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CHECK report for RVS on malbec1

This page was generated on 2021-05-06 12:28:57 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the RVS package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1606/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RVS 1.12.0  (landing page)
Thomas Sherman
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/RVS
Branch: RELEASE_3_12
Last Commit: a28e783
Last Changed Date: 2020-10-27 11:26:21 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: RVS
Version: 1.12.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:RVS.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings RVS_1.12.0.tar.gz
StartedAt: 2021-05-06 05:36:26 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:40:43 -0400 (Thu, 06 May 2021)
EllapsedTime: 256.9 seconds
RetCode: 0
Status:   OK  
CheckDir: RVS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:RVS.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings RVS_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/RVS.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RVS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RVS’ version ‘1.12.0’
* 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 ‘RVS’ 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
RVgene 16.832  0.312   19.01
* 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: OK


Installation output

RVS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL RVS
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘RVS’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (RVS)

Tests output

RVS.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(RVS)
> 
> test_check('RVS')
Founder  2  subped size  20 
Founder  4  subped size  11 
Founder  5  subped size  16 
Founder  9  subped size  5 
Founder  13  subped size  5 
Founder  14  subped size  3 
Founder  16  subped size  5 
[1] 0.01873 0.49970 0.48150
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (2)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 113 ]
> 
> proc.time()
   user  system elapsed 
111.344   0.252 111.911 

Example timings

RVS.Rcheck/RVS-Ex.timings

nameusersystemelapsed
ComputeKinshipPropCoef-methods0.0360.0040.039
GeneDrop0.0040.0000.001
RVgene16.832 0.31219.010
RVsharing-methods0.0640.0000.065
SnpMatrixToCount0.0000.0000.003
get.psubset0.9080.0720.985
multipleFamilyPValue0.9960.0041.003
ped2trio000
processPedigree-methods0.0040.0000.003