Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2022-01-24 13:06:39 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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

CHECK results for NanoMethViz on tokay2


To the developers/maintainers of the NanoMethViz package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1264/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoMethViz 2.0.0  (landing page)
Shian Su
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/NanoMethViz
git_branch: RELEASE_3_14
git_last_commit: ea1692c
git_last_commit_date: 2021-10-26 13:04:32 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NanoMethViz
Version: 2.0.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NanoMethViz.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings NanoMethViz_2.0.0.tar.gz
StartedAt: 2022-01-23 23:10:36 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 23:21:18 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 642.0 seconds
RetCode: 0
Status:   OK  
CheckDir: NanoMethViz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NanoMethViz.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings NanoMethViz_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/NanoMethViz.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NanoMethViz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NanoMethViz' version '2.0.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 whether package 'NanoMethViz' can be installed ... OK
* checking installed package size ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  'Homo.sapiens' 'Mus.musculus'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'ggthemes'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
karyogram: no visible global function definition for 'binMeans'
karyogram: no visible binding for global variable 'pos'
karyogram: no visible binding for global variable 'methy_prop'
karyogram: no visible global function definition for 'geom_tile'
karyogram: no visible global function definition for 'theme'
karyogram: no visible global function definition for 'margin'
karyogram: no visible global function definition for 'ggtitle'
Undefined global functions or variables:
  binMeans geom_tile ggtitle margin methy_prop pos theme
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/NanoMethViz/libs/i386/NanoMethViz.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/NanoMethViz/libs/x64/NanoMethViz.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
get_exons_homo_sapiens 17.17   2.20   19.38
get_exons_mus_musculus 15.50   0.92   16.42
plot_agg_regions        6.77   0.37    7.14
NanoMethResult-class    4.98   1.98    7.02
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
get_exons_homo_sapiens 21.53   0.75   22.28
get_exons_mus_musculus 17.14   0.35   17.48
plot_agg_regions        8.56   0.11    8.67
NanoMethResult-class    5.19   0.90    6.10
plot_region_heatmap     5.64   0.06    5.71
plot_gene_heatmap       4.97   0.05    5.01
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/NanoMethViz.Rcheck/00check.log'
for details.



Installation output

NanoMethViz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/NanoMethViz_2.0.0.tar.gz && rm -rf NanoMethViz.buildbin-libdir && mkdir NanoMethViz.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NanoMethViz.buildbin-libdir NanoMethViz_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL NanoMethViz_2.0.0.zip && rm NanoMethViz_2.0.0.tar.gz NanoMethViz_2.0.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  2 2676k    2 78087    0     0   500k      0  0:00:05 --:--:--  0:00:05  501k
100 2676k  100 2676k    0     0  3824k      0 --:--:-- --:--:-- --:--:-- 3823k

install for i386

* installing *source* package 'NanoMethViz' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o NanoMethViz.dll tmp.def RcppExports.o convert_methy_to_dss.o utils.o -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/NanoMethViz.buildbin-libdir/00LOCK-NanoMethViz/00new/NanoMethViz/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'NanoMethViz'
    finding HTML links ... done
    NanoMethResult-class                    html  
    NanoMethViz-package                     html  
    bsseq_to_edger                          html  
    bsseq_to_log_methy_ratio                html  
    convert_methy_format                    html  
    create_tabix_file                       html  
    exons-set                               html  
    exons                                   html  
    exons_to_genes                          html  
    get_example_exons_mus_musculus          html  
    get_exons_homo_sapiens                  html  
    get_exons_mus_musculus                  html  
    load_example_nanomethresult             html  
    methy-set                               html  
    methy                                   html  
    methy_col_names                         html  
    methy_to_bsseq                          html  
    plot_agg_regions                        html  
    plot_gene                               html  
    plot_gene_heatmap                       html  
    plot_grange                             html  
    plot_grange_heatmap                     html  
    plot_mds                                html  
    plot_pca                                html  
    plot_region                             html  
    plot_region_heatmap                     html  
    query_exons                             html  
    query_methy                             html  
    raw_methy_to_tabix                      html  
    samples-set                             html  
    samples                                 html  
    sort_methy_file                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'NanoMethViz' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o NanoMethViz.dll tmp.def RcppExports.o convert_methy_to_dss.o utils.o -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/NanoMethViz.buildbin-libdir/NanoMethViz/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NanoMethViz' as NanoMethViz_2.0.0.zip
* DONE (NanoMethViz)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'NanoMethViz' successfully unpacked and MD5 sums checked

