Package: MinimumDistance

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MinimumDistance_1.4.0.tar.gz

StartedAt: 2013-05-01 08:05:45 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 08:16:09 -0700 (Wed, 01 May 2013)

EllapsedTime: 624.6 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 Patched (2013-04-08 r62531)
* 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 '1.4.0'
* 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 ... [27s/28s] 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 ... [126s/131s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
computeBayesFactor 52.137  7.371  61.796
callDenovoSegments 23.596  0.443  24.557
TrioSetListLD       6.965  0.213   7.815
narrow              5.341  0.139   5.575
TrioSet             5.135  0.146   5.511
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'doRUnit.R' [232s/237s]
 [233s/238s] 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
** testing if installed package can be loaded
* DONE (MinimumDistance)

name	user	system	elapsed
Pedigree-class	0.035	0.006	0.040
Pedigree	0.044	0.005	0.049
TrioSet-class	4.303	0.171	4.849
TrioSet	5.135	0.146	5.511
TrioSetList-class	0.660	0.067	0.772
TrioSetListLD	6.965	0.213	7.815
calculateMindist	0.520	0.067	0.710
callDenovoSegments	23.596	0.443	24.557
computeBayesFactor	52.137	7.371	61.796
isDenovo	0.082	0.014	0.097
lrr.segs	0.009	0.009	0.018
mad2	0.602	0.112	0.727
narrow	5.341	0.139	5.575
phenoData	0.407	0.047	0.454
segment2	0.004	0.009	0.013
stackRangedDataList	0.303	0.017	0.320
trioSetList	2.968	0.126	3.175
trioSetListExample	0.563	0.072	0.659
xyplotTrio	1.658	0.099	1.793