Shian Su
| Snapshot Date: 2025-11-18 13:40 -0500 (Tue, 18 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) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-19 10:13 -0500 (Wed, 19 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4827 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4600 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4564 |
| 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 1420/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NanoMethViz 3.7.0 (landing page) Shian Su
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 3.7.0 |
| 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: 2025-11-18 22:41:52 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 22:54:51 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 778.7 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_3.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/NanoMethViz.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
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 14.0.3 (clang-1403.0.22.14.1)’
* 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 13.6Mb
* 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 74.940 4.289 80.099
get_exons_homo_sapiens 34.670 1.737 36.661
filter_methy 29.964 4.845 35.027
get_exons_mus_musculus 12.322 0.867 13.270
plot_gene 10.406 0.208 10.660
plot_region 9.371 0.267 9.693
plot_gene_heatmap 9.333 0.173 9.547
plot_grange 8.430 0.595 9.128
plot_grange_heatmap 6.525 0.109 6.676
plot_region_heatmap 6.355 0.109 6.506
NanoMethResult-class 4.871 1.304 6.227
plot_agg_regions 5.852 0.104 5.985
plot_agg_genes 5.209 0.098 5.330
* 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.
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/4.6-x86_64/Resources/library’
* installing *source* package ‘NanoMethViz’ ...
** this is package ‘NanoMethViz’ version ‘3.7.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++20
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o
clang++ -arch x86_64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c count_cg.cpp -o count_cg.o
clang++ -arch x86_64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c modbam.cpp -o modbam.o
clang++ -arch x86_64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o
clang++ -arch x86_64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-x86_64/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 Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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-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: [2025-11-18 22:52:34] creating intermediate files...
> test-bsseq_to_edger.R: [2025-11-18 22:52:34] parsing chr11...
> test-cluster_reads.R: Successfully created ModBamResult with 1 matched samples.
> test-bsseq_to_edger.R: [2025-11-18 22:52:35] parsing chr12...
> test-bsseq_to_edger.R: [2025-11-18 22:52:35] parsing chr18...
> test-bsseq_to_edger.R: [2025-11-18 22:52:35] parsing chr5...
> test-bsseq_to_edger.R: [2025-11-18 22:52:35] parsing chr7...
> test-bsseq_to_edger.R: [2025-11-18 22:52:35] parsing chrX...
> test-bsseq_to_edger.R: [2025-11-18 22:52:35] 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
> test-bsseq_to_edger.R: [2025-11-18 22:52:35] creating bsseq object...
> test-bsseq_to_edger.R: [2025-11-18 22:52:35] reading in parsed data...
> test-bsseq_to_edger.R: [2025-11-18 22:52:35] constructing matrices...
> test-bsseq_to_edger.R: [2025-11-18 22:52:35] done
> test-bsseq_to_edger.R: [2025-11-18 22:52:35] creating intermediate files...
> test-bsseq_to_edger.R: [2025-11-18 22:52:35] parsing chr11...
> test-bsseq_to_edger.R: [2025-11-18 22:52:36] parsing chr12...
> test-bsseq_to_edger.R: [2025-11-18 22:52:36] parsing chr18...
> test-bsseq_to_edger.R: [2025-11-18 22:52:36] parsing chr5...
> test-bsseq_to_edger.R: [2025-11-18 22:52:36] parsing chr7...
> test-bsseq_to_edger.R: [2025-11-18 22:52:36] parsing chrX...
> test-bsseq_to_edger.R: [2025-11-18 22:52:36] 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: [2025-11-18 22:52:36] creating bsseq object...
> test-bsseq_to_edger.R: [2025-11-18 22:52:36] reading in parsed data...
> test-bsseq_to_edger.R: [2025-11-18 22:52:36] constructing matrices...
> test-bsseq_to_edger.R: [2025-11-18 22:52:36] done
> test-bsseq_to_edger.R: [2025-11-18 22:52:36] creating intermediate files...
> test-bsseq_to_edger.R: [2025-11-18 22:52:36] parsing chr11...
> test-bsseq_to_edger.R: [2025-11-18 22:52:36] parsing chr12...
