/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-arm64/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-arm64/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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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: [2025-11-17 22:22:36] creating intermediate files...
> test-bsseq_to_edger.R: [2025-11-17 22:22:36] parsing chr11...
> test-NanoMethResults.R: Successfully matched 6 samples between data and annotation.
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chr12...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chr18...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chr5...
> test-cluster_reads.R: Successfully created ModBamResult with 1 matched samples.
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chr7...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chrX...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] 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: [2025-11-17 22:22:37] creating bsseq object...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] reading in parsed data...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] constructing matrices...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] done
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] creating intermediate files...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chr11...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chr12...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chr18...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chr5...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chr7...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chrX...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] 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: [2025-11-17 22:22:37] creating bsseq object...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] reading in parsed data...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] constructing matrices...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] done
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] creating intermediate files...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chr11...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chr12...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chr18...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chr5...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chr7...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] parsing chrX...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] 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: [2025-11-17 22:22:37] creating bsseq object...
> test-bsseq_to_edger.R: [2025-11-17 22:22:37] reading in parsed data...
> test-bsseq_to_edger.R: [2025-11-17 22:22:38] constructing matrices...
> test-bsseq_to_edger.R: [2025-11-17 22:22:38] 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: [2025-11-17 22:22:40] creating intermediate files...
> test-methy_to_bsseq.R: [2025-11-17 22:22:40] parsing chr11...
> test-methy_to_bsseq.R: [2025-11-17 22:22:40] parsing chr12...
> test-methy_to_bsseq.R: [2025-11-17 22:22:40] parsing chr18...
> test-methy_to_bsseq.R: [2025-11-17 22:22:40] parsing chr5...
> test-methy_to_bsseq.R: [2025-11-17 22:22:40] parsing chr7...
> test-methy_to_bsseq.R: [2025-11-17 22:22:40] parsing chrX...
> test-methy_to_bsseq.R: [2025-11-17 22:22:40] 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: [2025-11-17 22:22:40] creating bsseq object...
> test-methy_to_bsseq.R: [2025-11-17 22:22:40] reading in parsed data...
> test-methy_to_bsseq.R: [2025-11-17 22:22:40] constructing matrices...
> test-methy_to_bsseq.R: [2025-11-17 22:22:40] done
> test-methy_to_bsseq.R: [2025-11-17 22:22:40] creating intermediate files...
> test-methy_to_bsseq.R: [2025-11-17 22:22:40] parsing chr11...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] parsing chr12...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] parsing chr18...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] parsing chr5...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] parsing chr7...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] parsing chrX...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] 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: [2025-11-17 22:22:41] creating bsseq object...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] reading in parsed data...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] constructing matrices...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] done
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] creating intermediate files...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] parsing chr11...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] parsing chr12...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] parsing chr18...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] parsing chr5...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] parsing chr7...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] parsing chrX...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] 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: [2025-11-17 22:22:41] creating bsseq object...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] reading in parsed data...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] constructing matrices...
> test-methy_to_bsseq.R: [2025-11-17 22:22:41] done
> test-methy_to_bsseq.R: Successfully matched 6 samples between data and annotation.
> test-methy_to_bsseq.R: [2025-11-17 22:22:42] creating intermediate files...
> test-methy_to_bsseq.R: [2025-11-17 22:22:42] parsing chr11...
> test-methy_to_bsseq.R: [2025-11-17 22:22:42] parsing chr12...
> test-methy_to_bsseq.R: [2025-11-17 22:22:42] parsing chr18...
> test-methy_to_bsseq.R: [2025-11-17 22:22:42] parsing chr5...
> test-methy_to_bsseq.R: [2025-11-17 22:22:42] parsing chr7...
> test-methy_to_bsseq.R: [2025-11-17 22:22:42] parsing chrX...
> test-methy_to_bsseq.R: [2025-11-17 22:22:42] 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: [2025-11-17 22:22:42] creating bsseq object...
> test-methy_to_bsseq.R: [2025-11-17 22:22:42] reading in parsed data...
> test-methy_to_bsseq.R: [2025-11-17 22:22:42] constructing matrices...
> test-methy_to_bsseq.R: [2025-11-17 22:22:42] 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 [852ms]
> test-modbam_to_tabix.R: 
> test-modbam_to_tabix.R: i Sorting data
> test-modbam_to_tabix.R: v Sorting data [54ms]
> 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//RtmpMcvSLH/file8a427c6f531d.tsv.bgz
> test-modbam_to_tabix.R: i Compressing data
> test-modbam_to_tabix.R: v Compressing data [25ms]
> test-modbam_to_tabix.R: 
> test-modbam_to_tabix.R: i Tabix file created: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpM...
> test-modbam_to_tabix.R: v Tabix file created: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpM...
> 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//RtmpMmSNbG/file8a493bdde030.tsv.bgz' along with index file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMmSNbG/file8a493bdde030.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-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-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//RtmpMmSNbG/file8a493bdde030.tsv.bgz' along with index file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMmSNbG/file8a493bdde030.tsv.bgz.tbi'
> 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//RtmpMmSNbG/file8a493bdde030.tsv.bgz' along with index file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMmSNbG/file8a493bdde030.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: [2025-11-17 22:22:55] creating intermediate files...
> test-plot_mds.R: [2025-11-17 22:22:55] parsing chr11...
> test-plot_mds.R: [2025-11-17 22:22:55] parsing chr12...
> test-plot_mds.R: [2025-11-17 22:22:55] parsing chr18...
> test-plot_mds.R: [2025-11-17 22:22:55] parsing chr5...
> test-plot_mds.R: [2025-11-17 22:22:55] parsing chr7...
> test-plot_mds.R: [2025-11-17 22:22:56] parsing chrX...
> test-plot_mds.R: [2025-11-17 22:22:56] 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: [2025-11-17 22:22:56] creating bsseq object...
> test-plot_mds.R: [2025-11-17 22:22:56] reading in parsed data...
> test-plot_mds.R: [2025-11-17 22:22:56] constructing matrices...
> test-plot_mds.R: [2025-11-17 22:22:56] 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: [2025-11-17 22:22:57] creating intermediate files...
> test-plot_pca.R: [2025-11-17 22:22:57] parsing chr11...
> test-plot_pca.R: [2025-11-17 22:22:57] parsing chr12...
> test-plot_pca.R: [2025-11-17 22:22:57] parsing chr18...
> test-plot_pca.R: [2025-11-17 22:22:57] parsing chr5...
> test-plot_pca.R: [2025-11-17 22:22:57] parsing chr7...
> test-plot_pca.R: [2025-11-17 22:22:57] parsing chrX...
> test-plot_pca.R: [2025-11-17 22:22:57] 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: [2025-11-17 22:22:57] creating bsseq object...
> test-plot_pca.R: [2025-11-17 22:22:57] reading in parsed data...
> test-plot_pca.R: [2025-11-17 22:22:57] constructing matrices...
> test-plot_pca.R: [2025-11-17 22:22:57] 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-arm64/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-arm64/Resources/library/NanoMethViz/sample2_nanopolish.tsv.gz...
> test-tabix_utils.R: guessing file is produced by nanopolish...
> test-tabix_utils.R: [2025-11-17 22:23:04] sorting methylation table
> test-tabix_utils.R: [2025-11-17 22:23:04] compressing methylation table to tabix with index
> test-tabix_utils.R: [2025-11-17 22:23:04] creating intermediate files...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr1...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr2...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr3...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr4...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr5...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr6...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr7...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr8...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr9...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr10...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr11...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr12...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr13...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr14...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr15...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr16...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr17...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr18...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chr19...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chrM...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chrX...
> test-tabix_utils.R: [2025-11-17 22:23:04] parsing chrY...
> test-tabix_utils.R: [2025-11-17 22:23:04] 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: [2025-11-17 22:23:04] creating bsseq object...
> test-tabix_utils.R: [2025-11-17 22:23:04] reading in parsed data...
> test-tabix_utils.R: [2025-11-17 22:23:04] constructing matrices...
> test-tabix_utils.R: [2025-11-17 22:23:04] done
> test-tabix_utils.R: processing /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/NanoMethViz/megalodon_calls.txt.gz...
> test-tabix_utils.R: guessing file is produced by megalodon...
> test-tabix_utils.R: [2025-11-17 22:23:04] sorting methylation table
> test-tabix_utils.R: [2025-11-17 22:23:04] 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 
 88.615   4.747  61.003

