Shian Su
| Snapshot Date: 2025-12-08 13:45 -0500 (Mon, 08 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 2025-12-11 12:03 -0500 (Thu, 11 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" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4670 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4604 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings NanoMethViz_3.6.0.tar.gz |
| StartedAt: 2025-12-09 01:59:19 -0500 (Tue, 09 Dec 2025) |
| EndedAt: 2025-12-09 02:11:52 -0500 (Tue, 09 Dec 2025) |
| EllapsedTime: 752.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NanoMethViz.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings NanoMethViz_3.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/NanoMethViz.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... OK
Not all R platforms support C++20
* checking installed package size ... INFO
installed size is 17.2Mb
sub-directories of 1Mb or more:
libs 3.9Mb
* 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 loading without being on the library search path ... 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 67.627 2.582 70.291
get_exons_homo_sapiens 27.789 0.694 28.485
filter_methy 16.891 0.136 17.029
get_exons_mus_musculus 11.037 0.140 11.179
plot_gene 9.793 0.864 10.657
plot_gene_heatmap 8.107 0.661 8.768
plot_grange 7.267 0.449 7.717
plot_agg_genes 6.968 0.489 7.457
plot_region 7.071 0.349 7.421
plot_region_heatmap 5.693 0.334 6.027
plot_grange_heatmap 5.573 0.346 5.920
plot_agg_regions 5.241 0.556 5.798
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/NanoMethViz.Rcheck/00check.log’
for details.
NanoMethViz.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL NanoMethViz
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘NanoMethViz’ ...
** this is package ‘NanoMethViz’ version ‘3.6.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++20
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c count_cg.cpp -o count_cg.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c genome.cpp -o genome.o
genome.cpp: In member function ‘bool Genome::check_if_motif(const std::string&, int, const std::string&, int)’:
genome.cpp:43:21: warning: variable ‘chrom_view’ set but not used [-Wunused-but-set-variable]
43 | string_view chrom_view = this->bases_at(chrom, motif_start, motif_end);
| ^~~~~~~~~~
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c modbam.cpp -o modbam.o
modbam.cpp: In function ‘GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)’:
modbam.cpp:331:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::basic_string_view<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
331 | while ( mod_string_end < mm_tok.size() && std::isalnum(mm_tok[mod_string_end]) ) {
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
modbam.cpp:339:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::basic_string_view<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
339 | if (mod_string_end == mm_tok.size() || mm_tok[mod_string_end] == '?') {
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
modbam.cpp:363:17: warning: ‘target_base’ may be used uninitialized [-Wmaybe-uninitialized]
363 | if (seq.at(seq_ind) == target_base) {
| ^~
modbam.cpp:305:14: note: ‘target_base’ was declared here
305 | char target_base;
| ^~~~~~~~~~~
modbam.cpp:364:21: warning: ‘parse_mode’ may be used uninitialized [-Wmaybe-uninitialized]
364 | switch (parse_mode) {
| ^~~~~~
modbam.cpp:308:19: note: ‘parse_mode’ was declared here
308 | ParseMode parse_mode;
| ^~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_iterator.h:85,
from /usr/include/c++/13/bits/stl_algobase.h:67,
from /usr/include/c++/13/algorithm:60,
from modbam.cpp:1:
In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = char; _Args = {const char&}]’,
inlined from ‘static constexpr void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = char; _Args = {const char&}; _Tp = char]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21,
inlined from ‘constexpr void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const char&}; _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/13/bits/vector.tcc:468:28,
inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/13/bits/stl_vector.h:1292:21,
inlined from ‘GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)’ at modbam.cpp:368:50:
/usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘current_base’ may be used uninitialized [-Wmaybe-uninitialized]
97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
modbam.cpp: In function ‘GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)’:
modbam.cpp:304:14: note: ‘current_base’ was declared here
304 | char current_base;
| ^~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c utils.cpp -o utils.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o count_cg.o genome.o modbam.o utils.o -lz -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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-bsseq_to_edger.R: Successfully matched 6 samples between data and annotation.
> test-bsseq_to_edger.R: [2025-12-09 02:08:28] creating intermediate files...
> test-bsseq_to_edger.R: [2025-12-09 02:08:28] parsing chr11...
> test-bsseq_to_edger.R: [2025-12-09 02:08:28] parsing chr12...
> test-bsseq_to_edger.R: [2025-12-09 02:08:28] parsing chr18...
> test-bsseq_to_edger.R: [2025-12-09 02:08:28] parsing chr5...
> test-bsseq_to_edger.R: [2025-12-09 02:08:28] parsing chr7...
> test-bsseq_to_edger.R: [2025-12-09 02:08:28] parsing chrX...