> test-bsseq_to_edger.R: [2025-11-18 22:52:36] parsing chr18...
> test-bsseq_to_edger.R: [2025-11-18 22:52:37] parsing chr5...
> test-bsseq_to_edger.R: [2025-11-18 22:52:37] parsing chr7...
> test-bsseq_to_edger.R: [2025-11-18 22:52:37] parsing chrX...
> test-bsseq_to_edger.R: [2025-11-18 22:52:37] 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: [2025-11-18 22:52:37] creating bsseq object...
> test-bsseq_to_edger.R: [2025-11-18 22:52:37] reading in parsed data...
> test-bsseq_to_edger.R: [2025-11-18 22:52:37] constructing matrices...
> test-bsseq_to_edger.R: [2025-11-18 22:52:37] 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: [2025-11-18 22:52:45] creating intermediate files...
> test-methy_to_bsseq.R: [2025-11-18 22:52:45] parsing chr11...
> test-methy_to_bsseq.R: [2025-11-18 22:52:45] parsing chr12...
> test-methy_to_bsseq.R: [2025-11-18 22:52:45] parsing chr18...
> test-methy_to_bsseq.R: [2025-11-18 22:52:45] parsing chr5...
> test-methy_to_bsseq.R: [2025-11-18 22:52:45] parsing chr7...
> test-methy_to_bsseq.R: [2025-11-18 22:52:45] parsing chrX...
> test-methy_to_bsseq.R: [2025-11-18 22:52:45] 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: [2025-11-18 22:52:45] creating bsseq object...
> test-methy_to_bsseq.R: [2025-11-18 22:52:45] reading in parsed data...
> test-methy_to_bsseq.R: [2025-11-18 22:52:45] constructing matrices...
> test-methy_to_bsseq.R: [2025-11-18 22:52:46] done
> test-methy_to_bsseq.R: [2025-11-18 22:52:46] creating intermediate files...
> test-methy_to_bsseq.R: [2025-11-18 22:52:46] parsing chr11...
> test-methy_to_bsseq.R: [2025-11-18 22:52:46] parsing chr12...
> test-methy_to_bsseq.R: [2025-11-18 22:52:46] parsing chr18...
> test-methy_to_bsseq.R: [2025-11-18 22:52:46] parsing chr5...
> test-methy_to_bsseq.R: [2025-11-18 22:52:46] parsing chr7...
> test-methy_to_bsseq.R: [2025-11-18 22:52:46] parsing chrX...
> test-methy_to_bsseq.R: [2025-11-18 22:52:46] 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-methy_to_bsseq.R: [2025-11-18 22:52:46] creating bsseq object...
> test-methy_to_bsseq.R: [2025-11-18 22:52:46] reading in parsed data...
> test-methy_to_bsseq.R: [2025-11-18 22:52:46] constructing matrices...
> test-methy_to_bsseq.R: [2025-11-18 22:52:47] done
> test-methy_to_bsseq.R: [2025-11-18 22:52:47] creating intermediate files...
> test-methy_to_bsseq.R: [2025-11-18 22:52:47] parsing chr11...
> test-methy_to_bsseq.R: [2025-11-18 22:52:47] parsing chr12...
> test-methy_to_bsseq.R: [2025-11-18 22:52:47] parsing chr18...
> test-methy_to_bsseq.R: [2025-11-18 22:52:47] parsing chr5...
> test-methy_to_bsseq.R: [2025-11-18 22:52:47] parsing chr7...
> test-methy_to_bsseq.R: [2025-11-18 22:52:47] parsing chrX...
> test-methy_to_bsseq.R: [2025-11-18 22:52:47] 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: [2025-11-18 22:52:47] creating bsseq object...
> test-methy_to_bsseq.R: [2025-11-18 22:52:47] reading in parsed data...
> test-methy_to_bsseq.R: [2025-11-18 22:52:47] constructing matrices...
> test-methy_to_bsseq.R: [2025-11-18 22:52:48] done
> test-methy_to_bsseq.R: Successfully matched 6 samples between data and annotation.
