BioC 3.5: CHECK report for TVTB on veracruz2

Package: TVTB

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TVTB_1.2.0.tar.gz

StartedAt: 2017-10-18 09:57:26 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 10:03:51 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 384.6 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TVTB.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.2.0’
* 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 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 5.715  0.286   7.154
* 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	0.005
TVTBParam-class	0.387	0.018	0.466
VcfBasicRules-class	3.883	0.154	4.671
VcfFilterRules-class	2.108	0.121	2.654
addCountGenos-methods	1.119	0.094	1.392
addFrequencies-methods	0.457	0.080	0.576
addOverallFrequencies-methods	0.447	0.078	0.571
addPhenoLevelFrequencies-methods	0.616	0.085	0.835
autodetectGenotypes	0.473	0.084	0.644
countGenos-methods	0.475	0.080	0.643
dropInfo-methods	0.530	0.085	0.706
pairsInfo-methods	3.964	0.100	4.761
plotInfo-methods	5.715	0.286	7.154
readVcf-methods	0.370	0.030	0.498
tSVE	0.000	0.000	0.001
variantsInSamples-methods	0.478	0.081	0.736
vepInPhenoLevel-methods	0.628	0.073	0.773