Tests output

NanoMethViz.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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")
Loading required package: Mus.musculus
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:NanoMethViz':

    samples

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges

Attaching package: 'GenomicFeatures'

The following object is masked from 'package:NanoMethViz':

    exons

Loading required package: GO.db

Loading required package: org.Mm.eg.db

Loading required package: TxDb.Mmusculus.UCSC.mm10.knownGene
[2022-01-23 23:19:52] creating intermediate files...
[2022-01-23 23:19:52] parsing chr11...
[2022-01-23 23:19:52] parsing chr12...
[2022-01-23 23:19:52] parsing chr18...
[2022-01-23 23:19:52] parsing chr5...
[2022-01-23 23:19:52] parsing chr7...
[2022-01-23 23:19:52] parsing chrX...
[2022-01-23 23:19:52] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_bl6 B6Cast_Prom_1_cast 
[2022-01-23 23:19:52] creating bsseq object...
[2022-01-23 23:19:52] reading in parsed data...
[2022-01-23 23:19:53] constructing matrices...
[2022-01-23 23:19:54] done
[2022-01-23 23:19:54] creating intermediate files...
[2022-01-23 23:19:54] parsing chr11...
[2022-01-23 23:19:54] parsing chr12...
[2022-01-23 23:19:54] parsing chr18...
[2022-01-23 23:19:54] parsing chr5...
[2022-01-23 23:19:54] parsing chr7...
[2022-01-23 23:19:55] parsing chrX...
[2022-01-23 23:19:55] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_bl6 B6Cast_Prom_1_cast 
[2022-01-23 23:19:55] creating bsseq object...
[2022-01-23 23:19:55] reading in parsed data...
[2022-01-23 23:19:55] constructing matrices...
[2022-01-23 23:19:56] done
[2022-01-23 23:19:56] creating intermediate files...
[2022-01-23 23:19:56] parsing chr11...
[2022-01-23 23:19:56] parsing chr12...
[2022-01-23 23:19:56] parsing chr18...
[2022-01-23 23:19:56] parsing chr5...
[2022-01-23 23:19:56] parsing chr7...
[2022-01-23 23:19:56] parsing chrX...
[2022-01-23 23:19:56] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_bl6 B6Cast_Prom_1_cast 
[2022-01-23 23:19:56] creating bsseq object...
[2022-01-23 23:19:56] reading in parsed data...
[2022-01-23 23:19:57] constructing matrices...
[2022-01-23 23:19:58] done
[2022-01-23 23:20:19] creating methylation table
processing C:/Users/biocbuild/bbs-3.14-bioc/R/library/NanoMethViz/sample1_nanopolish.tsv.gz...
guessing file is produced by nanopolish...
processing C:/Users/biocbuild/bbs-3.14-bioc/R/library/NanoMethViz/sample2_nanopolish.tsv.gz...
guessing file is produced by nanopolish...
[2022-01-23 23:20:19] sorting methylation table
[2022-01-23 23:20:20] compressing methylation table to tabix with index
[2022-01-23 23:20:20] creating intermediate files...
[2022-01-23 23:20:20] parsing chr1...
[2022-01-23 23:20:20] parsing chr10...
[2022-01-23 23:20:20] parsing chr11...
[2022-01-23 23:20:20] parsing chr12...
[2022-01-23 23:20:20] parsing chr13...
[2022-01-23 23:20:20] parsing chr14...
[2022-01-23 23:20:20] parsing chr15...
[2022-01-23 23:20:20] parsing chr16...
[2022-01-23 23:20:20] parsing chr17...
[2022-01-23 23:20:20] parsing chr18...
[2022-01-23 23:20:20] parsing chr19...
[2022-01-23 23:20:20] parsing chr2...
[2022-01-23 23:20:20] parsing chr3...
[2022-01-23 23:20:20] parsing chr4...
[2022-01-23 23:20:20] parsing chr5...
[2022-01-23 23:20:20] parsing chr6...
[2022-01-23 23:20:20] parsing chr7...
[2022-01-23 23:20:20] parsing chr8...
[2022-01-23 23:20:20] parsing chr9...
[2022-01-23 23:20:20] parsing chrM...
[2022-01-23 23:20:20] parsing chrX...
[2022-01-23 23:20:20] parsing chrY...
[2022-01-23 23:20:20] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_bl6 B6Cast_Prom_1_cast sample1_nanopolish.tsv sample2_nanopolish.tsv 
[2022-01-23 23:20:20] creating bsseq object...
[2022-01-23 23:20:20] reading in parsed data...
[2022-01-23 23:20:20] constructing matrices...
[2022-01-23 23:20:21] done
[2022-01-23 23:20:21] creating methylation table
processing C:/Users/biocbuild/bbs-3.14-bioc/R/library/NanoMethViz/megalodon_calls.txt.gz...
guessing file is produced by megalodon...
[2022-01-23 23:20:21] sorting methylation table
[2022-01-23 23:20:22] compressing methylation table to tabix with index
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ]
> 
> proc.time()
   user  system elapsed 
  46.64    5.17   50.34 