> test-methy_to_bsseq.R: [2025-11-18 22:52:48] creating intermediate files...
> test-methy_to_bsseq.R: [2025-11-18 22:52:48] parsing chr11...
> test-methy_to_bsseq.R: [2025-11-18 22:52:48] parsing chr12...
> test-methy_to_bsseq.R: [2025-11-18 22:52:48] parsing chr18...
> test-methy_to_bsseq.R: [2025-11-18 22:52:49] parsing chr5...
> test-methy_to_bsseq.R: [2025-11-18 22:52:49] parsing chr7...
> test-methy_to_bsseq.R: [2025-11-18 22:52:49] parsing chrX...
> test-methy_to_bsseq.R: [2025-11-18 22:52:49] 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: [2025-11-18 22:52:49] creating bsseq object...
> test-methy_to_bsseq.R: [2025-11-18 22:52:49] reading in parsed data...
> test-methy_to_bsseq.R: [2025-11-18 22:52:49] constructing matrices...
> test-methy_to_bsseq.R: [2025-11-18 22:52:50] 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/RtmptraW9n/file113831155819f.tsv
> test-modbam_to_tabix.R: v Writing data to temporary file: /tmp/RtmptraW9n/file113831155819f.tsv [26ms]
> 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 [642ms]
> test-modbam_to_tabix.R:
> test-modbam_to_tabix.R: i Sorting data
> test-modbam_to_tabix.R: v Sorting data [149ms]
> 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/RtmptraW9n/file1138329b0c8f.tsv.bgz
> test-modbam_to_tabix.R: i Compressing data
> test-modbam_to_tabix.R: v Compressing data [55ms]
> test-modbam_to_tabix.R:
> test-modbam_to_tabix.R: i Tabix file created: /tmp/RtmptraW9n/file1138329b0c8f.tsv.bgz
> test-modbam_to_tabix.R: v Tabix file created: /tmp/RtmptraW9n/file1138329b0c8f.tsv.bgz [31ms]
> 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-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/RtmpBEt647/file113846f45d32e.tsv.bgz' along with index file '/tmp/RtmpBEt647/file113846f45d32e.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/RtmpBEt647/file113846f45d32e.tsv.bgz' along with index file '/tmp/RtmpBEt647/file113846f45d32e.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/RtmpBEt647/file113846f45d32e.tsv.bgz' along with index file '/tmp/RtmpBEt647/file113846f45d32e.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: [2025-11-18 22:53:36] creating intermediate files...
> test-plot_mds.R: [2025-11-18 22:53:36] parsing chr11...
> test-plot_mds.R: [2025-11-18 22:53:37] parsing chr12...
> test-plot_mds.R: [2025-11-18 22:53:37] parsing chr18...
> test-plot_mds.R: [2025-11-18 22:53:37] parsing chr5...
> test-plot_mds.R: [2025-11-18 22:53:37] parsing chr7...
> test-plot_mds.R: [2025-11-18 22:53:37] parsing chrX...
> test-plot_mds.R: [2025-11-18 22:53:37] 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-plot_mds.R: [2025-11-18 22:53:37] creating bsseq object...
> test-plot_mds.R: [2025-11-18 22:53:37] reading in parsed data...
> test-plot_mds.R: [2025-11-18 22:53:37] constructing matrices...
> test-plot_mds.R: [2025-11-18 22:53:37] 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: [2025-11-18 22:53:42] creating intermediate files...
> test-plot_pca.R: [2025-11-18 22:53:42] parsing chr11...
> test-plot_pca.R: [2025-11-18 22:53:42] parsing chr12...
> test-plot_pca.R: [2025-11-18 22:53:42] parsing chr18...
> test-plot_pca.R: [2025-11-18 22:53:42] parsing chr5...
> test-plot_pca.R: [2025-11-18 22:53:42] parsing chr7...
> test-plot_pca.R: [2025-11-18 22:53:42] parsing chrX...
> test-plot_pca.R: [2025-11-18 22:53:42] 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-plot_pca.R: [2025-11-18 22:53:42] creating bsseq object...
