Package: MinimumDistance

Version: 1.2.4

Command: rm -rf MinimumDistance.buildbin-libdir && mkdir MinimumDistance.buildbin-libdir && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MinimumDistance.buildbin-libdir MinimumDistance_1.2.4.tar.gz >MinimumDistance-install.out 2>&1 && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD check --library=MinimumDistance.buildbin-libdir --install="check:MinimumDistance-install.out" --force-multiarch --no-vignettes --timings MinimumDistance_1.2.4.tar.gz && mv MinimumDistance.buildbin-libdir/* MinimumDistance.Rcheck/ && rmdir MinimumDistance.buildbin-libdir

StartedAt: 2013-03-25 02:02:23 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:16:45 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 862.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MinimumDistance.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.11-bioc/meat/MinimumDistance.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.2.4'
* 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 whether package 'MinimumDistance' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
computeBayesFactor 49.39   0.26   49.66
callDenovoSegments 15.51   0.04   15.53
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
computeBayesFactor 37.20   0.06   37.26
callDenovoSegments 16.48   0.09   16.58
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'doRUnit.R'
 OK
** running tests for arch 'x64'
  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
  'D:/biocbld/bbs-2.11-bioc/meat/MinimumDistance.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'MinimumDistance' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MinimumDistance' as MinimumDistance_1.2.4.zip

* DONE (MinimumDistance)