BioC 2.12: CHECK report for bumphunter on moscato2

Package: bumphunter

Version: 1.0.2

Command: rm -rf bumphunter.buildbin-libdir && mkdir bumphunter.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bumphunter.buildbin-libdir bumphunter_1.0.2.tar.gz >bumphunter-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=bumphunter.buildbin-libdir --install="check:bumphunter-install.out" --force-multiarch --no-vignettes --timings bumphunter_1.0.2.tar.gz && mv bumphunter.buildbin-libdir/* bumphunter.Rcheck/ && rmdir bumphunter.buildbin-libdir

StartedAt: 2013-10-09 01:19:40 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:22:54 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 193.8 seconds

RetCode: 1

Status:  ERROR

CheckDir: bumphunter.Rcheck

Warnings: NA

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/bumphunter.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 'bumphunter/DESCRIPTION' ... OK
* this is package 'bumphunter' version '1.0.2'
* 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 'bumphunter' 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 ... 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 examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'bumphunter-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: smoother
> ### Title: Smooth genomic profiles
> ### Aliases: smoother
> 
> ### ** Examples
> 
>   dat <- dummyData()
> 
>   ## loessByCluster
>   smoothed <- smoother(y=dat$mat[,1], cluster=dat$cluster, smoothFunction=loessByCluster, 
+                        bpSpan = 1000, minNum=7, minInSpan=5, maxSpan=1)
Error in summary.connection(connection) : invalid connection
Calls: smoother ... sendData.SOCKnode -> serialize -> summary -> summary.connection
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'bumphunter-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: smoother
> ### Title: Smooth genomic profiles
> ### Aliases: smoother
> 
> ### ** Examples
> 
>   dat <- dummyData()
> 
>   ## loessByCluster
>   smoothed <- smoother(y=dat$mat[,1], cluster=dat$cluster, smoothFunction=loessByCluster, 
+                        bpSpan = 1000, minNum=7, minInSpan=5, maxSpan=1)
Error in summary.connection(connection) : invalid connection
Calls: smoother ... sendData.SOCKnode -> serialize -> summary -> summary.connection
Execution halted

install for i386

* installing *source* package 'bumphunter' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'bumphunter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bumphunter' as bumphunter_1.0.2.zip
* DONE (bumphunter)