Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2022-01-28 11:06:31 -0500 (Fri, 28 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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 nebbiolo1


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 1260/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoMethViz 2.1.2  (landing page)
Shian Su
Snapshot Date: 2022-01-27 13:55:17 -0500 (Thu, 27 Jan 2022)
git_url: https://git.bioconductor.org/packages/NanoMethViz
git_branch: master
git_last_commit: 32400e1
git_last_commit_date: 2021-12-07 01:06:18 -0500 (Tue, 07 Dec 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'S4Vectors' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NanoMethViz
Version: 2.1.2
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings NanoMethViz_2.1.2.tar.gz
StartedAt: 2022-01-27 20:11:21 -0500 (Thu, 27 Jan 2022)
EndedAt: 2022-01-27 20:17:41 -0500 (Thu, 27 Jan 2022)
EllapsedTime: 380.1 seconds
RetCode: 0
Status:   OK  
CheckDir: NanoMethViz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings NanoMethViz_2.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/NanoMethViz.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘2.1.2’
* 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 ... OK
* 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 16.826  0.979  17.805
get_exons_mus_musculus 13.911  0.676  14.588
plot_gene_heatmap      10.565  0.172  10.737
plot_region_heatmap    10.122  0.076  10.198
plot_agg_regions        7.712  0.115   7.828
plot_grange_heatmap     5.148  0.104   5.252
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/NanoMethViz.Rcheck/00check.log’
for details.



Installation output

NanoMethViz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL NanoMethViz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘NanoMethViz’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-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-3.15-bioc/R/lib -L/usr/local/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o utils.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
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
[2022-01-27 20:16:59] creating intermediate files...
[2022-01-27 20:16:59] parsing chr11...
[2022-01-27 20:16:59] parsing chr12...
[2022-01-27 20:16:59] parsing chr18...
[2022-01-27 20:16:59] parsing chr5...
[2022-01-27 20:16:59] parsing chr7...
[2022-01-27 20:16:59] parsing chrX...
[2022-01-27 20:16:59] 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 
[2022-01-27 20:16:59] creating bsseq object...
[2022-01-27 20:16:59] reading in parsed data...
[2022-01-27 20:16:59] constructing matrices...
[2022-01-27 20:17:00] done
[2022-01-27 20:17:00] creating intermediate files...
[2022-01-27 20:17:00] parsing chr11...
[2022-01-27 20:17:00] parsing chr12...
[2022-01-27 20:17:00] parsing chr18...
[2022-01-27 20:17:00] parsing chr5...
[2022-01-27 20:17:00] parsing chr7...
[2022-01-27 20:17:00] parsing chrX...
[2022-01-27 20:17:00] 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 
[2022-01-27 20:17:00] creating bsseq object...
[2022-01-27 20:17:00] reading in parsed data...
[2022-01-27 20:17:00] constructing matrices...
[2022-01-27 20:17:00] done
[2022-01-27 20:17:01] creating intermediate files...
[2022-01-27 20:17:01] parsing chr11...
[2022-01-27 20:17:01] parsing chr12...
[2022-01-27 20:17:01] parsing chr18...
[2022-01-27 20:17:01] parsing chr5...
[2022-01-27 20:17:01] parsing chr7...
[2022-01-27 20:17:01] parsing chrX...
[2022-01-27 20:17:01] 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 
[2022-01-27 20:17:01] creating bsseq object...
[2022-01-27 20:17:01] reading in parsed data...
[2022-01-27 20:17:01] constructing matrices...
[2022-01-27 20:17:02] done
processing /home/biocbuild/bbs-3.15-bioc/R/library/NanoMethViz/sample1_nanopolish.tsv.gz...
guessing file is produced by nanopolish...
processing /home/biocbuild/bbs-3.15-bioc/R/library/NanoMethViz/sample2_nanopolish.tsv.gz...
guessing file is produced by nanopolish...
[2022-01-27 20:17:36] sorting methylation table
[2022-01-27 20:17:36] compressing methylation table to tabix with index
[2022-01-27 20:17:36] creating intermediate files...
[2022-01-27 20:17:36] parsing chr1...
[2022-01-27 20:17:36] parsing chr2...
[2022-01-27 20:17:36] parsing chr3...
[2022-01-27 20:17:36] parsing chr4...
[2022-01-27 20:17:36] parsing chr5...
[2022-01-27 20:17:36] parsing chr6...
[2022-01-27 20:17:36] parsing chr7...
[2022-01-27 20:17:36] parsing chr8...
[2022-01-27 20:17:36] parsing chr9...
[2022-01-27 20:17:36] parsing chr10...
[2022-01-27 20:17:36] parsing chr11...
[2022-01-27 20:17:36] parsing chr12...
[2022-01-27 20:17:36] parsing chr13...
[2022-01-27 20:17:36] parsing chr14...
[2022-01-27 20:17:36] parsing chr15...
[2022-01-27 20:17:36] parsing chr16...
[2022-01-27 20:17:36] parsing chr17...
[2022-01-27 20:17:36] parsing chr18...
[2022-01-27 20:17:36] parsing chr19...
[2022-01-27 20:17:36] parsing chrM...
[2022-01-27 20:17:36] parsing chrX...
[2022-01-27 20:17:36] parsing chrY...
[2022-01-27 20:17:36] 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 
[2022-01-27 20:17:36] creating bsseq object...
[2022-01-27 20:17:36] reading in parsed data...
[2022-01-27 20:17:36] constructing matrices...
[2022-01-27 20:17:36] done
processing /home/biocbuild/bbs-3.15-bioc/R/library/NanoMethViz/megalodon_calls.txt.gz...
guessing file is produced by megalodon...
[2022-01-27 20:17:36] sorting methylation table
[2022-01-27 20:17:36] compressing methylation table to tabix with index
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ]
> 
> proc.time()
   user  system elapsed 
 54.798   2.218  56.567 

Example timings

NanoMethViz.Rcheck/NanoMethViz-Ex.timings

nameusersystemelapsed
NanoMethResult-class4.2420.3674.613
bsseq_to_edger0.8170.1080.873
bsseq_to_log_methy_ratio1.5950.0971.595
create_tabix_file0.1620.0180.182
exons0.0000.0030.003
exons_to_genes0.5470.0050.551
get_example_exons_mus_musculus1.5200.0601.579
get_exons_homo_sapiens16.826 0.97917.805
get_exons_mus_musculus13.911 0.67614.588
load_example_nanomethresult0.6040.0040.608
methy0.0010.0000.001
methy_col_names000
methy_to_bsseq1.4300.1471.451
plot_agg_regions7.7120.1157.828
plot_gene2.6420.0362.678
plot_gene_heatmap10.565 0.17210.737
plot_grange1.4420.0281.470
plot_grange_heatmap5.1480.1045.252
plot_mds1.7160.1231.653
plot_pca1.9560.1211.800
plot_region2.4250.0472.474
plot_region_heatmap10.122 0.07610.198
query_methy0.6810.0320.713
samples0.0000.0010.001