Package: ggbio

Version: 1.4.6

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ggbio_1.4.6.tar.gz

StartedAt: 2012-09-24 00:21:18 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:27:49 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 391.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: ggbio.Rcheck

Warnings: NA

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/ggbio.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ggbio/DESCRIPTION' ... OK
* this is package 'ggbio' version '1.4.6'
* 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 whether package 'ggbio' can be installed ... WARNING
Found the following significant warnings:
  Warning: found methods to import for function 'as.list' but not the generic itself
  Warning: found methods to import for function 'chartr' but not the generic itself
  Warning: found methods to import for function 'IQR' but not the generic itself
  Warning: found methods to import for function 'NROW' but not the generic itself
  Warning: found methods to import for function 'aggregate' but not the generic itself
  Warning: found methods to import for function 'cor' but not the generic itself
See '/Users/biocbuild/bbs-2.10-bioc/meat/ggbio.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 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
plotSingleChrom: no visible binding for global variable 'x1'
plotSingleChrom: no visible binding for global variable 'x2'
plotStackedOverview: no visible binding for global variable 'cytobands'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... ERROR
Running examples in 'ggbio-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot
> ### Title: Generic autoplot function
> ### Aliases: autoplot autoplot,GRanges-method autoplot,GRangesList-method
> ###   autoplot,IRanges-method autoplot,BSgenome-method
> ###   autoplot,GappedAlignments-method autoplot,BamFile-method
> ###   autoplot,TranscriptDb-method autoplot,character-method
> ###   autoplot,Rle-method autoplot,RleList-method
> ###   autoplot,ExpressionSet-method autoplot,GenomicRangesList-method
> ###   autoplot,VCF-method
> 
> ### ** Examples
> 
> library(ggbio)
> set.seed(1)
> N <- 200
> library(GenomicRanges)
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following object(s) are masked from 'package:stats':

    xtabs

The following object(s) are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
    colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
    rownames, sapply, setdiff, table, tapply, union, unique

Loading required package: IRanges
> gr <- GRanges(seqnames = sample(c("chr1", "chr2", "chr3"),
+                      size = N, replace = TRUE),
+               IRanges(start = sample(1:300, size = N, replace = TRUE),
+                       width = sample(70:75, size = N,replace = TRUE)),
+               strand = sample(c("+", "-", "*"), size = N, 
+                 replace = TRUE),
+               value = rnorm(N, 10, 3), score = rnorm(N, 100, 30),
+               group = sample(c("Normal", "Tumor"), 
+                 size = N, replace = TRUE),
+               pair = sample(letters, size = N, 
+                 replace = TRUE))
> autoplot(gr)
Error in rep.int("", ncol(r)) : incorrect type for second argument
Calls: print ... do.call -> <Anonymous> -> do.call -> <Anonymous> -> rep.int
Execution halted

* installing *source* package 'ggbio' ...
** R
** inst
** preparing package for lazy loading
Warning: found methods to import for function 'as.list' but not the generic itself
Warning: found methods to import for function 'chartr' but not the generic itself
Warning: found methods to import for function 'IQR' but not the generic itself
Warning: found methods to import for function 'NROW' but not the generic itself
Warning: found methods to import for function 'aggregate' but not the generic itself
Warning: found methods to import for function 'chartr' but not the generic itself
Warning: found methods to import for function 'cor' but not the generic itself
Creating a new generic function for 'rescale' in package 'ggbio'
Creating a generic function for 'summary' from package 'base' in package 'ggbio'
Creating a generic function for 'print' from package 'base' in package 'ggbio'
Creating a new generic function for 'xlim' in package 'ggbio'
Creating a generic function for 'update' from package 'stats' in package 'ggbio'
Creating a new generic function for 'geom_rect' in package 'ggbio'
Creating a new generic function for 'geom_segment' in package 'ggbio'
Creating a new generic function for 'geom_bar' in package 'ggbio'
Creating a new generic function for 'stat_identity' in package 'ggbio'
Warning in FUN(X[[1L]], ...) :
  Created a package name, '2012-09-24 00:21:34', when none found
** help
*** installing help indices
** building package indices
** installing vignettes
   'intro.Rnw' 
** testing if installed package can be loaded
Warning: found methods to import for function 'as.list' but not the generic itself
Warning: found methods to import for function 'chartr' but not the generic itself
Warning: found methods to import for function 'IQR' but not the generic itself
Warning: found methods to import for function 'NROW' but not the generic itself
Warning: found methods to import for function 'aggregate' but not the generic itself
Warning: found methods to import for function 'chartr' but not the generic itself
Warning: found methods to import for function 'cor' but not the generic itself

* DONE (ggbio)

name	user	system	elapsed
align.plots	17.766	1.034	18.869