Shian Su
| Snapshot Date: 2025-12-11 13:45 -0500 (Thu, 11 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/NanoMethViz |
| git_branch: RELEASE_3_22 |
| git_last_commit: 836d7c6 |
| git_last_commit_date: 2025-10-29 11:04:08 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-15 12:08 -0500 (Mon, 15 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 1439/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NanoMethViz 3.6.0 (landing page) Shian Su
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: NanoMethViz |
| Version: 3.6.0 |
| 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_3.6.0.tar.gz |
| StartedAt: 2025-12-13 15:24:57 -0500 (Sat, 13 Dec 2025) |
| EndedAt: 2025-12-13 15:44:31 -0500 (Sat, 13 Dec 2025) |
| EllapsedTime: 1174.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NanoMethViz.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_3.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/NanoMethViz.Rcheck’
* using R version 4.5.2 Patched (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 ‘3.6.0’
* 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-1500.0.40.1)’
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_exons 90.655 4.155 131.213
get_exons_homo_sapiens 39.248 2.255 54.387
filter_methy 23.439 2.217 35.379
get_exons_mus_musculus 14.044 0.547 20.747
plot_gene 9.562 0.253 13.208
plot_region_heatmap 8.099 0.678 12.237
plot_agg_genes 8.115 0.215 11.901
plot_gene_heatmap 7.604 0.139 10.186
plot_grange 7.318 0.117 9.913
plot_agg_regions 6.486 0.309 9.177
plot_region 6.619 0.093 9.413
NanoMethResult-class 5.548 0.935 9.063
plot_grange_heatmap 5.480 0.084 7.527
cluster_regions 4.023 0.100 5.719
* 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-3.22-bioc/meat/NanoMethViz.Rcheck/00check.log’
for details.
NanoMethViz.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NanoMethViz
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘NanoMethViz’ ...
** this is package ‘NanoMethViz’ version ‘3.6.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
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/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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)
NanoMethViz.Rcheck/tests/testthat.Rout
R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
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-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: [2025-12-13 15:40:52] creating intermediate files...
> test-bsseq_to_edger.R: [2025-12-13 15:40:52] parsing chr11...
> test-bsseq_to_edger.R: [2025-12-13 15:40:52] parsing chr12...
> test-bsseq_to_edger.R: [2025-12-13 15:40:52] parsing chr18...
> test-bsseq_to_edger.R: [2025-12-13 15:40:52] parsing chr5...
> test-cluster_reads.R: Successfully created ModBamResult with 1 matched samples.
> test-bsseq_to_edger.R: [2025-12-13 15:40:52] parsing chr7...
> test-bsseq_to_edger.R: [2025-12-13 15:40:53] parsing chrX...
> test-bsseq_to_edger.R: [2025-12-13 15:40:53] 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: [2025-12-13 15:40:53] creating bsseq object...
> test-bsseq_to_edger.R: [2025-12-13 15:40:53] reading in parsed data...
> test-bsseq_to_edger.R: [2025-12-13 15:40:53] constructing matrices...
> test-bsseq_to_edger.R: [2025-12-13 15:40:54] done
> test-bsseq_to_edger.R: [2025-12-13 15:40:54] creating intermediate files...
> test-bsseq_to_edger.R: [2025-12-13 15:40:54] parsing chr11...
> test-bsseq_to_edger.R: [2025-12-13 15:40:54] parsing chr12...
> test-bsseq_to_edger.R: [2025-12-13 15:40:54] parsing chr18...
> test-bsseq_to_edger.R: [2025-12-13 15:40:54] parsing chr5...
> test-bsseq_to_edger.R: [2025-12-13 15:40:54] parsing chr7...
> test-bsseq_to_edger.R: [2025-12-13 15:40:54] parsing chrX...
> test-bsseq_to_edger.R: [2025-12-13 15:40:55] 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: [2025-12-13 15:40:55] creating bsseq object...
> test-bsseq_to_edger.R: [2025-12-13 15:40:55] reading in parsed data...
> test-bsseq_to_edger.R: [2025-12-13 15:40:55] constructing matrices...
> test-bsseq_to_edger.R: [2025-12-13 15:40:55] done
> test-bsseq_to_edger.R: [2025-12-13 15:40:58] creating intermediate files...
