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This page was generated on 2022-01-14 13:05:29 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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 nebbiolo2


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: 2022-01-13 01:55:04 -0500 (Thu, 13 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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings NanoMethViz_2.0.0.tar.gz
StartedAt: 2022-01-13 08:41:30 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 08:46:58 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 328.2 seconds
RetCode: 0
Status:   OK  
CheckDir: NanoMethViz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings NanoMethViz_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/NanoMethViz.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 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_homo_sapiens 16.719  0.949  17.667
get_exons_mus_musculus 13.280  0.447  13.729
plot_agg_regions        4.993  0.072   5.066
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/NanoMethViz.Rcheck/00check.log’
for details.



Installation output

NanoMethViz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL NanoMethViz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘NanoMethViz’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o utils.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-NanoMethViz/00new/NanoMethViz/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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

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
[2022-01-13 08:46:34] creating intermediate files...
[2022-01-13 08:46:34] parsing chr11...
[2022-01-13 08:46:34] parsing chr12...
[2022-01-13 08:46:34] parsing chr18...
[2022-01-13 08:46:34] parsing chr5...
[2022-01-13 08:46:34] parsing chr7...
[2022-01-13 08:46:34] parsing chrX...
[2022-01-13 08:46:34] 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 
[2022-01-13 08:46:34] creating bsseq object...
[2022-01-13 08:46:34] reading in parsed data...
[2022-01-13 08:46:34] constructing matrices...
[2022-01-13 08:46:35] done
[2022-01-13 08:46:35] creating intermediate files...
[2022-01-13 08:46:35] parsing chr11...
[2022-01-13 08:46:35] parsing chr12...
[2022-01-13 08:46:35] parsing chr18...
[2022-01-13 08:46:35] parsing chr5...
[2022-01-13 08:46:35] parsing chr7...
[2022-01-13 08:46:35] parsing chrX...
[2022-01-13 08:46:35] 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 
[2022-01-13 08:46:35] creating bsseq object...
[2022-01-13 08:46:35] reading in parsed data...
[2022-01-13 08:46:35] constructing matrices...
[2022-01-13 08:46:36] done
[2022-01-13 08:46:37] creating intermediate files...
[2022-01-13 08:46:37] parsing chr11...
[2022-01-13 08:46:37] parsing chr12...
[2022-01-13 08:46:37] parsing chr18...
[2022-01-13 08:46:37] parsing chr5...
[2022-01-13 08:46:37] parsing chr7...
[2022-01-13 08:46:37] parsing chrX...
[2022-01-13 08:46:37] 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 
[2022-01-13 08:46:37] creating bsseq object...
[2022-01-13 08:46:37] reading in parsed data...
[2022-01-13 08:46:37] constructing matrices...
[2022-01-13 08:46:37] done
processing /home/biocbuild/bbs-3.14-bioc/R/library/NanoMethViz/sample1_nanopolish.tsv.gz...
guessing file is produced by nanopolish...
processing /home/biocbuild/bbs-3.14-bioc/R/library/NanoMethViz/sample2_nanopolish.tsv.gz...
guessing file is produced by nanopolish...
[2022-01-13 08:46:55] sorting methylation table
[2022-01-13 08:46:55] compressing methylation table to tabix with index
[2022-01-13 08:46:55] creating intermediate files...
[2022-01-13 08:46:55] parsing chr1...
[2022-01-13 08:46:55] parsing chr2...
[2022-01-13 08:46:55] parsing chr3...
[2022-01-13 08:46:55] parsing chr4...
[2022-01-13 08:46:55] parsing chr5...
[2022-01-13 08:46:55] parsing chr6...
[2022-01-13 08:46:55] parsing chr7...
[2022-01-13 08:46:55] parsing chr8...
[2022-01-13 08:46:55] parsing chr9...
[2022-01-13 08:46:55] parsing chr10...
[2022-01-13 08:46:55] parsing chr11...
[2022-01-13 08:46:55] parsing chr12...
[2022-01-13 08:46:55] parsing chr13...
[2022-01-13 08:46:55] parsing chr14...
[2022-01-13 08:46:55] parsing chr15...
[2022-01-13 08:46:55] parsing chr16...
[2022-01-13 08:46:55] parsing chr17...
[2022-01-13 08:46:55] parsing chr18...
[2022-01-13 08:46:55] parsing chr19...
[2022-01-13 08:46:55] parsing chrM...
[2022-01-13 08:46:55] parsing chrX...
[2022-01-13 08:46:55] parsing chrY...
[2022-01-13 08:46:55] 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 
[2022-01-13 08:46:55] creating bsseq object...
[2022-01-13 08:46:55] reading in parsed data...
[2022-01-13 08:46:55] constructing matrices...
[2022-01-13 08:46:55] done
processing /home/biocbuild/bbs-3.14-bioc/R/library/NanoMethViz/megalodon_calls.txt.gz...
guessing file is produced by megalodon...
[2022-01-13 08:46:55] sorting methylation table
[2022-01-13 08:46:55] compressing methylation table to tabix with index
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ]
> 
> proc.time()
   user  system elapsed 
 36.091   1.691  37.219 

Example timings

NanoMethViz.Rcheck/NanoMethViz-Ex.timings

nameusersystemelapsed
NanoMethResult-class4.1040.2244.329
bsseq_to_edger0.8300.0890.872
bsseq_to_log_methy_ratio2.3610.2322.488
create_tabix_file0.1460.0040.151
exons0.0020.0000.002
exons_to_genes0.4930.0200.513
get_example_exons_mus_musculus0.4790.0200.500
get_exons_homo_sapiens16.719 0.94917.667
get_exons_mus_musculus13.280 0.44713.729
load_example_nanomethresult0.4330.0040.437
methy0.0010.0000.001
methy_col_names0.0010.0000.000
methy_to_bsseq1.6830.1051.636
plot_agg_regions4.9930.0725.066
plot_gene2.1200.0242.143
plot_gene_heatmap4.2660.1044.371
plot_grange1.2880.0281.316
plot_grange_heatmap2.2120.0202.231
plot_mds1.7660.0701.639
plot_pca1.8290.0721.610
plot_region1.8980.0401.938
plot_region_heatmap4.2110.0324.242
query_methy0.5840.0160.599
samples0.0000.0010.001