Package: VariantAnnotation

Version: 1.0.5

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch VariantAnnotation_1.0.5.tar.gz

StartedAt: 2012-03-24 04:47:07 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 05:00:04 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 776.4 seconds

RetCode: 0

Status:  OK

CheckDir: VariantAnnotation.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/VariantAnnotation.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'VariantAnnotation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'VariantAnnotation' version '1.0.5'
* 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 'VariantAnnotation' 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 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 ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'VariantAnnotation_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

* installing *source* package 'VariantAnnotation' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'as.list' when loading 'AnnotationDbi'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'VariantAnnotation.Rnw' 
** testing if installed package can be loaded
Warning message:
replacing previous import 'as.list' when loading 'AnnotationDbi' 

* DONE (VariantAnnotation)

name	user	system	elapsed
MatrixToSnpMatrix	1.107	0.018	1.141
PolyPhenDb-class	1.734	0.423	3.249
SIFTDb-class	4.601	0.637	6.675
VAFilter-class	0.001	0.000	0.000
VAFilterResult-class	0.000	0.001	0.000
VAUtil-class	0.002	0.000	0.002
getTranscriptSeqs	20.109	1.724	23.912
globalToLocal	0.001	0.001	0.001
locateVariants	54.583	44.045	103.733
predictCoding	11.155	1.628	14.393
readVcf	1.012	0.017	1.039
vaFilter	133.072	89.178	229.168
variant	0.023	0.001	0.025