> test-bsseq_to_edger.R: [2025-12-13 15:40:58] parsing chr11...
> test-bsseq_to_edger.R: [2025-12-13 15:40:58] parsing chr12...
> test-bsseq_to_edger.R: [2025-12-13 15:40:58] parsing chr18...
> test-bsseq_to_edger.R: [2025-12-13 15:40:58] parsing chr5...
> test-bsseq_to_edger.R: [2025-12-13 15:40:58] parsing chr7...
> test-bsseq_to_edger.R: [2025-12-13 15:40:59] parsing chrX...
> test-bsseq_to_edger.R: [2025-12-13 15:40:59] 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: [2025-12-13 15:40:59] creating bsseq object...
> test-bsseq_to_edger.R: [2025-12-13 15:40:59] reading in parsed data...
> test-bsseq_to_edger.R: [2025-12-13 15:40:59] constructing matrices...
> test-bsseq_to_edger.R: [2025-12-13 15:40:59] 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: [2025-12-13 15:41:11] creating intermediate files...
> test-methy_to_bsseq.R: [2025-12-13 15:41:11] parsing chr11...
> test-methy_to_bsseq.R: [2025-12-13 15:41:11] parsing chr12...
> test-methy_to_bsseq.R: [2025-12-13 15:41:11] parsing chr18...
> test-methy_to_bsseq.R: [2025-12-13 15:41:11] parsing chr5...
> test-methy_to_bsseq.R: [2025-12-13 15:41:11] parsing chr7...
> test-methy_to_bsseq.R: [2025-12-13 15:41:12] parsing chrX...
> test-methy_to_bsseq.R: [2025-12-13 15:41:12] 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-methy_to_bsseq.R: [2025-12-13 15:41:12] creating bsseq object...
> test-methy_to_bsseq.R: [2025-12-13 15:41:12] reading in parsed data...
> test-methy_to_bsseq.R: [2025-12-13 15:41:12] constructing matrices...
> test-methy_to_bsseq.R: [2025-12-13 15:41:13] done
> test-methy_to_bsseq.R: [2025-12-13 15:41:13] creating intermediate files...
> test-methy_to_bsseq.R: [2025-12-13 15:41:13] parsing chr11...
> test-methy_to_bsseq.R: [2025-12-13 15:41:13] parsing chr12...
> test-methy_to_bsseq.R: [2025-12-13 15:41:13] parsing chr18...
> test-methy_to_bsseq.R: [2025-12-13 15:41:13] parsing chr5...
> test-methy_to_bsseq.R: [2025-12-13 15:41:13] parsing chr7...
> test-methy_to_bsseq.R: [2025-12-13 15:41:14] parsing chrX...
> test-methy_to_bsseq.R: [2025-12-13 15:41:14] 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: [2025-12-13 15:41:14] creating bsseq object...
> test-methy_to_bsseq.R: [2025-12-13 15:41:14] reading in parsed data...
> test-methy_to_bsseq.R: [2025-12-13 15:41:14] constructing matrices...
> test-methy_to_bsseq.R: [2025-12-13 15:41:15] done
> test-methy_to_bsseq.R: [2025-12-13 15:41:15] creating intermediate files...
> test-methy_to_bsseq.R: [2025-12-13 15:41:15] parsing chr11...
> test-methy_to_bsseq.R: [2025-12-13 15:41:15] parsing chr12...
> test-methy_to_bsseq.R: [2025-12-13 15:41:15] parsing chr18...
> test-methy_to_bsseq.R: [2025-12-13 15:41:15] parsing chr5...
> test-methy_to_bsseq.R: [2025-12-13 15:41:15] parsing chr7...
> test-methy_to_bsseq.R: [2025-12-13 15:41:16] parsing chrX...
> test-methy_to_bsseq.R: [2025-12-13 15:41:16] 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: [2025-12-13 15:41:16] creating bsseq object...
> test-methy_to_bsseq.R: [2025-12-13 15:41:16] reading in parsed data...
> test-methy_to_bsseq.R: [2025-12-13 15:41:16] constructing matrices...
> test-methy_to_bsseq.R: [2025-12-13 15:41:17] done
> test-methy_to_bsseq.R: Successfully matched 6 samples between data and annotation.
> test-methy_to_bsseq.R: [2025-12-13 15:41:17] creating intermediate files...
