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CHECK report for TVTB on celaya2

This page was generated on 2019-10-16 12:59:02 -0400 (Wed, 16 Oct 2019).

Package 1689/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TVTB 1.10.0
Kevin Rue-Albrecht
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/TVTB
Branch: RELEASE_3_9
Last Commit: 9d486bd
Last Changed Date: 2019-05-02 11:54:04 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: TVTB
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TVTB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TVTB_1.10.0.tar.gz
StartedAt: 2019-10-16 07:35:36 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:44:32 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 536.3 seconds
RetCode: 0
Status:  OK 
CheckDir: TVTB.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TVTB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TVTB_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TVTB.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TVTB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TVTB’ version ‘1.10.0’
* 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 ‘TVTB’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotInfo-methods 9.429  0.623  10.156
* 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

TVTB.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TVTB
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘TVTB’ ...
** 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 (TVTB)

Tests output

TVTB.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(TVTB)
> 
> test_check("TVTB")
Class: Genotypes
  @ref (hom. ref.): "REF" {0/0}
  @het (heter.)   : "HET" {0/1, 1/0}
  @alt (hom. alt.): "ALT" {1/1}class: TVTBparam
@genos: class: Genotypes
    @ref (hom. ref.): "REF" {0|0}
    @het (heter.): "HET" {0|1, 1|0}
    @alt (hom. alt.): "ALT" {1|1}
  @ranges: 0 GRanges on 0 sequence(s)
  @aaf (alt. allele freq.): "AAF"
  @maf (minor allele freq.): "MAF"
  @vep (Ensembl VEP key): "CSQ"
  @svp: 
  @bp: 
rs199764262 rs189224179 rs373895181 rs201294244 rs199841831 rs182642366 
       TRUE       FALSE       FALSE       FALSE       FALSE       FALSE 
  rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672 
       TRUE        TRUE       FALSE       FALSE        TRUE       FALSE 
rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382 
       TRUE       FALSE        TRUE        TRUE       FALSE       FALSE 
rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600 
      FALSE       FALSE       FALSE       FALSE       FALSE       FALSE 
rs550201688 rs565338261 rs201239799 rs200461129 rs146726548 
      FALSE       FALSE       FALSE       FALSE        TRUE 
rs199764262 rs189224179 rs373895181 rs201294244 rs199841831 rs182642366 
      FALSE       FALSE       FALSE       FALSE       FALSE       FALSE 
  rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672 
      FALSE       FALSE       FALSE       FALSE       FALSE       FALSE 
rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382 
      FALSE       FALSE       FALSE       FALSE       FALSE       FALSE 
rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600 
      FALSE       FALSE       FALSE       FALSE       FALSE       FALSE 
rs550201688 rs565338261 rs201239799 rs200461129 rs146726548 
      FALSE       FALSE       FALSE       FALSE       FALSE 
rs199764262 rs189224179 rs373895181 rs201294244 rs199841831 rs182642366 
       TRUE       FALSE       FALSE       FALSE       FALSE       FALSE 
  rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672 
       TRUE        TRUE       FALSE       FALSE        TRUE       FALSE 
rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382 
       TRUE       FALSE        TRUE        TRUE       FALSE       FALSE 
rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600 
      FALSE       FALSE       FALSE       FALSE       FALSE       FALSE 
rs550201688 rs565338261 rs201239799 rs200461129 rs146726548 
      FALSE       FALSE       FALSE       FALSE        TRUE 
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 227 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 55.475   5.229  60.796 

Example timings

TVTB.Rcheck/TVTB-Ex.timings

nameusersystemelapsed
Genotypes-class0.0040.0010.005
TVTBParam-class0.2960.0140.310
VcfBasicRules-class3.7840.4564.244
VcfFilterRules-class2.2650.2142.482
addCountGenos-methods1.2150.2131.429
addFrequencies-methods1.0460.2041.251
addOverallFrequencies-methods1.1180.1931.312
addPhenoLevelFrequencies-methods1.0290.2221.255
autodetectGenotypes0.9800.2271.206
countGenos-methods0.9050.2061.121
dropInfo-methods1.1210.1941.319
pairsInfo-methods2.2690.2342.506
plotInfo-methods 9.429 0.62310.156
readVcf-methods0.5660.0030.573
tSVE000
variantsInSamples-methods0.9470.2351.182
vepInPhenoLevel-methods1.2010.2651.469