Package: VariantAnnotation

Version: 1.0.5

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch VariantAnnotation_1.0.5.tar.gz

StartedAt: 2012-01-09 06:07:53 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 06:16:29 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 515.5 seconds

RetCode: 0

Status:  OK

CheckDir: VariantAnnotation.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/VariantAnnotation.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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 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	0.87	0.00	0.90
PolyPhenDb-class	1.03	0.09	8.33
SIFTDb-class	4.18	0.25	7.96
VAFilter-class	0	0	0
VAFilterResult-class	0	0	0
VAUtil-class	0.01	0.00	0.01
getTranscriptSeqs	16.24	0.28	43.97
globalToLocal	0	0	0
locateVariants	28.50	11.24	44.05
predictCoding	7.54	0.43	8.31
readVcf	0.66	0.02	0.67
vaFilter	68.73	23.01	92.56
variant	0.01	0.00	0.02