> test-methy_to_bsseq.R: [2025-12-13 15:41:17] parsing chr11...
> test-methy_to_bsseq.R: [2025-12-13 15:41:18] parsing chr12...
> test-methy_to_bsseq.R: [2025-12-13 15:41:18] parsing chr18...
> test-methy_to_bsseq.R: [2025-12-13 15:41:18] parsing chr5...
> test-methy_to_bsseq.R: [2025-12-13 15:41:18] parsing chr7...
> test-methy_to_bsseq.R: [2025-12-13 15:41:18] parsing chrX...
> test-methy_to_bsseq.R: [2025-12-13 15:41:18] 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: [2025-12-13 15:41:18] creating bsseq object...
> test-methy_to_bsseq.R: [2025-12-13 15:41:18] reading in parsed data...
> test-methy_to_bsseq.R: [2025-12-13 15:41:19] constructing matrices...
> test-methy_to_bsseq.R: [2025-12-13 15:41:20] done
> test-modbam_to_tabix.R: Successfully created ModBamResult with 1 matched samples.
> test-modbam_to_tabix.R: i Writing data to temporary file: /tmp/RtmpLC69he/file11e536fdf3ef0.tsv
> test-modbam_to_tabix.R: v Writing data to temporary file: /tmp/RtmpLC69he/file11e536fdf3ef0.tsv [31ms]
> 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 [848ms]
> test-modbam_to_tabix.R:
> test-modbam_to_tabix.R: i Sorting data
> test-modbam_to_tabix.R: v Sorting data [184ms]
> test-modbam_to_tabix.R:
> test-modbam_to_tabix.R: i Compressing data
> test-modbam_to_tabix.R: i Moving data to final location: /tmp/RtmpLC69he/file11e5344b59f15.tsv.bgz
> test-modbam_to_tabix.R: i Compressing data
> test-modbam_to_tabix.R: v Compressing data [71ms]
> test-modbam_to_tabix.R:
> test-modbam_to_tabix.R: i Tabix file created: /tmp/RtmpLC69he/file11e5344b59f15.tsv.bgz
> test-modbam_to_tabix.R: v Tabix file created: /tmp/RtmpLC69he/file11e5344b59f15.tsv.bgz [28ms]
> 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 '/tmp/RtmpZ2tISD/file11e56454c7ec5.tsv.bgz' along with index file '/tmp/RtmpZ2tISD/file11e56454c7ec5.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-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 '/tmp/RtmpZ2tISD/file11e56454c7ec5.tsv.bgz' along with index file '/tmp/RtmpZ2tISD/file11e56454c7ec5.tsv.bgz.tbi'
> test-filter_methy.R: 21,798 of 224,267 (9.72%) entries kept after filtering
> test-filter_methy.R: results written to '/tmp/RtmpZ2tISD/file11e56454c7ec5.tsv.bgz' along with index file '/tmp/RtmpZ2tISD/file11e56454c7ec5.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: [2025-12-13 15:42:22] creating intermediate files...
> test-plot_mds.R: [2025-12-13 15:42:22] parsing chr11...
> test-plot_mds.R: [2025-12-13 15:42:23] parsing chr12...
> test-plot_mds.R: [2025-12-13 15:42:23] parsing chr18...
> test-plot_mds.R: [2025-12-13 15:42:23] parsing chr5...
> test-plot_mds.R: [2025-12-13 15:42:23] parsing chr7...
> test-plot_mds.R: [2025-12-13 15:42:23] parsing chrX...
> test-plot_mds.R: [2025-12-13 15:42:23] 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: [2025-12-13 15:42:23] creating bsseq object...
> test-plot_mds.R: [2025-12-13 15:42:23] reading in parsed data...
> test-plot_mds.R: [2025-12-13 15:42:23] constructing matrices...
> test-plot_mds.R: [2025-12-13 15:42:24] 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: [2025-12-13 15:42:30] creating intermediate files...
> test-plot_pca.R: [2025-12-13 15:42:30] parsing chr11...
> test-plot_pca.R: [2025-12-13 15:42:30] parsing chr12...
> test-plot_pca.R: [2025-12-13 15:42:30] parsing chr18...
> test-plot_pca.R: [2025-12-13 15:42:30] parsing chr5...
> test-plot_pca.R: [2025-12-13 15:42:30] parsing chr7...
