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This page was generated on 2025-11-22 11:37 -0500 (Sat, 22 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4829
lconwaymacOS 12.7.6 Montereyx86_64R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" 4603
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4567
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Package 1422/2327HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoMethViz 3.7.0  (landing page)
Shian Su
Snapshot Date: 2025-11-21 13:40 -0500 (Fri, 21 Nov 2025)
git_url: https://git.bioconductor.org/packages/NanoMethViz
git_branch: devel
git_last_commit: 4349b36
git_last_commit_date: 2025-10-29 11:04:08 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'bsseq' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'BiocSingular' which is only available as a source package that needs compilation

CHECK results for NanoMethViz on nebbiolo1

To the developers/maintainers of the NanoMethViz package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NanoMethViz.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: NanoMethViz
Version: 3.7.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings NanoMethViz_3.7.0.tar.gz
StartedAt: 2025-11-22 01:57:46 -0500 (Sat, 22 Nov 2025)
EndedAt: 2025-11-22 02:10:19 -0500 (Sat, 22 Nov 2025)
EllapsedTime: 753.2 seconds
RetCode: 0
Status:   OK  
CheckDir: NanoMethViz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings NanoMethViz_3.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/NanoMethViz.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘3.7.0’
* 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: ‘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 15.5Mb
  sub-directories of 1Mb or more:
    libs   2.1Mb
* 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 ... 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              67.478  3.063  70.593
get_exons_homo_sapiens 27.977  0.745  28.730
filter_methy           17.282  0.185  17.466
get_exons_mus_musculus 11.048  0.154  11.202
plot_gene               9.220  0.160   9.380
plot_region             7.340  0.174   7.514
plot_gene_heatmap       7.465  0.017   7.483
plot_grange             6.940  0.032   6.972
cluster_regions         5.337  0.282   5.639
plot_grange_heatmap     5.345  0.033   5.378
plot_region_heatmap     5.312  0.047   5.359
plot_agg_regions        5.007  0.230   5.237
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/NanoMethViz.Rcheck/00check.log’
for details.

Installation output

NanoMethViz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL NanoMethViz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘NanoMethViz’ ...
** this is package ‘NanoMethViz’ version ‘3.7.0’
** 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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-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-3.23-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-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-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)

