BioC 2.12: CHECK report for VariantTools on george2

Package: VariantTools

Version: 1.2.2

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings VariantTools_1.2.2.tar.gz

StartedAt: 2013-10-09 05:24:35 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 05:35:37 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 661.5 seconds

RetCode: 0

Status:  OK

CheckDir: VariantTools.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/VariantTools.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.2.2’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘VariantTools’ can be installed ... [47s/48s] OK
* checking installed package size ... OK
* checking package 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 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
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’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable ‘read.pos.mean’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable ‘read.pos.mean.ref’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable ‘read.pos.var’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable ‘read.pos.var.ref’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable ‘count’
ReadPositionTTestFilter : <anonymous>: no visible binding for global
  variable ‘count.ref’
* 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 ... [231s/186s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
callSampleSpecificVariants 65.431  2.452  75.745
callVariants               40.292  2.240  11.717
callWildtype               31.201  1.884  30.934
variantGR2Vcf              20.617  2.916  14.167
postFilterVariants         21.429  1.452  18.544
tallyVariants               8.000  1.136   5.841
qaVariants                  7.397  1.204   5.126
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘VariantTools_unit_tests.R’ [0s/0s]
 [1s/1s] 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 were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-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
** testing if installed package can be loaded
* DONE (VariantTools)

name	user	system	elapsed
callSampleSpecificVariants	65.431	2.452	75.745
callVariants	40.292	2.240	11.717
callWildtype	31.201	1.884	30.934
postFilterVariants	21.429	1.452	18.544
qaVariants	7.397	1.204	5.126
tallyVariants	8.000	1.136	5.841
variantGR2Vcf	20.617	2.916	14.167