BioC 3.6: CHECK report for TVTB on malbec1

Package: TVTB

Version: 1.3.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TVTB_1.3.1.tar.gz

StartedAt: 2017-08-16 02:55:17 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 03:00:28 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 311.5 seconds

RetCode: 0

Status:  OK

CheckDir: TVTB.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TVTB_1.3.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/TVTB.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.3.1’
* 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
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotInfo-methods 4.732   0.08   5.568
* 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	0.000	0.000	0.003
TVTBParam-class	0.232	0.000	0.234
VcfBasicRules-class	3.080	0.056	3.138
VcfFilterRules-class	1.420	0.012	1.435
addCountGenos-methods	0.352	0.016	0.366
addFrequencies-methods	0.328	0.012	0.341
addOverallFrequencies-methods	0.328	0.008	0.335
addPhenoLevelFrequencies-methods	0.416	0.012	0.426
autodetectGenotypes	0.288	0.020	0.310
countGenos-methods	0.316	0.020	0.335
dropInfo-methods	0.344	0.008	0.353
pairsInfo-methods	2.756	0.012	2.768
plotInfo-methods	4.732	0.080	5.568
readVcf-methods	0.256	0.000	0.259
tSVE	0	0	0
variantsInSamples-methods	0.320	0.012	0.333
vepInPhenoLevel-methods	0.524	0.020	0.548