BioC 3.5: CHECK report for TVTB on toluca2

Package: TVTB

Version: 1.1.12

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TVTB_1.1.12.tar.gz

StartedAt: 2017-04-23 11:00:02 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 11:07:15 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 433.0 seconds

RetCode: 0

Status:  OK

CheckDir: TVTB.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TVTB_1.1.12.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TVTB.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.12’
* 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 6.524  0.222   8.111
* 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	0.005	0.001	0.005
TVTBParam-class	0.353	0.015	0.380
VcfBasicRules-class	3.908	0.118	4.917
VcfFilterRules-class	2.252	0.122	3.003
addCountGenos-methods	0.550	0.076	0.783
addFrequencies-methods	0.513	0.070	0.585
addOverallFrequencies-methods	0.489	0.081	0.570
addPhenoLevelFrequencies-methods	0.588	0.074	0.662
autodetectGenotypes	0.447	0.072	0.520
countGenos-methods	0.469	0.076	0.546
dropInfo-methods	0.506	0.075	0.582
pairsInfo-methods	3.957	0.086	4.296
plotInfo-methods	6.524	0.222	8.111
readVcf-methods	0.379	0.026	0.556
tSVE	0.001	0.000	0.001
variantsInSamples-methods	0.546	0.084	0.748
vepInPhenoLevel-methods	0.783	0.079	0.874