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CHECK report for methyvim on malbec2

This page was generated on 2020-06-07 15:04:10 -0400 (Sun, 07 Jun 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE methyvim PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1067/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methyvim 1.10.0
Nima Hejazi
Snapshot Date: 2020-06-06 16:50:24 -0400 (Sat, 06 Jun 2020)
URL: https://git.bioconductor.org/packages/methyvim
Branch: RELEASE_3_11
Last Commit: 9bcf5ef
Last Changed Date: 2020-04-27 15:11:00 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: methyvim
Version: 1.10.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:methyvim.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings methyvim_1.10.0.tar.gz
StartedAt: 2020-06-07 05:49:33 -0400 (Sun, 07 Jun 2020)
EndedAt: 2020-06-07 05:55:57 -0400 (Sun, 07 Jun 2020)
EllapsedTime: 384.2 seconds
RetCode: 0
Status:  OK 
CheckDir: methyvim.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:methyvim.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings methyvim_1.10.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/methyvim.Rcheck’
* using R version 4.0.0 (2020-04-24)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methyvim/DESCRIPTION’ ... OK
* this is package ‘methyvim’ version ‘1.10.0’
* 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 ‘methyvim’ 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 ... OK
* 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 ... NOTE
Package unavailable to check Rd xrefs: ‘tmle.npvi’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
methyheat      19.731  0.569  20.346
plot.methytmle 14.363  0.056  14.420
methyvolc      12.884  0.064  12.951
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/methyvim.Rcheck/00check.log’
for details.



Installation output

methyvim.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL methyvim
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘methyvim’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (methyvim)

Tests output

methyvim.Rcheck/tests/testthat.Rout


R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 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(methyvim)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
methyvim v1.10.0: Targeted, Robust, and Model-free Differential Methylation Analysis
> 
> set.seed(43719)
> test_check("methyvim")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 46 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 28.445   1.498  29.945 

Example timings

methyvim.Rcheck/methyvim-Ex.timings

nameusersystemelapsed
fdr_msa0.0020.0000.002
methyheat19.731 0.56920.346
methytmle-class0.6110.0170.627
methyvim1.9130.0121.988
methyvolc12.884 0.06412.951
plot.methytmle14.363 0.05614.420