> test-plot_pca.R: [2025-11-18 22:53:42] reading in parsed data...
> test-plot_pca.R: [2025-11-18 22:53:42] constructing matrices...
> test-plot_pca.R: [2025-11-18 22:53:43] 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-x86_64/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-x86_64/Resources/library/NanoMethViz/sample2_nanopolish.tsv.gz...
> test-tabix_utils.R: guessing file is produced by nanopolish...
> test-tabix_utils.R: [2025-11-18 22:54:01] sorting methylation table
> test-tabix_utils.R: [2025-11-18 22:54:01] compressing methylation table to tabix with index
> test-tabix_utils.R: [2025-11-18 22:54:01] creating intermediate files...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr1...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr2...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr3...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr4...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr5...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr6...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr7...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr8...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr9...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr10...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr11...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr12...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr13...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr14...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr15...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr16...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr17...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr18...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chr19...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chrM...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chrX...
> test-tabix_utils.R: [2025-11-18 22:54:01] parsing chrY...
> test-tabix_utils.R: [2025-11-18 22:54:01] 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: [2025-11-18 22:54:01] creating bsseq object...
> test-tabix_utils.R: [2025-11-18 22:54:01] reading in parsed data...
> test-tabix_utils.R: [2025-11-18 22:54:01] constructing matrices...
> test-tabix_utils.R: [2025-11-18 22:54:02] done
> test-tabix_utils.R: processing /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/NanoMethViz/megalodon_calls.txt.gz...
> test-tabix_utils.R: guessing file is produced by megalodon...
> test-tabix_utils.R: [2025-11-18 22:54:02] sorting methylation table
> test-tabix_utils.R: [2025-11-18 22:54:02] 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
261.031 18.857 166.572
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
| name | user | system | elapsed | |
| NanoMethResult-class | 4.871 | 1.304 | 6.227 | |
| bsseq_to_edger | 0.986 | 0.036 | 1.031 | |
| bsseq_to_log_methy_ratio | 2.358 | 0.039 | 2.413 | |
| cluster_regions | 3.468 | 0.111 | 3.598 | |
| create_tabix_file | 1.851 | 0.392 | 2.296 | |
| exons_to_genes | 0.359 | 0.014 | 0.377 | |
| filter_methy | 29.964 | 4.845 | 35.027 | |
| get_example_exons_mus_musculus | 0.296 | 0.010 | 0.307 | |
| get_exons | 74.940 | 4.289 | 80.099 | |
| get_exons_homo_sapiens | 34.670 | 1.737 | 36.661 | |
| get_exons_mus_musculus | 12.322 | 0.867 | 13.270 | |
| load_example_modbamresult | 0.324 | 0.019 | 0.345 | |
| load_example_nanomethresult | 0.330 | 0.015 | 0.346 | |
| methy | 0.002 | 0.001 | 0.003 | |
| methy_col_names | 0 | 0 | 0 | |
| methy_to_bsseq | 1.159 | 0.042 | 1.211 | |
| methy_to_edger | 1.385 | 0.114 | 1.509 | |
| modbam_to_tabix | 0.591 | 0.307 | 0.729 | |
| plot_agg_genes | 5.209 | 0.098 | 5.330 | |
| plot_agg_regions | 5.852 | 0.104 | 5.985 | |
| plot_gene | 10.406 | 0.208 | 10.660 | |
| plot_gene_heatmap | 9.333 | 0.173 | 9.547 | |
| plot_grange | 8.430 | 0.595 | 9.128 | |
| plot_grange_heatmap | 6.525 | 0.109 | 6.676 | |
| plot_mds | 1.821 | 0.043 | 1.873 | |
| plot_pca | 1.904 | 0.037 | 1.947 | |
| plot_region | 9.371 | 0.267 | 9.693 | |
| plot_region_heatmap | 6.355 | 0.109 | 6.506 | |
| plot_violin | 2.777 | 0.040 | 2.832 | |
| query_methy | 0.450 | 0.010 | 0.462 | |
| region_methy_stats | 1.087 | 0.017 | 1.109 | |