[Bioc-sig-seq] srapply / as.list / multicore weird interaction

[Janet Young]

Hi,

I'm learning how to use srapply - it looks like it'll be really useful for me.     

I think I might have found a bug, or at least behavior that's a bit odd.  I've written an srapply function on a DNAStringSet.  My goal is to put a wrapper on pairwiseAlign to align a bunch of shortReads to several subject sequences of interest and return a list of all the scores. After a struggle I've got it working but I needed to work around what might be a bug(?)

I've got a toy example too (see below). This example (and my real function) work fine when multicore is not loaded (I know, the whole point of srapply is to use multicore, right, but I was trying to track down the problem). However, it doesn't work after I load multicore, because as.list now seems to struggle on the DNAStringSet.  It's a problem whether I load ShortRead or multicore first.   If I force as.list on my DNAStringSet object, it works - but should I have to do that?

I think I've included all you need to know below (that was on my Mac, but I get the same thing on 64-bit linux). Does this make any sense to you?

thanks,

Janet




R version 2.13.0 (2011-04-13)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

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[R.app GUI 1.40 (5751) i386-apple-darwin9.8.0]

> library(ShortRead)
Loading required package: IRanges

Attaching package: 'IRanges'

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

    cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin,
    pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools
> 
> testseqs <- DNAStringSet(c("CTCGACCAGTAT", "TTGAGGCTGT"))
> names(testseqs) <- c("seq1","seq2")
> 
> 
> testfunction2 <- function (myseqs) {
+     srapply(myseqs, function(x, ... ) { class(x) } )
+ }
> testfunction2(testseqs)
$seq1
[1] "DNAString"
attr(,"package")
[1] "Biostrings"

$seq2
[1] "DNAString"
attr(,"package")
[1] "Biostrings"

> 
> 
> 
> library(multicore)

Attaching package: 'multicore'

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

    parallel

> 
> testfunction2 <- function (myseqs) {
+     srapply(myseqs, function(x, ... ) { class(x) } )
+ }
> testfunction2(testseqs)
$seq1
[1] "Error in as.list.default(X) : \n  no method for coercing this S4 class to a vector\n"

$seq2
[1] "Error in as.list.default(X) : \n  no method for coercing this S4 class to a vector\n"

> 
> 
> testfunction3 <- function (myseqs) {
+     srapply(as.list(myseqs), function(x, ... ) { class(x) } )
+ }
> testfunction3(testseqs)
$seq1
[1] "DNAString"
attr(,"package")
[1] "Biostrings"

$seq2
[1] "DNAString"
attr(,"package")
[1] "Biostrings"

> 
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: i386-apple-darwin9.8.0/i386 (32-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     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] multicore_0.1-5     ShortRead_1.10.0    Rsamtools_1.4.0     lattice_0.19-23    
[5] Biostrings_2.20.0   GenomicRanges_1.4.0 IRanges_1.10.0     

loaded via a namespace (and not attached):
[1] Biobase_2.12.0 grid_2.13.0    hwriter_1.3