Package: MinimumDistance

Version: 1.1.7

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MinimumDistance_1.1.7.tar.gz

StartedAt: 2012-06-21 01:42:18 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 01:49:27 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 428.7 seconds

RetCode: 0

Status:  OK

CheckDir: MinimumDistance.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/MinimumDistance.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MinimumDistance/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MinimumDistance' version '1.1.7'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doSNOW'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'MinimumDistance' 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 ... NOTE
xyplotTrioListLrrBaf: no visible global function definition for
  'xyplotTrioLrrBaf'
xyplotTrioSetList: no visible global function definition for 'ss'
* 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 installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'doRUnit.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 were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/MinimumDistance.Rcheck/00check.log'
for details.

* installing *source* package 'MinimumDistance' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'MinimumDistance.Rnw' 
** testing if installed package can be loaded

* DONE (MinimumDistance)

name	user	system	elapsed
Pedigree-class	0.020	0.001	0.021
Pedigree	0.050	0.003	0.053
TrioSet-class	2.967	0.160	3.148
TrioSet	4.500	0.104	4.665
TrioSetList-class	0.042	0.002	0.045
TrioSetListLD	0.104	0.008	0.113
calculateMindist	3.454	0.203	3.680
callDenovoSegments	15.268	0.275	15.688
computeBayesFactor	96.019	23.066	121.263
isDenovo	0.068	0.003	0.071
lrr.segs	0.005	0.002	0.007
mad2	0.334	0.064	0.404
narrow	3.237	0.100	3.376
phenoData	0.208	0.014	0.223
segment2	0.001	0.001	0.000
stackRangedDataList	0.572	0.004	0.579
trioSetList	2.823	0.070	2.926
trioSetListExample	0.334	0.032	0.374
xyplotTrio	1.936	0.058	2.029