Shian Su
| Snapshot Date: 2025-11-24 13:45 -0500 (Mon, 24 Nov 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 2025-11-27 12:04 -0500 (Thu, 27 Nov 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" | 4876 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4656 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4602 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 | NA | |||||||||
| 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: 2025-11-26 17:05:19 -0500 (Wed, 26 Nov 2025) |
| EndedAt: 2025-11-26 17:26:46 -0500 (Wed, 26 Nov 2025) |
| EllapsedTime: 1287.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NanoMethViz.Rcheck |
| Warnings: 0 |
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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_3.6.0.tar.gz
###
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* 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 94.704 4.588 141.449
get_exons_homo_sapiens 39.503 1.675 63.572
filter_methy 22.840 2.162 38.121
get_exons_mus_musculus 16.623 1.046 26.723
plot_gene 9.846 0.246 15.290
plot_region 8.111 0.369 12.897
plot_gene_heatmap 7.934 0.129 12.179
plot_grange 7.463 0.119 11.629
plot_agg_regions 6.631 0.188 10.351
NanoMethResult-class 5.609 0.940 10.178
plot_region_heatmap 5.821 0.222 9.505
plot_grange_heatmap 5.850 0.085 9.127
plot_agg_genes 5.506 0.156 8.052
cluster_regions 4.159 0.103 6.617
* 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
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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/4.5-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: [2025-11-26 17:22:45] creating intermediate files...
> test-bsseq_to_edger.R: [2025-11-26 17:22:45] parsing chr11...
> test-bsseq_to_edger.R: [2025-11-26 17:22:46] parsing chr12...
> test-cluster_reads.R: Successfully created ModBamResult with 1 matched samples.
> test-bsseq_to_edger.R: [2025-11-26 17:22:46] parsing chr18...
> test-bsseq_to_edger.R: [2025-11-26 17:22:46] parsing chr5...
> test-bsseq_to_edger.R: [2025-11-26 17:22:46] parsing chr7...
> test-bsseq_to_edger.R: [2025-11-26 17:22:46] parsing chrX...
> test-bsseq_to_edger.R: [2025-11-26 17:22:46] 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: [2025-11-26 17:22:46] creating bsseq object...
> test-bsseq_to_edger.R: [2025-11-26 17:22:46] reading in parsed data...
> test-bsseq_to_edger.R: [2025-11-26 17:22:47] constructing matrices...
> test-bsseq_to_edger.R: [2025-11-26 17:22:47] done
> test-bsseq_to_edger.R: [2025-11-26 17:22:47] creating intermediate files...
> test-bsseq_to_edger.R: [2025-11-26 17:22:47] parsing chr11...
> test-bsseq_to_edger.R: [2025-11-26 17:22:47] parsing chr12...
> test-bsseq_to_edger.R: [2025-11-26 17:22:48] parsing chr18...
> test-bsseq_to_edger.R: [2025-11-26 17:22:48] parsing chr5...
> test-bsseq_to_edger.R: [2025-11-26 17:22:48] parsing chr7...
> test-bsseq_to_edger.R: [2025-11-26 17:22:48] parsing chrX...
> test-bsseq_to_edger.R: [2025-11-26 17:22:48] 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: [2025-11-26 17:22:48] creating bsseq object...
> test-bsseq_to_edger.R: [2025-11-26 17:22:48] reading in parsed data...
> test-bsseq_to_edger.R: [2025-11-26 17:22:48] constructing matrices...
> test-bsseq_to_edger.R: [2025-11-26 17:22:49] done
> test-bsseq_to_edger.R: [2025-11-26 17:22:49] creating intermediate files...
> test-bsseq_to_edger.R: [2025-11-26 17:22:49] parsing chr11...
> test-bsseq_to_edger.R: [2025-11-26 17:22:49] parsing chr12...
> test-bsseq_to_edger.R: [2025-11-26 17:22:49] parsing chr18...
> test-bsseq_to_edger.R: [2025-11-26 17:22:50] parsing chr5...
