Package: RmiR

Version: 1.5.0

Command: D:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings RmiR_1.5.0.tar.gz

StartedAt: 2010-10-14 06:30:32 -0700 (Thu, 14 Oct 2010)

EndedAt: 2010-10-14 06:31:46 -0700 (Thu, 14 Oct 2010)

EllapsedTime: 74.2 seconds

RetCode: 1

Status:  ERROR

CheckDir: RmiR.Rcheck

Warnings: NA

* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/RmiR.Rcheck'
* using R version 2.12.0 RC (2010-10-11 r53293)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RmiR/DESCRIPTION' ... OK
* this is package 'RmiR' version '1.5.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'RmiR' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 data for non-ASCII characters ... OK
* checking examples ... ERROR
Running examples in 'RmiR-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotRmiRtc
> ### Title: Plot object from read.mir or a selected gene and respective
> ###   miRNAs from
> ### Aliases: plotRmiRtc
> 
> ### ** Examples
> 
> 	
>         data(RmiR)
>         res1 <- read.mir(genes=gene1, mirna=mir1, annotation="hgug4112a.db")
Loading required package: hgug4112a.db
Loading required package: AnnotationDbi
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: org.Hs.eg.db
>         res2 <- read.mir(genes=gene2, mirna=mir2, annotation="hgug4112a.db")
>         res3 <- read.mir(genes=gene3, mirna=mir3, annotation="hgug4112a.db")
> 
>         res_tc <- RmiRtc(timeline=c("res1", "res2", "res3"),
+ 			 timevalue=c(12, 48, 72))
>         res <- readRmiRtc(res_tc, correlation=-0.9, exprLev=1,
+ 			  annotation="hgug4112a.db")
> 
> 	## List of genes with anti-correlated miRNAs:
>         
> 	res$reps
  symbol miRNAs gene_id
2    APP      3     351
3  VLDLR      3    7436
1  CENPV      1  201161
> 
> 	## Plot of the first gene of the list:
> 	plotRmiRtc (res, gene_id=351, timeunit="Hours")
> 
> 	## Setting the position of the legend:
> 	
> 	plotRmiRtc (res,gene_id=351, legend.x=50, legend.y=0, timeunit="Hours")
> 
> 	## Plot with RSVGTipsDevice:
> 	
> 	plotRmiRtc (res,gene_id=351, legend.x=50, legend.y=0, timeunit="Hours",
+ 

* installing *source* package 'RmiR' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: DBI
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (RmiR)

name	user	system	elapsed
RmiR	19.24	0.62	25.61
RmiRtc	6.12	0.13	6.28
data	0.03	0.00	0.03