Package: VariantTools

Version: 1.0.1

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings VariantTools_1.0.1.tar.gz

StartedAt: 2013-03-25 05:27:51 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:34:14 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 382.6 seconds

RetCode: 0

Status:  OK

CheckDir: VariantTools.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/VariantTools.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VariantTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VariantTools’ version ‘1.0.1’
* 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 whether package ‘VariantTools’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 for unstated 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 ... NOTE
BinomialLRFilter : <anonymous>: no visible binding for global variable
  ‘high.quality’
BinomialLRFilter : <anonymous>: no visible binding for global variable
  ‘high.quality.total’
BinomialLRFilter : <anonymous>: no visible binding for global variable
  ‘count’
BinomialLRFilter : <anonymous>: no visible binding for global variable
  ‘count.total’
FisherStrandFilter : <anonymous>: no visible binding for global
  variable ‘count.pos.ref’
FisherStrandFilter : <anonymous>: no visible binding for global
  variable ‘count.neg.ref’
FisherStrandFilter : <anonymous>: no visible binding for global
  variable ‘count.pos’
FisherStrandFilter : <anonymous>: no visible binding for global
  variable ‘count.neg’
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
  global variable ‘high.quality’
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
  global variable ‘high.quality.total’
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
  global variable ‘count’
LowerFrequencyInOtherFilter : <anonymous>: no visible binding for
  global variable ‘count.total’
* 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 examples ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
callSampleSpecificVariants 43.767  0.884  45.564
variantGR2Vcf              11.809  0.304  12.220
callVariants               11.061  0.260  11.355
qaVariants                  5.984  0.144   6.134
tallyVariants               5.780  0.116   5.932
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘VariantTools_unit_tests.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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/VariantTools.Rcheck/00check.log’
for details.

* installing *source* package ‘VariantTools’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘VariantTools.Rnw’ 
** testing if installed package can be loaded

* DONE (VariantTools)

name	user	system	elapsed
callSampleSpecificVariants	43.767	0.884	45.564
callVariants	11.061	0.260	11.355
qaVariants	5.984	0.144	6.134
tallyVariants	5.780	0.116	5.932
variantGR2Vcf	11.809	0.304	12.220