> test-bsseq_to_edger.R: [2025-11-26 17:22:50] parsing chr7...
> test-bsseq_to_edger.R: [2025-11-26 17:22:50] parsing chrX...
> test-bsseq_to_edger.R: [2025-11-26 17:22:50] 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: [2025-11-26 17:22:50] creating bsseq object...
> test-bsseq_to_edger.R: [2025-11-26 17:22:50] reading in parsed data...
> test-bsseq_to_edger.R: [2025-11-26 17:22:50] constructing matrices...
> test-bsseq_to_edger.R: [2025-11-26 17:22:51] 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: [2025-11-26 17:23:06] creating intermediate files...
> test-methy_to_bsseq.R: [2025-11-26 17:23:06] parsing chr11...
> test-methy_to_bsseq.R: [2025-11-26 17:23:06] parsing chr12...
> test-methy_to_bsseq.R: [2025-11-26 17:23:06] parsing chr18...
> test-methy_to_bsseq.R: [2025-11-26 17:23:06] parsing chr5...
> test-methy_to_bsseq.R: [2025-11-26 17:23:06] parsing chr7...
> test-methy_to_bsseq.R: [2025-11-26 17:23:07] parsing chrX...
> test-methy_to_bsseq.R: [2025-11-26 17:23:07] 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: [2025-11-26 17:23:07] creating bsseq object...
> test-methy_to_bsseq.R: [2025-11-26 17:23:07] reading in parsed data...
> test-methy_to_bsseq.R: [2025-11-26 17:23:07] constructing matrices...
> test-methy_to_bsseq.R: [2025-11-26 17:23:08] done
> test-methy_to_bsseq.R: [2025-11-26 17:23:08] creating intermediate files...
> test-methy_to_bsseq.R: [2025-11-26 17:23:08] parsing chr11...
> test-methy_to_bsseq.R: [2025-11-26 17:23:08] parsing chr12...
> test-methy_to_bsseq.R: [2025-11-26 17:23:08] parsing chr18...
> test-methy_to_bsseq.R: [2025-11-26 17:23:08] parsing chr5...
> test-methy_to_bsseq.R: [2025-11-26 17:23:09] parsing chr7...
> test-methy_to_bsseq.R: [2025-11-26 17:23:09] parsing chrX...
> test-methy_to_bsseq.R: [2025-11-26 17:23:09] 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-methy_to_bsseq.R: [2025-11-26 17:23:09] creating bsseq object...
> test-methy_to_bsseq.R: [2025-11-26 17:23:09] reading in parsed data...
> test-methy_to_bsseq.R: [2025-11-26 17:23:09] constructing matrices...
> test-methy_to_bsseq.R: [2025-11-26 17:23:10] done
> test-methy_to_bsseq.R: [2025-11-26 17:23:10] creating intermediate files...
> test-methy_to_bsseq.R: [2025-11-26 17:23:10] parsing chr11...
> test-methy_to_bsseq.R: [2025-11-26 17:23:10] parsing chr12...
> test-methy_to_bsseq.R: [2025-11-26 17:23:10] parsing chr18...
> test-methy_to_bsseq.R: [2025-11-26 17:23:11] parsing chr5...
> test-methy_to_bsseq.R: [2025-11-26 17:23:11] parsing chr7...
> test-methy_to_bsseq.R: [2025-11-26 17:23:11] parsing chrX...
> test-methy_to_bsseq.R: [2025-11-26 17:23:11] 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: [2025-11-26 17:23:11] creating bsseq object...
> test-methy_to_bsseq.R: [2025-11-26 17:23:11] reading in parsed data...
> test-methy_to_bsseq.R: [2025-11-26 17:23:11] constructing matrices...
> test-methy_to_bsseq.R: [2025-11-26 17:23:12] done
> test-methy_to_bsseq.R: Successfully matched 6 samples between data and annotation.
> test-methy_to_bsseq.R: [2025-11-26 17:23:13] creating intermediate files...
