Package: MinimumDistance

Version: 1.3.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings MinimumDistance_1.3.3.tar.gz

StartedAt: 2013-01-08 03:59:36 -0800 (Tue, 08 Jan 2013)

EndedAt: 2013-01-08 04:12:49 -0800 (Tue, 08 Jan 2013)

EllapsedTime: 793.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MinimumDistance.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/MinimumDistance.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MinimumDistance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MinimumDistance’ version ‘1.3.3’
* 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 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 ... 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
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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
computeBayesFactor 69.024  0.068  69.133
callDenovoSegments 34.450  0.128  34.666
TrioSet             6.308  0.044   6.387
TrioSet-class       5.296  0.072   5.374
* 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 were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-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	0.716	0.004	0.721
Pedigree	0.036	0.004	0.043
TrioSet-class	5.296	0.072	5.374
TrioSet	6.308	0.044	6.387
TrioSetList-class	0.592	0.016	0.606
TrioSetListLD	0.204	0.004	0.214
calculateMindist	4.501	0.016	4.517
callDenovoSegments	34.450	0.128	34.666
computeBayesFactor	69.024	0.068	69.133
isDenovo	0.168	0.000	0.167
lrr.segs	0.008	0.000	0.008
mad2	0.492	0.016	0.509
narrow	4.413	0.004	4.420
phenoData	0.260	0.012	0.272
segment2	0.004	0.000	0.004
stackRangedDataList	0.256	0.000	0.255
trioSetList	2.484	0.020	2.504
trioSetListExample	0.340	0.012	0.352
xyplotTrio	1.392	0.016	1.405