> test-bsseq_to_edger.R: [2025-12-09 02:08:28] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6
> test-bsseq_to_edger.R: [2025-12-09 02:08:28] creating bsseq object...
> test-bsseq_to_edger.R: [2025-12-09 02:08:28] reading in parsed data...
> test-bsseq_to_edger.R: [2025-12-09 02:08:28] constructing matrices...
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] done
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] creating intermediate files...
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] parsing chr11...
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] parsing chr12...
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] parsing chr18...
> test-NanoMethResults.R: Successfully matched 6 samples between data and annotation.
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] parsing chr5...
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] parsing chr7...
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] parsing chrX...
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] creating bsseq object...
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] reading in parsed data...
> test-NanoMethResults.R: Successfully matched 6 samples between data and annotation.
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] constructing matrices...
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] done
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] creating intermediate files...
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] parsing chr11...
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] parsing chr12...
> test-cluster_reads.R: Successfully created ModBamResult with 1 matched samples.
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] parsing chr18...
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] parsing chr5...
> test-bsseq_to_edger.R: [2025-12-09 02:08:29] parsing chr7...
> test-bsseq_to_edger.R: [2025-12-09 02:08:30] parsing chrX...
> test-bsseq_to_edger.R: [2025-12-09 02:08:30] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6
> test-bsseq_to_edger.R: [2025-12-09 02:08:30] creating bsseq object...
> test-bsseq_to_edger.R: [2025-12-09 02:08:30] reading in parsed data...
> test-bsseq_to_edger.R: [2025-12-09 02:08:30] constructing matrices...
> test-bsseq_to_edger.R: [2025-12-09 02:08:30] 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: [2025-12-09 02:08:35] creating intermediate files...
> test-methy_to_bsseq.R: [2025-12-09 02:08:35] parsing chr11...
> test-methy_to_bsseq.R: [2025-12-09 02:08:35] parsing chr12...
> test-methy_to_bsseq.R: [2025-12-09 02:08:35] parsing chr18...
> test-methy_to_bsseq.R: [2025-12-09 02:08:35] parsing chr5...
> test-methy_to_bsseq.R: [2025-12-09 02:08:35] parsing chr7...
> test-methy_to_bsseq.R: [2025-12-09 02:08:35] parsing chrX...
> test-methy_to_bsseq.R: [2025-12-09 02:08:36] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6
> test-methy_to_bsseq.R: [2025-12-09 02:08:36] creating bsseq object...
> test-methy_to_bsseq.R: [2025-12-09 02:08:36] reading in parsed data...
> test-methy_to_bsseq.R: [2025-12-09 02:08:36] constructing matrices...
> test-methy_to_bsseq.R: [2025-12-09 02:08:36] done
> test-methy_to_bsseq.R: [2025-12-09 02:08:36] creating intermediate files...
> test-methy_to_bsseq.R: [2025-12-09 02:08:36] parsing chr11...
> test-methy_to_bsseq.R: [2025-12-09 02:08:36] parsing chr12...
> test-methy_to_bsseq.R: [2025-12-09 02:08:36] parsing chr18...
> test-methy_to_bsseq.R: [2025-12-09 02:08:36] parsing chr5...
> test-methy_to_bsseq.R: [2025-12-09 02:08:36] parsing chr7...
> test-methy_to_bsseq.R: [2025-12-09 02:08:36] parsing chrX...
> test-methy_to_bsseq.R: [2025-12-09 02:08:36] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6
> test-methy_to_bsseq.R: [2025-12-09 02:08:36] creating bsseq object...
> test-methy_to_bsseq.R: [2025-12-09 02:08:36] reading in parsed data...
> test-methy_to_bsseq.R: [2025-12-09 02:08:36] constructing matrices...
> test-methy_to_bsseq.R: [2025-12-09 02:08:37] done
> test-methy_to_bsseq.R: [2025-12-09 02:08:37] creating intermediate files...
> test-methy_to_bsseq.R: [2025-12-09 02:08:37] parsing chr11...
> test-methy_to_bsseq.R: [2025-12-09 02:08:37] parsing chr12...
> test-methy_to_bsseq.R: [2025-12-09 02:08:37] parsing chr18...
> test-methy_to_bsseq.R: [2025-12-09 02:08:37] parsing chr5...
> test-methy_to_bsseq.R: [2025-12-09 02:08:37] parsing chr7...
> test-methy_to_bsseq.R: [2025-12-09 02:08:37] parsing chrX...
> test-methy_to_bsseq.R: [2025-12-09 02:08:37] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6
> test-methy_to_bsseq.R: [2025-12-09 02:08:37] creating bsseq object...