> test-methy_to_bsseq.R: [2025-11-26 17:23:13] parsing chr11...
> test-methy_to_bsseq.R: [2025-11-26 17:23:13] parsing chr12...
> test-methy_to_bsseq.R: [2025-11-26 17:23:14] parsing chr18...
> test-methy_to_bsseq.R: [2025-11-26 17:23:14] parsing chr5...
> test-methy_to_bsseq.R: [2025-11-26 17:23:14] parsing chr7...
> test-methy_to_bsseq.R: [2025-11-26 17:23:14] parsing chrX...
> test-methy_to_bsseq.R: [2025-11-26 17:23:14] 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: [2025-11-26 17:23:14] creating bsseq object...
> test-methy_to_bsseq.R: [2025-11-26 17:23:14] reading in parsed data...
> test-methy_to_bsseq.R: [2025-11-26 17:23:14] constructing matrices...
> test-methy_to_bsseq.R: [2025-11-26 17:23:16] 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/RtmpqzKeUE/filef2574d9f0f55.tsv
> test-modbam_to_tabix.R: v Writing data to temporary file: /tmp/RtmpqzKeUE/filef2574d9f0f55.tsv [40ms]
> 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 [1s]
> test-modbam_to_tabix.R:
> test-modbam_to_tabix.R: i Sorting data
> test-modbam_to_tabix.R: v Sorting data [248ms]
> 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/RtmpqzKeUE/filef2574124a834.tsv.bgz
> test-modbam_to_tabix.R: i Compressing data
> test-modbam_to_tabix.R: v Compressing data [74ms]
> test-modbam_to_tabix.R:
> test-modbam_to_tabix.R: i Tabix file created: /tmp/RtmpqzKeUE/filef2574124a834.tsv.bgz
> test-modbam_to_tabix.R: v Tabix file created: /tmp/RtmpqzKeUE/filef2574124a834.tsv.bgz [28ms]
> test-modbam_to_tabix.R:
> test-filter_methy.R: 21,798 of 224,267 (9.72%) entries kept after filtering
> test-filter_methy.R: results written to '/tmp/RtmpLw5o31/filef256377710fe.tsv.bgz' along with index file '/tmp/RtmpLw5o31/filef256377710fe.tsv.bgz.tbi'
> 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-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 '/tmp/RtmpLw5o31/filef256377710fe.tsv.bgz' along with index file '/tmp/RtmpLw5o31/filef256377710fe.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 '/tmp/RtmpLw5o31/filef256377710fe.tsv.bgz' along with index file '/tmp/RtmpLw5o31/filef256377710fe.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: [2025-11-26 17:24:11] creating intermediate files...
> test-plot_mds.R: [2025-11-26 17:24:11] parsing chr11...
> test-plot_mds.R: [2025-11-26 17:24:11] parsing chr12...
> test-plot_mds.R: [2025-11-26 17:24:11] parsing chr18...
> test-plot_mds.R: [2025-11-26 17:24:11] parsing chr5...
> test-plot_mds.R: [2025-11-26 17:24:11] parsing chr7...
> test-plot_mds.R: [2025-11-26 17:24:12] parsing chrX...
> test-plot_mds.R: [2025-11-26 17:24:12] 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-plot_mds.R: [2025-11-26 17:24:12] creating bsseq object...
> test-plot_mds.R: [2025-11-26 17:24:12] reading in parsed data...
> test-plot_mds.R: [2025-11-26 17:24:12] constructing matrices...
> test-plot_mds.R: [2025-11-26 17:24:12] 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: [2025-11-26 17:24:19] creating intermediate files...
> test-plot_pca.R: [2025-11-26 17:24:19] parsing chr11...
> test-plot_pca.R: [2025-11-26 17:24:19] parsing chr12...
> test-plot_pca.R: [2025-11-26 17:24:19] parsing chr18...
> test-plot_pca.R: [2025-11-26 17:24:19] parsing chr5...
> test-plot_pca.R: [2025-11-26 17:24:20] parsing chr7...
