Shian Su
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 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 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:05:40 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 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 | ||||
|
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. |
| Package 1264/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NanoMethViz 2.0.0 (landing page) Shian Su
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| 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: 2022-04-12 08:25:52 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 08:32:01 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 369.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NanoMethViz.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 4.1.3 (2022-03-10)
* 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 16.409 0.947 17.357
get_exons_mus_musculus 13.982 0.416 14.400
plot_gene_heatmap 10.266 0.123 10.391
plot_region_heatmap 10.116 0.083 10.199
plot_agg_regions 6.074 0.052 6.126
plot_grange_heatmap 5.146 0.044 5.190
* 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.
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)
NanoMethViz.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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
[2022-04-12 08:31:20] creating intermediate files...
[2022-04-12 08:31:20] parsing chr11...
[2022-04-12 08:31:20] parsing chr12...
[2022-04-12 08:31:20] parsing chr18...
[2022-04-12 08:31:20] parsing chr5...
[2022-04-12 08:31:20] parsing chr7...
[2022-04-12 08:31:20] parsing chrX...
[2022-04-12 08:31:20] 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
[2022-04-12 08:31:20] creating bsseq object...
[2022-04-12 08:31:20] reading in parsed data...
[2022-04-12 08:31:20] constructing matrices...
[2022-04-12 08:31:21] done
[2022-04-12 08:31:21] creating intermediate files...
[2022-04-12 08:31:21] parsing chr11...
[2022-04-12 08:31:21] parsing chr12...
[2022-04-12 08:31:21] parsing chr18...
[2022-04-12 08:31:21] parsing chr5...
[2022-04-12 08:31:21] parsing chr7...
[2022-04-12 08:31:21] parsing chrX...
[2022-04-12 08:31:21] 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
[2022-04-12 08:31:21] creating bsseq object...
[2022-04-12 08:31:21] reading in parsed data...
[2022-04-12 08:31:21] constructing matrices...
[2022-04-12 08:31:22] done
[2022-04-12 08:31:22] creating intermediate files...
[2022-04-12 08:31:22] parsing chr11...
[2022-04-12 08:31:22] parsing chr12...
[2022-04-12 08:31:22] parsing chr18...
[2022-04-12 08:31:22] parsing chr5...
[2022-04-12 08:31:22] parsing chr7...
[2022-04-12 08:31:22] parsing chrX...
[2022-04-12 08:31:22] 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
[2022-04-12 08:31:22] creating bsseq object...
[2022-04-12 08:31:22] reading in parsed data...
[2022-04-12 08:31:22] constructing matrices...
[2022-04-12 08:31:23] 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...
[2022-04-12 08:31:58] sorting methylation table
[2022-04-12 08:31:58] compressing methylation table to tabix with index
[2022-04-12 08:31:58] creating intermediate files...
[2022-04-12 08:31:58] parsing chr1...
[2022-04-12 08:31:58] parsing chr2...
[2022-04-12 08:31:58] parsing chr3...
[2022-04-12 08:31:58] parsing chr4...
[2022-04-12 08:31:58] parsing chr5...
[2022-04-12 08:31:58] parsing chr6...
[2022-04-12 08:31:58] parsing chr7...
[2022-04-12 08:31:58] parsing chr8...
[2022-04-12 08:31:58] parsing chr9...
[2022-04-12 08:31:58] parsing chr10...
[2022-04-12 08:31:58] parsing chr11...
[2022-04-12 08:31:58] parsing chr12...
[2022-04-12 08:31:58] parsing chr13...
[2022-04-12 08:31:58] parsing chr14...
[2022-04-12 08:31:58] parsing chr15...
[2022-04-12 08:31:58] parsing chr16...
[2022-04-12 08:31:58] parsing chr17...
[2022-04-12 08:31:58] parsing chr18...
[2022-04-12 08:31:58] parsing chr19...
[2022-04-12 08:31:58] parsing chrM...
[2022-04-12 08:31:58] parsing chrX...
[2022-04-12 08:31:58] parsing chrY...
[2022-04-12 08:31:58] 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
[2022-04-12 08:31:58] creating bsseq object...
[2022-04-12 08:31:58] reading in parsed data...
[2022-04-12 08:31:58] constructing matrices...
[2022-04-12 08:31:58] done
processing /home/biocbuild/bbs-3.14-bioc/R/library/NanoMethViz/megalodon_calls.txt.gz...
guessing file is produced by megalodon...
[2022-04-12 08:31:58] sorting methylation table
[2022-04-12 08:31:59] compressing methylation table to tabix with index
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ]
>
> proc.time()
user system elapsed
53.448 2.013 55.018
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
| name | user | system | elapsed | |
| NanoMethResult-class | 4.242 | 0.264 | 4.507 | |
| bsseq_to_edger | 0.862 | 0.098 | 0.911 | |
| bsseq_to_log_methy_ratio | 1.435 | 0.120 | 1.451 | |
| create_tabix_file | 0.151 | 0.005 | 0.156 | |
| exons | 0.003 | 0.000 | 0.002 | |
| exons_to_genes | 0.493 | 0.008 | 0.501 | |
| get_example_exons_mus_musculus | 0.624 | 0.012 | 0.635 | |
| get_exons_homo_sapiens | 16.409 | 0.947 | 17.357 | |
| get_exons_mus_musculus | 13.982 | 0.416 | 14.400 | |
| load_example_nanomethresult | 0.481 | 0.000 | 0.481 | |
| methy | 0.000 | 0.000 | 0.001 | |
| methy_col_names | 0 | 0 | 0 | |
| methy_to_bsseq | 1.345 | 0.102 | 1.286 | |
| plot_agg_regions | 6.074 | 0.052 | 6.126 | |
| plot_gene | 2.410 | 0.039 | 2.450 | |
| plot_gene_heatmap | 10.266 | 0.123 | 10.391 | |
| plot_grange | 1.491 | 0.032 | 1.522 | |
| plot_grange_heatmap | 5.146 | 0.044 | 5.190 | |
| plot_mds | 1.783 | 0.074 | 1.642 | |
| plot_pca | 1.891 | 0.099 | 1.702 | |
| plot_region | 2.208 | 0.016 | 2.224 | |
| plot_region_heatmap | 10.116 | 0.083 | 10.199 | |
| query_methy | 0.633 | 0.004 | 0.637 | |
| samples | 0.001 | 0.000 | 0.001 | |