Package: MinimumDistance

Version: 1.2.4

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MinimumDistance_1.2.4.tar.gz

StartedAt: 2013-03-25 00:25:02 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:37:13 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 731.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MinimumDistance.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/MinimumDistance.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.2.4'
* 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 '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 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
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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'Pedigree,ANY,ANY,ANY'
  generic '[' and siglist 'TrioSet,ANY,ANY,ANY'
  generic '[' and siglist 'TrioSetList,ANY,ANY,ANY'
  generic '[' and siglist 'ff_array,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
Examples with CPU or elapsed time > 5s
                     user system elapsed
computeBayesFactor 62.058 13.183  77.011
callDenovoSegments 22.992  0.426  23.656
TrioSetListLD       5.089  0.154   5.264
narrow              4.728  0.139   5.506
* 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
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	0.018	0.003	0.019
Pedigree	0.032	0.009	0.041
TrioSet-class	4.191	0.196	4.438
TrioSet	3.979	0.132	4.165
TrioSetList-class	0.447	0.038	0.487
TrioSetListLD	5.089	0.154	5.264
calculateMindist	1.387	0.226	1.651
callDenovoSegments	22.992	0.426	23.656
computeBayesFactor	62.058	13.183	77.011
isDenovo	0.135	0.005	0.140
lrr.segs	0.004	0.001	0.006
mad2	0.546	0.092	0.663
narrow	4.728	0.139	5.506
phenoData	0.386	0.042	0.758
segment2	0.000	0.001	0.000
stackRangedDataList	0.324	0.005	0.387
trioSetList	2.566	0.098	2.798
trioSetListExample	0.419	0.049	0.499
xyplotTrio	1.450	0.083	1.559