> test-plot_pca.R: [2025-11-26 17:24:20] parsing chrX...
> test-plot_pca.R: [2025-11-26 17:24:20] 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: [2025-11-26 17:24:20] creating bsseq object...
> test-plot_pca.R: [2025-11-26 17:24:20] reading in parsed data...
> test-plot_pca.R: [2025-11-26 17:24:20] constructing matrices...
> test-plot_pca.R: [2025-11-26 17:24:20] 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: [2025-11-26 17:24:53] sorting methylation table
> test-tabix_utils.R: [2025-11-26 17:24:53] compressing methylation table to tabix with index
> test-tabix_utils.R: [2025-11-26 17:24:53] creating intermediate files...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr1...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr2...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr3...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr4...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr5...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr6...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr7...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr8...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr9...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr10...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr11...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr12...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr13...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr14...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr15...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr16...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr17...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr18...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chr19...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chrM...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chrX...
> test-tabix_utils.R: [2025-11-26 17:24:53] parsing chrY...
> test-tabix_utils.R: [2025-11-26 17:24:53] 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 sample1_nanopolish.tsv sample2_nanopolish.tsv
> test-tabix_utils.R: [2025-11-26 17:24:53] creating bsseq object...
> test-tabix_utils.R: [2025-11-26 17:24:53] reading in parsed data...
> test-tabix_utils.R: [2025-11-26 17:24:53] constructing matrices...
> test-tabix_utils.R: [2025-11-26 17:24:54] 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: [2025-11-26 17:24:55] sorting methylation table
> test-tabix_utils.R: [2025-11-26 17:24:55] 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
273.866 14.937 295.848
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
| name | user | system | elapsed | |
| NanoMethResult-class | 5.609 | 0.940 | 10.178 | |
| bsseq_to_edger | 1.258 | 0.039 | 1.834 | |
| bsseq_to_log_methy_ratio | 2.779 | 0.039 | 4.444 | |
| cluster_regions | 4.159 | 0.103 | 6.617 | |
| create_tabix_file | 1.524 | 0.212 | 2.695 | |
| exons_to_genes | 1.992 | 0.028 | 3.103 | |
| filter_methy | 22.840 | 2.162 | 38.121 | |
| get_example_exons_mus_musculus | 0.326 | 0.010 | 0.436 | |
| get_exons | 94.704 | 4.588 | 141.449 | |
| get_exons_homo_sapiens | 39.503 | 1.675 | 63.572 | |
| get_exons_mus_musculus | 16.623 | 1.046 | 26.723 | |
| load_example_modbamresult | 0.349 | 0.012 | 0.523 | |
| load_example_nanomethresult | 0.320 | 0.012 | 0.485 | |
| methy | 0.003 | 0.000 | 0.002 | |
| methy_col_names | 0 | 0 | 0 | |
| methy_to_bsseq | 1.407 | 0.042 | 2.310 | |
| methy_to_edger | 1.525 | 0.046 | 2.546 | |
| modbam_to_tabix | 1.155 | 0.182 | 1.999 | |
| plot_agg_genes | 5.506 | 0.156 | 8.052 | |
| plot_agg_regions | 6.631 | 0.188 | 10.351 | |
| plot_gene | 9.846 | 0.246 | 15.290 | |
| plot_gene_heatmap | 7.934 | 0.129 | 12.179 | |
| plot_grange | 7.463 | 0.119 | 11.629 | |
| plot_grange_heatmap | 5.850 | 0.085 | 9.127 | |
| plot_mds | 2.062 | 0.039 | 3.158 | |
| plot_pca | 2.128 | 0.040 | 3.255 | |
| plot_region | 8.111 | 0.369 | 12.897 | |
| plot_region_heatmap | 5.821 | 0.222 | 9.505 | |
| plot_violin | 3.108 | 0.070 | 4.801 | |
| query_methy | 0.479 | 0.014 | 0.735 | |
| region_methy_stats | 1.258 | 0.029 | 1.942 | |