BioC 2.14: CHECK report for MinimumDistance on zin2

Package: MinimumDistance

Version: 1.8.1

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings MinimumDistance_1.8.1.tar.gz

StartedAt: 2014-10-08 01:06:10 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:12:30 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 379.1 seconds

RetCode: 0

Status:  OK

CheckDir: MinimumDistance.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings MinimumDistance_1.8.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/MinimumDistance.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.8.1’
* 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 ... [20s/20s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... [64s/64s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
computeBayesFactor 23.942  0.044  24.079
callDenovoSegments 13.988  0.064  14.094
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [123s/123s]
 [123s/123s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

* 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	0.012	0.000	0.014
Pedigree	0.024	0.000	0.025
TrioSet-class	2.192	0.016	2.209
TrioSet	2.516	0.024	2.557
TrioSetList-class	0.328	0.012	0.339
TrioSetListLD	3.793	0.056	3.856
calculateMindist	0.328	0.008	0.334
callDenovoSegments	13.988	0.064	14.094
computeBayesFactor	23.942	0.044	24.079
isDenovo	0.06	0.00	0.06
lrr.segs	0.004	0.000	0.003
mad2	0.352	0.000	0.352
narrow	4.180	0.016	4.204
phenoData	0.272	0.008	0.279
segment2	0.000	0.000	0.001
stackRangedDataList	0.192	0.000	0.196
trioSetList	1.744	0.000	1.747
trioSetListExample	0.284	0.000	0.283
xyplotTrio	1.212	0.008	1.220