BioC 2.12: CHECK report for MinimumDistance on moscato2

Package: MinimumDistance

Version: 1.4.0

Command: rm -rf MinimumDistance.buildbin-libdir && mkdir MinimumDistance.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MinimumDistance.buildbin-libdir MinimumDistance_1.4.0.tar.gz >MinimumDistance-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=MinimumDistance.buildbin-libdir --install="check:MinimumDistance-install.out" --force-multiarch --no-vignettes --timings MinimumDistance_1.4.0.tar.gz && mv MinimumDistance.buildbin-libdir/* MinimumDistance.Rcheck/ && rmdir MinimumDistance.buildbin-libdir

StartedAt: 2013-10-09 03:03:13 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:17:41 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 867.3 seconds

RetCode: 0

Status:  OK

CheckDir: MinimumDistance.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/MinimumDistance.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [88s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
computeBayesFactor 40.23   0.86   41.11
callDenovoSegments 15.32   0.14   15.47
** running examples for arch 'x64' ... [102s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
computeBayesFactor 44.32   1.41   45.72
callDenovoSegments 17.47   0.12   17.63
narrow              6.01   0.03    6.07
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'doRUnit.R' [209s]
 [209s] OK
** running tests for arch 'x64'
  Running 'doRUnit.R' [181s]
 [182s] 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
  'E:/biocbld/bbs-2.12-bioc/meat/MinimumDistance.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'MinimumDistance' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MinimumDistance' as MinimumDistance_1.4.0.zip
* DONE (MinimumDistance)