Example timings

NanoMethViz.Rcheck/NanoMethViz-Ex.timings

nameusersystemelapsed
NanoMethResult-class1.7260.3042.104
bsseq_to_edger0.4240.0130.441
bsseq_to_log_methy_ratio0.4650.0130.481
cluster_regions1.7770.0341.863
create_tabix_file0.5150.0620.610
exons_to_genes0.1030.0030.112
filter_methy 9.521 0.68410.361
get_example_exons_mus_musculus0.0870.0020.102
get_exons31.536 1.71334.349
get_exons_homo_sapiens14.772 0.85116.123
get_exons_mus_musculus5.1160.3595.583
load_example_modbamresult0.0990.0050.110
load_example_nanomethresult0.0870.0050.093
methy0.0010.0000.001
methy_col_names000
methy_to_bsseq0.4450.0170.463
methy_to_edger0.5810.0300.638
modbam_to_tabix0.2320.1540.282
plot_agg_genes1.7560.0491.869
plot_agg_regions2.0210.0552.145
plot_gene3.0880.0773.313
plot_gene_heatmap2.7240.1193.044
plot_grange2.5700.3783.070
plot_grange_heatmap1.7450.0421.875
plot_mds0.6860.0160.717
plot_pca0.6610.0200.692
plot_region2.2550.0432.389
plot_region_heatmap1.7470.0381.834
plot_violin1.0150.0251.072
query_methy0.1420.0030.154
region_methy_stats0.3960.0080.412