[Bioc-sig-seq] strand problem in GenomicRanges

[Joseph Scandura]

I recently updated BioC to 2.12.1 and now find a new issue when assigning strand to a GRanges object. 

The problem must be something straightforward but I have not been able to track it down. 

################### Example: 
> z=GRanges(seqnames=paste("chr",seq(3), sep=""), ranges = IRanges(start=c(1,300,600), width=50), strand=c("+", "-", "*"))
> strand(z)
	'factor' Rle of length 3 with 3 runs
	  Lengths: 1 1 1
	  Values : + - *
	Levels(3): + - *
> strand(z) = "*"  #this used to assign a strand of "*" to all elements in z
Error in x[[name, exact = FALSE]] : 
  missing '[[' method for Sequence class GRanges

> traceback()
10: stop("missing '[[' method for Sequence class ", class(x))
9: x[[name, exact = FALSE]]
8: x[[name, exact = FALSE]]
7: object$call
6: object$call
5: update.default(x, strand = value)
4: update(x, strand = value)
3: update(x, strand = value)
2: `strand<-`(`*tmp*`, value = "*")
1: `strand<-`(`*tmp*`, value = "*")

>sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats   utils   methods base   

other attached packages:
[1] GenomicRanges_1.2.3 IRanges_1.8.8       Biobase_2.10.0     

loaded via a namespace (and not attached):
 [1] annotate_1.28.0                     AnnotationDbi_1.12.0                biomaRt_2.6.0                      
 [4] Biostrings_2.18.2                   BSgenome_1.18.2                     BSgenome.Ecoli.NCBI.20080805_1.3.16
 [7] ChIPpeakAnno_1.6.0                  DBI_0.2-5                           DESeq_1.2.1                        
[10] gdata_2.8.1                         genefilter_1.32.0                   geneplotter_1.28.0                 
[13] GO.db_2.4.5                         gplots_2.8.0                        graphics_2.12.1                    
[16] grDevices_2.12.1                    grid_2.12.1                         gtools_2.6.2                       
[19] limma_3.6.9                         MASS_7.3-9                          multtest_2.6.0                     
[22] org.Hs.eg.db_2.4.6                  RColorBrewer_1.0-2                  RCurl_1.5-0                        
[25] RMySQL_0.7-5                        RSQLite_0.9-4                       splines_2.12.1                     
[28] survival_2.36-2                     tools_2.12.1                        XML_3.2-0                          
[31] xtable_1.5-6       
###################
Joe