Package: MinimumDistance

Version: 1.3.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MinimumDistance_1.3.7.tar.gz

StartedAt: 2013-03-24 07:43:00 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 07:53:13 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 612.7 seconds

RetCode: 0

Status:  OK

CheckDir: MinimumDistance.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MinimumDistance.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MinimumDistance/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MinimumDistance' version '1.3.7'
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'MinimumDistance' can be installed ... [26s/26s] 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
.map_trioSet: no visible global function definition for 'ocSamples'
.map_trioSet: no visible binding for global variable 'i'
.map_trioSetList: no visible global function definition for 'ocSamples'
.map_trioSetList: no visible binding for global variable 'i'
computeBayesFactorTrioSet: no visible global function definition for
  'joint4'
close,TrioSet: no visible global function definition for 'isFF'
open,TrioSet: no visible global function definition for 'isFF'
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [121s/122s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
computeBayesFactor 48.248  7.012  55.648
callDenovoSegments 22.705  0.321  23.133
TrioSetListLD       6.686  0.186   6.919
narrow              5.834  0.176   6.018
TrioSet             4.941  0.121   5.132
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'doRUnit.R' [228s/232s]
 [229s/232s] 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 was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/MinimumDistance.Rcheck/00check.log'
for details.

* installing *source* package 'MinimumDistance' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'xyplot' from package 'lattice' in package 'MinimumDistance'
** 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	0.025	0.004	0.030
Pedigree	0.046	0.006	0.053
TrioSet-class	4.656	0.171	4.844
TrioSet	4.941	0.121	5.132
TrioSetList-class	0.697	0.067	0.801
TrioSetListLD	6.686	0.186	6.919
calculateMindist	0.524	0.069	0.623
callDenovoSegments	22.705	0.321	23.133
computeBayesFactor	48.248	7.012	55.648
isDenovo	0.167	0.019	0.186
lrr.segs	0.010	0.009	0.019
mad2	0.601	0.109	0.827
narrow	5.834	0.176	6.018
phenoData	0.398	0.040	0.437
segment2	0.005	0.010	0.015
stackRangedDataList	0.306	0.020	0.327
trioSetList	2.636	0.095	2.810
trioSetListExample	0.555	0.074	0.629
xyplotTrio	1.672	0.095	1.770