> test-methy_to_bsseq.R: [2025-12-09 02:08:37] reading in parsed data...
> test-methy_to_bsseq.R: [2025-12-09 02:08:37] constructing matrices...
> test-methy_to_bsseq.R: [2025-12-09 02:08:38] done
> test-methy_to_bsseq.R: Successfully matched 6 samples between data and annotation.
> test-methy_to_bsseq.R: [2025-12-09 02:08:38] creating intermediate files...
> test-methy_to_bsseq.R: [2025-12-09 02:08:38] parsing chr11...
> test-methy_to_bsseq.R: [2025-12-09 02:08:38] parsing chr12...
> test-methy_to_bsseq.R: [2025-12-09 02:08:38] parsing chr18...
> test-methy_to_bsseq.R: [2025-12-09 02:08:38] parsing chr5...
> test-methy_to_bsseq.R: [2025-12-09 02:08:38] parsing chr7...
> test-methy_to_bsseq.R: [2025-12-09 02:08:38] parsing chrX...
> test-methy_to_bsseq.R: [2025-12-09 02:08:38] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6
> test-methy_to_bsseq.R: [2025-12-09 02:08:38] creating bsseq object...
> test-methy_to_bsseq.R: [2025-12-09 02:08:38] reading in parsed data...
> test-methy_to_bsseq.R: [2025-12-09 02:08:38] constructing matrices...
> test-methy_to_bsseq.R: [2025-12-09 02:08:39] 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/Rtmp9TZOrP/file2d9b4e4966af9c.tsv
> test-modbam_to_tabix.R: v Writing data to temporary file: /tmp/Rtmp9TZOrP/file2d9b4e4966af9c.tsv [25ms]
> 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 [1.9s]
> test-modbam_to_tabix.R:
> test-modbam_to_tabix.R: i Sorting data
> test-modbam_to_tabix.R: v Sorting data [44ms]
> 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/Rtmp9TZOrP/file2d9b4e49e46b62.tsv.bgz
> test-modbam_to_tabix.R: i Compressing data
> test-modbam_to_tabix.R: v Compressing data [40ms]
> test-modbam_to_tabix.R:
> test-modbam_to_tabix.R: i Tabix file created: /tmp/Rtmp9TZOrP/file2d9b4e49e46b62.tsv.bgz
> test-modbam_to_tabix.R: v Tabix file created: /tmp/Rtmp9TZOrP/file2d9b4e49e46b62.tsv.bgz [25ms]
> 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/RtmpnwLScC/file2d9b536b5b11e6.tsv.bgz' along with index file '/tmp/RtmpnwLScC/file2d9b536b5b11e6.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-filter_methy.R: 21,798 of 224,267 (9.72%) entries kept after filtering
> test-filter_methy.R: results written to '/tmp/RtmpnwLScC/file2d9b536b5b11e6.tsv.bgz' along with index file '/tmp/RtmpnwLScC/file2d9b536b5b11e6.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/RtmpnwLScC/file2d9b536b5b11e6.tsv.bgz' along with index file '/tmp/RtmpnwLScC/file2d9b536b5b11e6.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: [2025-12-09 02:09:05] creating intermediate files...
> test-plot_mds.R: [2025-12-09 02:09:05] parsing chr11...
> test-plot_mds.R: [2025-12-09 02:09:05] parsing chr12...
> test-plot_mds.R: [2025-12-09 02:09:05] parsing chr18...
> test-plot_mds.R: [2025-12-09 02:09:05] parsing chr5...
> test-plot_mds.R: [2025-12-09 02:09:05] parsing chr7...
> test-plot_mds.R: [2025-12-09 02:09:05] parsing chrX...
> test-plot_mds.R: [2025-12-09 02:09:06] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6
> test-plot_mds.R: [2025-12-09 02:09:06] creating bsseq object...
> test-plot_mds.R: [2025-12-09 02:09:06] reading in parsed data...
> test-plot_mds.R: [2025-12-09 02:09:06] constructing matrices...
> test-plot_mds.R: [2025-12-09 02:09:06] 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: [2025-12-09 02:09:09] creating intermediate files...
> test-plot_pca.R: [2025-12-09 02:09:09] parsing chr11...
> test-plot_pca.R: [2025-12-09 02:09:09] parsing chr12...
> test-plot_pca.R: [2025-12-09 02:09:09] parsing chr18...
> test-plot_pca.R: [2025-12-09 02:09:09] parsing chr5...
> test-plot_pca.R: [2025-12-09 02:09:09] parsing chr7...
> test-plot_pca.R: [2025-12-09 02:09:09] parsing chrX...