Tests output

NanoMethViz.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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-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: [2025-11-22 02:06:55] creating intermediate files...
> test-bsseq_to_edger.R: [2025-11-22 02:06:55] parsing chr11...
> test-bsseq_to_edger.R: [2025-11-22 02:06:55] parsing chr12...
> test-bsseq_to_edger.R: [2025-11-22 02:06:55] parsing chr18...
> test-bsseq_to_edger.R: [2025-11-22 02:06:55] parsing chr5...
> test-bsseq_to_edger.R: [2025-11-22 02:06:55] parsing chr7...
> test-bsseq_to_edger.R: [2025-11-22 02:06:56] parsing chrX...
> test-bsseq_to_edger.R: [2025-11-22 02:06:56] 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: [2025-11-22 02:06:56] creating bsseq object...
> test-bsseq_to_edger.R: [2025-11-22 02:06:56] reading in parsed data...
> test-cluster_reads.R: Successfully created ModBamResult with 1 matched samples.
> test-bsseq_to_edger.R: [2025-11-22 02:06:56] constructing matrices...
> test-bsseq_to_edger.R: [2025-11-22 02:06:56] done
> test-bsseq_to_edger.R: [2025-11-22 02:06:56] creating intermediate files...
> test-bsseq_to_edger.R: [2025-11-22 02:06:56] parsing chr11...
> test-bsseq_to_edger.R: [2025-11-22 02:06:56] parsing chr12...
> test-bsseq_to_edger.R: [2025-11-22 02:06:56] parsing chr18...
> test-bsseq_to_edger.R: [2025-11-22 02:06:56] parsing chr5...
> test-bsseq_to_edger.R: [2025-11-22 02:06:56] parsing chr7...
> test-bsseq_to_edger.R: [2025-11-22 02:06:56] parsing chrX...
> test-bsseq_to_edger.R: [2025-11-22 02:06:56] 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: [2025-11-22 02:06:56] creating bsseq object...
> test-bsseq_to_edger.R: [2025-11-22 02:06:56] reading in parsed data...
> test-bsseq_to_edger.R: [2025-11-22 02:06:56] constructing matrices...
> test-bsseq_to_edger.R: [2025-11-22 02:06:56] done
> test-bsseq_to_edger.R: [2025-11-22 02:06:57] creating intermediate files...
> test-bsseq_to_edger.R: [2025-11-22 02:06:57] parsing chr11...
> test-bsseq_to_edger.R: [2025-11-22 02:06:57] parsing chr12...
> test-bsseq_to_edger.R: [2025-11-22 02:06:57] parsing chr18...
> test-bsseq_to_edger.R: [2025-11-22 02:06:57] parsing chr5...
> test-bsseq_to_edger.R: [2025-11-22 02:06:57] parsing chr7...
> test-bsseq_to_edger.R: [2025-11-22 02:06:57] parsing chrX...
> test-bsseq_to_edger.R: [2025-11-22 02:06:57] 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: [2025-11-22 02:06:57] creating bsseq object...
> test-bsseq_to_edger.R: [2025-11-22 02:06:57] reading in parsed data...
> test-bsseq_to_edger.R: [2025-11-22 02:06:57] constructing matrices...
> test-bsseq_to_edger.R: [2025-11-22 02:06:57] 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: [2025-11-22 02:07:04] creating intermediate files...
> test-methy_to_bsseq.R: [2025-11-22 02:07:04] parsing chr11...
> test-methy_to_bsseq.R: [2025-11-22 02:07:04] parsing chr12...
> test-methy_to_bsseq.R: [2025-11-22 02:07:04] parsing chr18...
> test-methy_to_bsseq.R: [2025-11-22 02:07:04] parsing chr5...
> test-methy_to_bsseq.R: [2025-11-22 02:07:04] parsing chr7...
> test-methy_to_bsseq.R: [2025-11-22 02:07:04] parsing chrX...
> test-methy_to_bsseq.R: [2025-11-22 02:07:04] 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: [2025-11-22 02:07:04] creating bsseq object...
> test-methy_to_bsseq.R: [2025-11-22 02:07:04] reading in parsed data...
> test-methy_to_bsseq.R: [2025-11-22 02:07:04] constructing matrices...
> test-methy_to_bsseq.R: [2025-11-22 02:07:05] done
> test-methy_to_bsseq.R: [2025-11-22 02:07:05] creating intermediate files...
> test-methy_to_bsseq.R: [2025-11-22 02:07:05] parsing chr11...
> test-methy_to_bsseq.R: [2025-11-22 02:07:05] parsing chr12...
> test-methy_to_bsseq.R: [2025-11-22 02:07:05] parsing chr18...
> test-methy_to_bsseq.R: [2025-11-22 02:07:05] parsing chr5...
> test-methy_to_bsseq.R: [2025-11-22 02:07:05] parsing chr7...
> test-methy_to_bsseq.R: [2025-11-22 02:07:05] parsing chrX...
> test-methy_to_bsseq.R: [2025-11-22 02:07:05] 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: [2025-11-22 02:07:05] creating bsseq object...
> test-methy_to_bsseq.R: [2025-11-22 02:07:05] reading in parsed data...
> test-methy_to_bsseq.R: [2025-11-22 02:07:05] constructing matrices...
> test-methy_to_bsseq.R: [2025-11-22 02:07:06] done
> test-methy_to_bsseq.R: [2025-11-22 02:07:06] creating intermediate files...
> test-methy_to_bsseq.R: [2025-11-22 02:07:06] parsing chr11...
> test-methy_to_bsseq.R: [2025-11-22 02:07:06] parsing chr12...
> test-methy_to_bsseq.R: [2025-11-22 02:07:06] parsing chr18...
> test-methy_to_bsseq.R: [2025-11-22 02:07:06] parsing chr5...
> test-methy_to_bsseq.R: [2025-11-22 02:07:06] parsing chr7...
> test-methy_to_bsseq.R: [2025-11-22 02:07:06] parsing chrX...
> test-methy_to_bsseq.R: [2025-11-22 02:07:06] 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-methy_to_bsseq.R: [2025-11-22 02:07:06] creating bsseq object...
> test-methy_to_bsseq.R: [2025-11-22 02:07:06] reading in parsed data...
> test-methy_to_bsseq.R: [2025-11-22 02:07:06] constructing matrices...
> test-methy_to_bsseq.R: [2025-11-22 02:07:07] done
> test-methy_to_bsseq.R: Successfully matched 6 samples between data and annotation.
> test-methy_to_bsseq.R: [2025-11-22 02:07:07] creating intermediate files...
> test-methy_to_bsseq.R: [2025-11-22 02:07:07] parsing chr11...
> test-methy_to_bsseq.R: [2025-11-22 02:07:07] parsing chr12...
> test-methy_to_bsseq.R: [2025-11-22 02:07:07] parsing chr18...
> test-methy_to_bsseq.R: [2025-11-22 02:07:07] parsing chr5...
> test-methy_to_bsseq.R: [2025-11-22 02:07:07] parsing chr7...
> test-methy_to_bsseq.R: [2025-11-22 02:07:07] parsing chrX...