NanoMethViz.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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")
Loading required package: Mus.musculus
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:NanoMethViz':

    samples

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges

Attaching package: 'GenomicFeatures'

The following object is masked from 'package:NanoMethViz':

    exons

Loading required package: GO.db

Loading required package: org.Mm.eg.db

Loading required package: TxDb.Mmusculus.UCSC.mm10.knownGene
[2022-01-23 23:20:42] creating intermediate files...
[2022-01-23 23:20:42] parsing chr11...
[2022-01-23 23:20:42] parsing chr12...
[2022-01-23 23:20:42] parsing chr18...
[2022-01-23 23:20:42] parsing chr5...
[2022-01-23 23:20:42] parsing chr7...
[2022-01-23 23:20:42] parsing chrX...
[2022-01-23 23:20:42] samples found: B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_cast B6Cast_Prom_1_bl6 B6Cast_Prom_1_cast 
[2022-01-23 23:20:42] creating bsseq object...
[2022-01-23 23:20:42] reading in parsed data...
[2022-01-23 23:20:43] constructing matrices...
[2022-01-23 23:20:43] done
[2022-01-23 23:20:43] creating intermediate files...
[2022-01-23 23:20:43] parsing chr11...
[2022-01-23 23:20:43] parsing chr12...
[2022-01-23 23:20:43] parsing chr18...
[2022-01-23 23:20:43] parsing chr5...
[2022-01-23 23:20:44] parsing chr7...
[2022-01-23 23:20:44] parsing chrX...
[2022-01-23 23:20:44] samples found: B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_cast B6Cast_Prom_1_bl6 B6Cast_Prom_1_cast 
[2022-01-23 23:20:44] creating bsseq object...
[2022-01-23 23:20:44] reading in parsed data...
[2022-01-23 23:20:44] constructing matrices...
[2022-01-23 23:20:45] done
[2022-01-23 23:20:45] creating intermediate files...
[2022-01-23 23:20:45] parsing chr11...
[2022-01-23 23:20:45] parsing chr12...
[2022-01-23 23:20:45] parsing chr18...
[2022-01-23 23:20:45] parsing chr5...
[2022-01-23 23:20:46] parsing chr7...
[2022-01-23 23:20:46] parsing chrX...
[2022-01-23 23:20:46] samples found: B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_cast B6Cast_Prom_1_bl6 B6Cast_Prom_1_cast 
[2022-01-23 23:20:46] creating bsseq object...
[2022-01-23 23:20:46] reading in parsed data...
[2022-01-23 23:20:46] constructing matrices...
[2022-01-23 23:20:48] done
[2022-01-23 23:21:07] creating methylation table
processing C:/Users/biocbuild/bbs-3.14-bioc/R/library/NanoMethViz/sample1_nanopolish.tsv.gz...
guessing file is produced by nanopolish...
processing C:/Users/biocbuild/bbs-3.14-bioc/R/library/NanoMethViz/sample2_nanopolish.tsv.gz...
guessing file is produced by nanopolish...
[2022-01-23 23:21:07] sorting methylation table
[2022-01-23 23:21:08] compressing methylation table to tabix with index
[2022-01-23 23:21:08] creating intermediate files...
[2022-01-23 23:21:08] parsing chr1...
[2022-01-23 23:21:08] parsing chr10...
[2022-01-23 23:21:08] parsing chr11...
[2022-01-23 23:21:08] parsing chr12...
[2022-01-23 23:21:08] parsing chr13...
[2022-01-23 23:21:08] parsing chr14...
[2022-01-23 23:21:08] parsing chr15...
[2022-01-23 23:21:08] parsing chr16...
[2022-01-23 23:21:08] parsing chr17...
[2022-01-23 23:21:08] parsing chr18...
[2022-01-23 23:21:08] parsing chr19...
[2022-01-23 23:21:08] parsing chr2...
[2022-01-23 23:21:08] parsing chr3...
[2022-01-23 23:21:08] parsing chr4...
[2022-01-23 23:21:08] parsing chr5...
[2022-01-23 23:21:08] parsing chr6...
[2022-01-23 23:21:08] parsing chr7...
[2022-01-23 23:21:08] parsing chr8...
[2022-01-23 23:21:08] parsing chr9...
[2022-01-23 23:21:08] parsing chrM...
[2022-01-23 23:21:08] parsing chrX...
[2022-01-23 23:21:08] parsing chrY...
[2022-01-23 23:21:08] samples found: B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_cast B6Cast_Prom_1_bl6 B6Cast_Prom_1_cast sample1_nanopolish.tsv sample2_nanopolish.tsv 
[2022-01-23 23:21:08] creating bsseq object...
[2022-01-23 23:21:08] reading in parsed data...
[2022-01-23 23:21:09] constructing matrices...
[2022-01-23 23:21:10] done
[2022-01-23 23:21:10] creating methylation table
processing C:/Users/biocbuild/bbs-3.14-bioc/R/library/NanoMethViz/megalodon_calls.txt.gz...
guessing file is produced by megalodon...
[2022-01-23 23:21:10] sorting methylation table
[2022-01-23 23:21:10] compressing methylation table to tabix with index
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ]
> 
> proc.time()
   user  system elapsed 
  46.39    2.51   47.76 