> test-plot_pca.R: [2025-12-09 02:09:09] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6
> test-plot_pca.R: [2025-12-09 02:09:09] creating bsseq object...
> test-plot_pca.R: [2025-12-09 02:09:09] reading in parsed data...
> test-plot_pca.R: [2025-12-09 02:09:09] constructing matrices...
> test-plot_pca.R: [2025-12-09 02:09:10] 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 /home/biocbuild/bbs-3.22-bioc/R/site-library/NanoMethViz/sample1_nanopolish.tsv.gz...
> test-tabix_utils.R: guessing file is produced by nanopolish...
> test-tabix_utils.R: processing /home/biocbuild/bbs-3.22-bioc/R/site-library/NanoMethViz/sample2_nanopolish.tsv.gz...
> test-tabix_utils.R: guessing file is produced by nanopolish...
> test-tabix_utils.R: [2025-12-09 02:09:24] sorting methylation table
> test-tabix_utils.R: [2025-12-09 02:09:24] compressing methylation table to tabix with index
> test-tabix_utils.R: [2025-12-09 02:09:24] creating intermediate files...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr1...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr2...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr3...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr4...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr5...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr6...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr7...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr8...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr9...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr10...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr11...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr12...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr13...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr14...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr15...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr16...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr17...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr18...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chr19...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chrM...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chrX...
> test-tabix_utils.R: [2025-12-09 02:09:24] parsing chrY...
> test-tabix_utils.R: [2025-12-09 02:09:24] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6 sample1_nanopolish.tsv sample2_nanopolish.tsv
> test-tabix_utils.R: [2025-12-09 02:09:24] creating bsseq object...
> test-tabix_utils.R: [2025-12-09 02:09:24] reading in parsed data...
> test-tabix_utils.R: [2025-12-09 02:09:24] constructing matrices...
> test-tabix_utils.R: [2025-12-09 02:09:24] done
> test-tabix_utils.R: processing /home/biocbuild/bbs-3.22-bioc/R/site-library/NanoMethViz/megalodon_calls.txt.gz...
> test-tabix_utils.R: guessing file is produced by megalodon...
> test-tabix_utils.R: [2025-12-09 02:09:25] sorting methylation table
> test-tabix_utils.R: [2025-12-09 02:09:25] 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
208.202 11.933 141.191
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
| name | user | system | elapsed | |
| NanoMethResult-class | 2.881 | 0.210 | 3.092 | |
| bsseq_to_edger | 0.595 | 0.013 | 0.610 | |
| bsseq_to_log_methy_ratio | 0.978 | 0.015 | 0.993 | |
| cluster_regions | 4.055 | 0.242 | 4.298 | |
| create_tabix_file | 2.213 | 0.123 | 2.338 | |
| exons_to_genes | 0.234 | 0.001 | 0.236 | |
| filter_methy | 16.891 | 0.136 | 17.029 | |
| get_example_exons_mus_musculus | 0.206 | 0.005 | 0.212 | |
| get_exons | 67.627 | 2.582 | 70.291 | |
| get_exons_homo_sapiens | 27.789 | 0.694 | 28.485 | |
| get_exons_mus_musculus | 11.037 | 0.140 | 11.179 | |
| load_example_modbamresult | 0.384 | 0.002 | 0.387 | |
| load_example_nanomethresult | 0.218 | 0.002 | 0.221 | |
| methy | 0.002 | 0.000 | 0.003 | |
| methy_col_names | 0 | 0 | 0 | |
| methy_to_bsseq | 0.815 | 0.007 | 0.822 | |
| methy_to_edger | 0.927 | 0.022 | 0.949 | |
| modbam_to_tabix | 0.319 | 0.563 | 0.857 | |
| plot_agg_genes | 6.968 | 0.489 | 7.457 | |
| plot_agg_regions | 5.241 | 0.556 | 5.798 | |
| plot_gene | 9.793 | 0.864 | 10.657 | |
| plot_gene_heatmap | 8.107 | 0.661 | 8.768 | |
| plot_grange | 7.267 | 0.449 | 7.717 | |
| plot_grange_heatmap | 5.573 | 0.346 | 5.920 | |
| plot_mds | 1.374 | 0.049 | 1.424 | |
| plot_pca | 1.438 | 0.069 | 1.508 | |
| plot_region | 7.071 | 0.349 | 7.421 | |
| plot_region_heatmap | 5.693 | 0.334 | 6.027 | |
| plot_violin | 2.479 | 0.057 | 2.537 | |
| query_methy | 0.352 | 0.015 | 0.368 | |
| region_methy_stats | 0.937 | 0.066 | 1.004 | |