BioC 2.14: CHECK report for VariantTools on zin2

Package: VariantTools

Version: 1.6.1

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings VariantTools_1.6.1.tar.gz

StartedAt: 2014-10-08 03:31:34 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 03:35:57 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 263.0 seconds

RetCode: 0

Status:  OK

CheckDir: VariantTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings VariantTools_1.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/VariantTools.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.6.1’
* 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 ... 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 ... [24s/24s] 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’ ‘IRanges:::mseq’
  ‘gmapR:::normalizeIndelAlleles’ ‘gmapR:::showSlots’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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.plus.ref’
FisherStrandFilter : <anonymous>: no visible binding for global
  variable ‘count.minus.ref’
FisherStrandFilter : <anonymous>: no visible binding for global
  variable ‘count.plus’
FisherStrandFilter : <anonymous>: no visible binding for global
  variable ‘count.minus’
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’
makeVRangesFromVariantGRanges: no visible binding for global variable
  ‘high.quality.total’
makeVRangesFromVariantGRanges: no visible binding for global variable
  ‘high.quality.ref’
makeVRangesFromVariantGRanges: no visible binding for global variable
  ‘high.quality’
* 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 ... [38s/39s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
postFilterVariants 8.845  0.348   9.251
callWildtype       8.816  0.252   9.098
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘VariantTools_unit_tests.R’ [0s/0s]
 [0s/0s] 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-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	3.304	0.304	3.632
callVariants	1.845	0.216	2.086
callWildtype	8.816	0.252	9.098
pileupVariants	0.668	0.108	0.788
postFilterVariants	8.845	0.348	9.251
qaVariants	0.844	0.176	1.035
tallyVariants	0.588	0.192	0.799
variantGR2Vcf	0.000	0.000	0.001