* using log directory 'E:/biocbld/bbs-2.10-bioc/meat/ggbio.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 'E:/biocbld/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 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
* 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
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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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
** running examples for arch 'x64' ... 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