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This page was generated on 2022-10-19 13:23:21 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 merida1


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? 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 1296/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoMethViz 2.2.0  (landing page)
Shian Su
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/NanoMethViz
git_branch: RELEASE_3_15
git_last_commit: ccc98e8
git_last_commit_date: 2022-04-26 12:10:18 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NanoMethViz
Version: 2.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NanoMethViz_2.2.0.tar.gz
StartedAt: 2022-10-19 05:20:06 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 05:32:32 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 745.8 seconds
RetCode: 0
Status:   OK  
CheckDir: NanoMethViz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NanoMethViz_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/NanoMethViz.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.2.0’
* 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cluster_regions: no visible binding for global variable ‘pos’
cluster_regions: no visible global function definition for ‘quantile’
cluster_regions: no visible global function definition for ‘hist’
cluster_regions: no visible global function definition for ‘approxfun’
cluster_regions : sample_methy_grid: no visible global function
  definition for ‘approxfun’
cluster_regions: no visible global function definition for ‘prcomp’
cluster_regions: no visible global function definition for ‘kmeans’
plot_agg_regions: no visible global function definition for ‘sd’
Undefined global functions or variables:
  approxfun hist kmeans pos prcomp quantile sd
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "approxfun", "kmeans", "prcomp", "quantile", "sd")
to your NAMESPACE file.
* 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 25.590  1.320  26.966
get_exons_mus_musculus 23.882  1.083  25.049
plot_gene_heatmap      21.031  0.157  21.226
plot_region_heatmap    20.670  0.172  20.873
plot_agg_regions       12.637  0.121  12.771
NanoMethResult-class    7.052  0.816   7.880
plot_grange_heatmap     7.465  0.052   7.525
cluster_regions         6.590  0.217   6.816
plot_gene               4.953  0.069   5.037
* 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
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/NanoMethViz.Rcheck/00check.log’
for details.



