BioC 2.12: CHECK report for MinimumDistance on george2

Package: MinimumDistance

Version: 1.4.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings MinimumDistance_1.4.0.tar.gz

StartedAt: 2013-10-09 03:17:59 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:33:56 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 957.1 seconds

RetCode: 0

Status:  OK

CheckDir: MinimumDistance.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/MinimumDistance.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.4.0’
* 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 ... [35s/36s] 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 ... [167s/168s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
computeBayesFactor 72.089  0.184  72.434
callDenovoSegments 38.422  0.200  39.207
TrioSetListLD      10.677  0.140  10.832
TrioSet             7.740  0.072   7.859
TrioSet-class       7.017  0.096   7.117
narrow              6.484  0.024   6.514
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [323s/463s]
 [323s/464s] 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
  ‘/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
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	0.028	0.000	0.030
Pedigree	0.052	0.000	0.053
TrioSet-class	7.017	0.096	7.117
TrioSet	7.740	0.072	7.859
TrioSetList-class	0.776	0.028	0.805
TrioSetListLD	10.677	0.140	10.832
calculateMindist	0.436	0.060	0.534
callDenovoSegments	38.422	0.200	39.207
computeBayesFactor	72.089	0.184	72.434
isDenovo	0.092	0.004	0.095
lrr.segs	0.016	0.000	0.015
mad2	0.664	0.012	0.675
narrow	6.484	0.024	6.514
phenoData	0.364	0.008	0.374
segment2	0.012	0.000	0.012
stackRangedDataList	0.436	0.000	0.434
trioSetList	3.441	0.020	3.480
trioSetListExample	0.580	0.016	0.597
xyplotTrio	1.804	0.020	1.825