BioC 3.4: CHECK report for TVTB on malbec1

Package: TVTB

Version: 1.0.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings TVTB_1.0.2.tar.gz

StartedAt: 2017-04-15 01:45:10 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:49:32 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 262.7 seconds

RetCode: 0

Status:  OK

CheckDir: TVTB.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings TVTB_1.0.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/TVTB.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.2’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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

* installing *source* package ‘TVTB’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TVTB)

name	user	system	elapsed
Genotypes-class	0.004	0.000	0.003
TVTBParam-class	0.096	0.000	0.095
VcfBasicRules-class	1.096	0.024	1.119
VcfFilterRules-class	0.908	0.012	0.922
addCountGenos-methods	0.384	0.008	0.392
addFrequencies-methods	0.932	0.008	0.945
addOverallFrequencies-methods	0.336	0.024	0.363
addPhenoLevelFrequencies-methods	0.364	0.008	0.373
countGenos-methods	0.320	0.012	0.332
dropInfo-methods	0.360	0.004	0.365
readVcf-methods	0.252	0.004	0.259
tSVE	0	0	0
variantsInSamples-methods	0.344	0.004	0.348
vepInPhenoLevel-methods	0.356	0.024	0.379