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BioC 2.14: CHECK report for MinimumDistance on zin2

This page was generated on 2014-10-08 08:49:30 -0700 (Wed, 08 Oct 2014).

Package 499/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MinimumDistance 1.8.1
Robert B Scharpf
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/MinimumDistance
Last Changed Rev: 94681 / Revision: 95116
Last Changed Date: 2014-09-29 18:28:20 -0700 (Mon, 29 Sep 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

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

Command output

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


* 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

MinimumDistance.Rcheck/00install.out:

* 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)

MinimumDistance.Rcheck/MinimumDistance-Ex.timings:

nameusersystemelapsed
Pedigree-class0.0120.0000.014
Pedigree0.0240.0000.025
TrioSet-class2.1920.0162.209
TrioSet2.5160.0242.557
TrioSetList-class0.3280.0120.339
TrioSetListLD3.7930.0563.856
calculateMindist0.3280.0080.334
callDenovoSegments13.988 0.06414.094
computeBayesFactor23.942 0.04424.079
isDenovo0.060.000.06
lrr.segs0.0040.0000.003
mad20.3520.0000.352
narrow4.1800.0164.204
phenoData0.2720.0080.279
segment20.0000.0000.001
stackRangedDataList0.1920.0000.196
trioSetList1.7440.0001.747
trioSetListExample0.2840.0000.283
xyplotTrio1.2120.0081.220