> test-methy_to_bsseq.R: [2025-11-22 02:07:07] 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: [2025-11-22 02:07:07] creating bsseq object...
> test-methy_to_bsseq.R: [2025-11-22 02:07:07] reading in parsed data...
> test-methy_to_bsseq.R: [2025-11-22 02:07:07] constructing matrices...
> test-methy_to_bsseq.R: [2025-11-22 02:07:08] 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/RtmpXRbIA6/file18f5cb559a8fa4.tsv
> test-modbam_to_tabix.R: v Writing data to temporary file: /tmp/RtmpXRbIA6/file18f5cb559a8fa4.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 [808ms]
> test-modbam_to_tabix.R: 
> test-modbam_to_tabix.R: i Sorting data
> test-modbam_to_tabix.R: v Sorting data [47ms]
> 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/RtmpXRbIA6/file18f5cb3ae5e01d.tsv.bgz
> test-modbam_to_tabix.R: i Compressing data
> test-modbam_to_tabix.R: v Compressing data [44ms]
> test-modbam_to_tabix.R: 
> test-modbam_to_tabix.R: i Tabix file created: /tmp/RtmpXRbIA6/file18f5cb3ae5e01d.tsv.bgz
> test-modbam_to_tabix.R: v Tabix file created: /tmp/RtmpXRbIA6/file18f5cb3ae5e01d.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-filter_methy.R: 21,798 of 224,267 (9.72%) entries kept after filtering
> test-filter_methy.R: results written to '/tmp/Rtmpre2Kbq/file18f5cc2200ffdb.tsv.bgz' along with index file '/tmp/Rtmpre2Kbq/file18f5cc2200ffdb.tsv.bgz.tbi'
> 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/Rtmpre2Kbq/file18f5cc2200ffdb.tsv.bgz' along with index file '/tmp/Rtmpre2Kbq/file18f5cc2200ffdb.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/Rtmpre2Kbq/file18f5cc2200ffdb.tsv.bgz' along with index file '/tmp/Rtmpre2Kbq/file18f5cc2200ffdb.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: [2025-11-22 02:07:31] creating intermediate files...
> test-plot_mds.R: [2025-11-22 02:07:31] parsing chr11...
> test-plot_mds.R: [2025-11-22 02:07:31] parsing chr12...
> test-plot_mds.R: [2025-11-22 02:07:31] parsing chr18...
> test-plot_mds.R: [2025-11-22 02:07:31] parsing chr5...
> test-plot_mds.R: [2025-11-22 02:07:32] parsing chr7...
> test-plot_mds.R: [2025-11-22 02:07:32] parsing chrX...
> test-plot_mds.R: [2025-11-22 02:07:32] 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: [2025-11-22 02:07:32] creating bsseq object...
> test-plot_mds.R: [2025-11-22 02:07:32] reading in parsed data...
> test-plot_mds.R: [2025-11-22 02:07:32] constructing matrices...
> test-plot_mds.R: [2025-11-22 02:07:32] 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: [2025-11-22 02:07:35] creating intermediate files...
> test-plot_pca.R: [2025-11-22 02:07:35] parsing chr11...
> test-plot_pca.R: [2025-11-22 02:07:35] parsing chr12...
> test-plot_pca.R: [2025-11-22 02:07:35] parsing chr18...
> test-plot_pca.R: [2025-11-22 02:07:35] parsing chr5...
> test-plot_pca.R: [2025-11-22 02:07:35] parsing chr7...
> test-plot_pca.R: [2025-11-22 02:07:35] parsing chrX...
> test-plot_pca.R: [2025-11-22 02:07:35] 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: [2025-11-22 02:07:35] creating bsseq object...
> test-plot_pca.R: [2025-11-22 02:07:35] reading in parsed data...
> test-plot_pca.R: [2025-11-22 02:07:35] constructing matrices...
> test-plot_pca.R: [2025-11-22 02:07:36] 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-3.23-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-3.23-bioc/R/site-library/NanoMethViz/sample2_nanopolish.tsv.gz...
> test-tabix_utils.R: guessing file is produced by nanopolish...
> test-tabix_utils.R: [2025-11-22 02:07:49] sorting methylation table
> test-tabix_utils.R: [2025-11-22 02:07:49] compressing methylation table to tabix with index
> test-tabix_utils.R: [2025-11-22 02:07:49] creating intermediate files...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr1...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr2...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr3...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr4...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr5...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr6...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr7...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr8...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr9...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr10...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr11...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr12...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr13...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr14...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr15...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr16...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr17...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr18...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chr19...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chrM...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chrX...
> test-tabix_utils.R: [2025-11-22 02:07:49] parsing chrY...
> test-tabix_utils.R: [2025-11-22 02:07:49] 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: [2025-11-22 02:07:49] creating bsseq object...
> test-tabix_utils.R: [2025-11-22 02:07:49] reading in parsed data...
> test-tabix_utils.R: [2025-11-22 02:07:49] constructing matrices...
> test-tabix_utils.R: [2025-11-22 02:07:50] done
> test-tabix_utils.R: processing /home/biocbuild/bbs-3.23-bioc/R/site-library/NanoMethViz/megalodon_calls.txt.gz...
> test-tabix_utils.R: guessing file is produced by megalodon...
> test-tabix_utils.R: [2025-11-22 02:07:50] sorting methylation table
> test-tabix_utils.R: [2025-11-22 02:07:50] 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 
205.070  11.000 138.798