Example timings

NanoMethViz.Rcheck/examples_i386/NanoMethViz-Ex.timings

nameusersystemelapsed
NanoMethResult-class4.981.987.02
bsseq_to_edger2.040.212.16
bsseq_to_log_methy_ratio2.960.283.03
create_tabix_file0.940.341.09
exons000
exons_to_genes0.670.080.75
get_example_exons_mus_musculus0.620.220.85
get_exons_homo_sapiens17.17 2.2019.38
get_exons_mus_musculus15.50 0.9216.42
load_example_nanomethresult0.520.030.55
methy000
methy_col_names000
methy_to_bsseq2.140.272.16
plot_agg_regions6.770.377.14
plot_gene2.431.113.55
plot_gene_heatmap4.830.114.94
plot_grange1.350.051.39
plot_grange_heatmap2.360.012.37
plot_mds2.530.202.46
plot_pca2.750.182.54
plot_region2.280.042.33
plot_region_heatmap4.800.084.88
query_methy0.620.030.65
samples000

NanoMethViz.Rcheck/examples_x64/NanoMethViz-Ex.timings

nameusersystemelapsed
NanoMethResult-class5.190.906.10
bsseq_to_edger1.750.211.78
bsseq_to_log_methy_ratio2.360.222.38
create_tabix_file0.940.420.82
exons0.010.000.02
exons_to_genes1.560.081.64
get_example_exons_mus_musculus0.490.010.50
get_exons_homo_sapiens21.53 0.7522.28
get_exons_mus_musculus17.14 0.3517.48
load_example_nanomethresult0.450.060.51
methy000
methy_col_names000
methy_to_bsseq2.160.102.11
plot_agg_regions8.560.118.67
plot_gene2.310.032.35
plot_gene_heatmap4.970.055.01
plot_grange1.500.031.54
plot_grange_heatmap3.090.033.12
plot_mds2.350.172.31
plot_pca2.470.172.35
plot_region2.440.082.52
plot_region_heatmap5.640.065.71
query_methy0.810.100.91
samples0.020.000.01