Installation output

NanoMethViz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NanoMethViz
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘NanoMethViz’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.cpp -o utils.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
[2022-10-19 05:31:06] creating intermediate files...
[2022-10-19 05:31:06] parsing chr11...
[2022-10-19 05:31:06] parsing chr12...
[2022-10-19 05:31:06] parsing chr18...
[2022-10-19 05:31:06] parsing chr5...
[2022-10-19 05:31:06] parsing chr7...
[2022-10-19 05:31:07] parsing chrX...
[2022-10-19 05:31:07] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 
[2022-10-19 05:31:07] creating bsseq object...
[2022-10-19 05:31:07] reading in parsed data...
[2022-10-19 05:31:07] constructing matrices...
[2022-10-19 05:31:07] done
[2022-10-19 05:31:09] creating intermediate files...
[2022-10-19 05:31:09] parsing chr11...
[2022-10-19 05:31:09] parsing chr12...
[2022-10-19 05:31:09] parsing chr18...
[2022-10-19 05:31:09] parsing chr5...
[2022-10-19 05:31:09] parsing chr7...
[2022-10-19 05:31:09] parsing chrX...
[2022-10-19 05:31:09] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 
[2022-10-19 05:31:09] creating bsseq object...
[2022-10-19 05:31:09] reading in parsed data...
[2022-10-19 05:31:10] constructing matrices...
[2022-10-19 05:31:10] done
[2022-10-19 05:31:10] creating intermediate files...
[2022-10-19 05:31:10] parsing chr11...
[2022-10-19 05:31:10] parsing chr12...
[2022-10-19 05:31:11] parsing chr18...
[2022-10-19 05:31:11] parsing chr5...
[2022-10-19 05:31:11] parsing chr7...
[2022-10-19 05:31:11] parsing chrX...
[2022-10-19 05:31:11] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 
[2022-10-19 05:31:11] creating bsseq object...
[2022-10-19 05:31:11] reading in parsed data...
[2022-10-19 05:31:11] constructing matrices...
[2022-10-19 05:31:12] done
[2022-10-19 05:31:12] creating intermediate files...
[2022-10-19 05:31:12] parsing chr11...
[2022-10-19 05:31:13] parsing chr12...
[2022-10-19 05:31:13] parsing chr18...
[2022-10-19 05:31:13] parsing chr5...
[2022-10-19 05:31:13] parsing chr7...
[2022-10-19 05:31:13] parsing chrX...
[2022-10-19 05:31:13] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 
[2022-10-19 05:31:13] creating bsseq object...
[2022-10-19 05:31:13] reading in parsed data...
[2022-10-19 05:31:13] constructing matrices...
[2022-10-19 05:31:14] done
processing /Library/Frameworks/R.framework/Versions/4.2/Resources/library/NanoMethViz/sample1_nanopolish.tsv.gz...
guessing file is produced by nanopolish...
processing /Library/Frameworks/R.framework/Versions/4.2/Resources/library/NanoMethViz/sample2_nanopolish.tsv.gz...
guessing file is produced by nanopolish...
[2022-10-19 05:32:20] sorting methylation table
[2022-10-19 05:32:20] compressing methylation table to tabix with index
[2022-10-19 05:32:20] creating intermediate files...
[2022-10-19 05:32:20] parsing chr1...
[2022-10-19 05:32:20] parsing chr2...
[2022-10-19 05:32:20] parsing chr3...
[2022-10-19 05:32:20] parsing chr4...
[2022-10-19 05:32:20] parsing chr5...
[2022-10-19 05:32:20] parsing chr6...
[2022-10-19 05:32:20] parsing chr7...
[2022-10-19 05:32:20] parsing chr8...
[2022-10-19 05:32:20] parsing chr9...
[2022-10-19 05:32:20] parsing chr10...
[2022-10-19 05:32:20] parsing chr11...
[2022-10-19 05:32:20] parsing chr12...
[2022-10-19 05:32:20] parsing chr13...
[2022-10-19 05:32:20] parsing chr14...
[2022-10-19 05:32:20] parsing chr15...
[2022-10-19 05:32:20] parsing chr16...
[2022-10-19 05:32:20] parsing chr17...
[2022-10-19 05:32:20] parsing chr18...
[2022-10-19 05:32:20] parsing chr19...
[2022-10-19 05:32:20] parsing chrM...
[2022-10-19 05:32:20] parsing chrX...
[2022-10-19 05:32:20] parsing chrY...
[2022-10-19 05:32:20] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 sample1_nanopolish.tsv sample2_nanopolish.tsv 
[2022-10-19 05:32:20] creating bsseq object...
[2022-10-19 05:32:20] reading in parsed data...
[2022-10-19 05:32:20] constructing matrices...
[2022-10-19 05:32:21] done
processing /Library/Frameworks/R.framework/Versions/4.2/Resources/library/NanoMethViz/megalodon_calls.txt.gz...
guessing file is produced by megalodon...
[2022-10-19 05:32:22] sorting methylation table
[2022-10-19 05:32:22] compressing methylation table to tabix with index
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 51 ]

[ FAIL 0 | WARN 9 | SKIP 0 | PASS 51 ]
> 
> proc.time()
   user  system elapsed 
107.857   2.676 110.146 

Example timings

NanoMethViz.Rcheck/NanoMethViz-Ex.timings

nameusersystemelapsed
NanoMethResult-class7.0520.8167.880
bsseq_to_edger1.6130.0721.636
bsseq_to_log_methy_ratio3.7360.0993.767
cluster_regions6.5900.2176.816
create_tabix_file0.3250.0340.362
exons0.0040.0000.004
exons_to_genes0.9750.0251.001
filter_methy3.8120.1503.979
get_example_exons_mus_musculus0.8980.0250.926
get_exons_homo_sapiens25.590 1.32026.966
get_exons_mus_musculus23.882 1.08325.049
load_example_nanomethresult0.9470.0290.977
methy0.0000.0000.001
methy_col_names0.0010.0000.000
methy_to_bsseq2.4700.0882.489
methy_to_edger2.8470.0982.833
plot_agg_regions12.637 0.12112.771
plot_gene4.9530.0695.037
plot_gene_heatmap21.031 0.15721.226
plot_grange2.7170.0382.760
plot_grange_heatmap7.4650.0527.525
plot_mds3.3340.0903.291
plot_pca3.3510.0783.273
plot_region4.6510.0554.717
plot_region_heatmap20.670 0.17220.873
query_methy1.1930.0251.219
region_methy_stats2.7240.0362.763
samples0.0010.0000.002