Example timings

NanoMethViz.Rcheck/NanoMethViz-Ex.timings

nameusersystemelapsed
NanoMethResult-class2.8490.2633.112
bsseq_to_edger0.5870.0340.622
bsseq_to_log_methy_ratio0.9970.0091.006
cluster_regions5.3370.2825.639
create_tabix_file1.0740.0741.149
exons_to_genes0.2420.0060.248
filter_methy17.282 0.18517.466
get_example_exons_mus_musculus0.2190.0030.223
get_exons67.478 3.06370.593
get_exons_homo_sapiens27.977 0.74528.730
get_exons_mus_musculus11.048 0.15411.202
load_example_modbamresult0.2160.0130.229
load_example_nanomethresult0.2160.0020.217
methy0.0020.0000.002
methy_col_names000
methy_to_bsseq0.8200.0110.831
methy_to_edger2.9080.0592.968
modbam_to_tabix0.4430.5350.772
plot_agg_genes4.1700.0984.268
plot_agg_regions5.0070.2305.237
plot_gene9.220.169.38
plot_gene_heatmap7.4650.0177.483
plot_grange6.9400.0326.972
plot_grange_heatmap5.3450.0335.378
plot_mds1.3500.0121.362
plot_pca1.3880.0441.432
plot_region7.3400.1747.514
plot_region_heatmap5.3120.0475.359
plot_violin2.3600.0572.417
query_methy0.3390.0100.349
region_methy_stats1.0170.0181.035