> test-plot_pca.R: [2025-12-13 15:42:31] parsing chrX...
> test-plot_pca.R: [2025-12-13 15:42:31] 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: [2025-12-13 15:42:31] creating bsseq object...
> test-plot_pca.R: [2025-12-13 15:42:31] reading in parsed data...
> test-plot_pca.R: [2025-12-13 15:42:31] constructing matrices...
> test-plot_pca.R: [2025-12-13 15:42:31] 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/4.5-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/4.5-arm64/Resources/library/NanoMethViz/sample2_nanopolish.tsv.gz...
> test-tabix_utils.R: guessing file is produced by nanopolish...
> test-tabix_utils.R: [2025-12-13 15:43:02] sorting methylation table
> test-tabix_utils.R: [2025-12-13 15:43:02] compressing methylation table to tabix with index
> test-tabix_utils.R: [2025-12-13 15:43:02] creating intermediate files...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr1...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr2...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr3...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr4...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr5...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr6...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr7...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr8...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr9...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr10...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr11...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr12...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr13...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr14...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr15...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr16...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr17...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr18...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chr19...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chrM...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chrX...
> test-tabix_utils.R: [2025-12-13 15:43:02] parsing chrY...
> test-tabix_utils.R: [2025-12-13 15:43:02] 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: [2025-12-13 15:43:02] creating bsseq object...
> test-tabix_utils.R: [2025-12-13 15:43:02] reading in parsed data...
> test-tabix_utils.R: [2025-12-13 15:43:02] constructing matrices...
> test-tabix_utils.R: [2025-12-13 15:43:03] done
> test-tabix_utils.R: processing /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/NanoMethViz/megalodon_calls.txt.gz...
> test-tabix_utils.R: guessing file is produced by megalodon...
> test-tabix_utils.R: [2025-12-13 15:43:04] sorting methylation table
> test-tabix_utils.R: [2025-12-13 15:43:04] 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
279.934 14.327 268.766
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
| name | user | system | elapsed | |
| NanoMethResult-class | 5.548 | 0.935 | 9.063 | |
| bsseq_to_edger | 1.263 | 0.041 | 1.788 | |
| bsseq_to_log_methy_ratio | 3.003 | 0.051 | 4.419 | |
| cluster_regions | 4.023 | 0.100 | 5.719 | |
| create_tabix_file | 3.276 | 0.240 | 4.905 | |
| exons_to_genes | 0.322 | 0.008 | 0.463 | |
| filter_methy | 23.439 | 2.217 | 35.379 | |
| get_example_exons_mus_musculus | 0.315 | 0.010 | 0.427 | |
| get_exons | 90.655 | 4.155 | 131.213 | |
| get_exons_homo_sapiens | 39.248 | 2.255 | 54.387 | |
| get_exons_mus_musculus | 14.044 | 0.547 | 20.747 | |
| load_example_modbamresult | 0.318 | 0.011 | 0.498 | |
| load_example_nanomethresult | 0.305 | 0.009 | 0.492 | |
| methy | 0.002 | 0.000 | 0.003 | |
| methy_col_names | 0.001 | 0.000 | 0.000 | |
| methy_to_bsseq | 1.381 | 0.036 | 2.039 | |
| methy_to_edger | 2.022 | 0.066 | 3.060 | |
| modbam_to_tabix | 0.600 | 0.146 | 0.843 | |
| plot_agg_genes | 8.115 | 0.215 | 11.901 | |
| plot_agg_regions | 6.486 | 0.309 | 9.177 | |
| plot_gene | 9.562 | 0.253 | 13.208 | |
| plot_gene_heatmap | 7.604 | 0.139 | 10.186 | |
| plot_grange | 7.318 | 0.117 | 9.913 | |
| plot_grange_heatmap | 5.480 | 0.084 | 7.527 | |
| plot_mds | 1.991 | 0.043 | 2.864 | |
| plot_pca | 2.143 | 0.041 | 2.697 | |
| plot_region | 6.619 | 0.093 | 9.413 | |
| plot_region_heatmap | 8.099 | 0.678 | 12.237 | |
| plot_violin | 3.203 | 0.149 | 4.841 | |
| query_methy | 0.475 | 0.036 | 0.734 | |
| region_methy_stats | 1.251 | 0.058 | 1.871 | |