Hi,

sorry, the sequence in my original posting got screwed during copy/paste, 
this is the "real" sequence:

>
CTATGTGTGAGGGCAGCAACCAGAACTGTCTGCCCTGACTTCGCTCAGGATGCTGTGAACATGTGGCTCAGATGGTGCTA
GGCATTTTCCTCTAGAGTCAGAAACGTGGACAGAGAGTCATCTCCTCTGGCTTCCCAGGCATGTCTGCCACTCTGAAGGT
CTGAAGGTCTGGGTCTCCCTCCCATGGGATTTGAGTGCAGAGAGCTGTGTGACTGGGTCCCTTCAGATCCAGGTGGTGTC
TGGACTGTAGCGTTGAGTGCCCTATCTTCCTGGTCTCAGAGCACCTATACAGTTTCCTCTTGGGCCAGGGATGTGGGCAG
TGGTGGGCTGTACTGGAAGTCTCTCCTGTCCTGCAGTCTCAGGAGTGGCCACCTGTCTGGGTGGTGAGCTCTCTCTCCCA
TGGGGTTAGGGAGCAGGGAGGTTTTGCAAGATTCAGATTTAAGGTCACATTTTATCATCATAATGGAGGACATTAGGAAG
GTCAGAAATAACTCCCTTAAGGAAATACTTGACAACACAAGCAAACTAGTAGAAATCTTTTTAAAAGGAAACACAAAAGT
ATTTTAAAGAATTACAGCAAACCACAACCAAATAGGAGAGGAAATTGAACAAAATCATCCAGGAGTTAAATATGGAAATA
GAAACAATGAAGAGAGCACACAGCGAGACAACCCTGGAGATAGAAAATCTAAGGAAGAGATCAGGAGTCATAGATGCAAG
CATCACTGACGGACTACATGAGATAGAAGAGAGAATTTTGGGAGCAGAAGATATCATAGAAAACATTGACACAACCTTCA
AAGAGAACGTAAATAGGAAAAAGCTCCTAGCCCTAAACATGCAGGAAATCAGGAAACAAATCAAAGATCAAACCTAAATA
TATCAGGTATAGAAGAGAGTGAAGACTCCCAACATAAAGGGATGGTAAATATCTTCAACAATATAAACAATATAAAGGAA
AACATCCCTAACCAAAAGAAATAAATGTCCATAAATAGACATGAAGCCTGCAGAATTCCAAATAGAATGGACCAGAAAAT
AAATTCCTCCTGTCACATAATAGTCAAAACACCAAATGCACAAAACAAAGAATGAATATTAAAAGCATTAACGGATAAAG
GTCAAGTACATTTAAAGGCAGACATGTCAGAATTACACCAGAATTCTTACCATGGACTATGAAAGCCAGAAGACAGATGT

It doesn't matter which sequence one uses to get the DNAStringSet error, 
it just has to be long and
there have to be many of them, here's a more generic example:

> myseq.bs = DNAStringSet(rep(paste(rep("A", 100), collapse=""), 2000))
> myseq.bs = DNAStringSet(rep(paste(rep("A", 100), collapse=""), 2000000))
> myseq.bs = DNAStringSet(rep(paste(rep("A", 1200), collapse=""), 2000))
> myseq.bs = DNAStringSet(rep(paste(rep("A", 1200), collapse=""), 
2000000))
Error in .Call("new_SharedRaw_from_STRSXP", x, start(solved_SEW), 
width(solved_SEW),  : 
  negative length vectors are not allowed

Arne






arne.mueller@novartis.com 
Sent by: bioconductor-bounces@stat.math.ethz.ch
10/07/2010 05:55 PM

To
bioconductor@stat.math.ethz.ch
cc

Subject
[BioC] Biostrings bug?






Dear All,

I came across the following error in DNAStringSet from the Biostrings 
package:

> myseq = 
"CTATGTGTGAGGGCAGCAACCAGAACTGTCTGCCCTGACTTCGCTCAGGATGCTGTGAACATGTGGCTCAGATGGTGCTAGGCATTTTCCTCTAGAGTCAGAAACGTGGACAGAGAGTCATCTCCTCTGGCTTCCCAGGCATGTCTGCCACTCTGAAGGTCTGAAGGTCTGGGTCTCCCTCCCATGGGATTTGAGTGCAGAGAGCTGTGTGACTGGGTCCCTTCAGATCCAGGTGGTGTCTGGACTGTAGCGTTGAGTGCCCTATCTTCCTGGTCTCAGAGCACCTATACAGTTTCCTCTTGGGCCAGGGATGTGGGCAGTGGTGGGCTGTACTGGAAGTCTCTCCTGTCCTGCAGTCTCAGGAGTGGCCACCTGTCTGGGTGGTGAGCTCTCTCTCCCATGGGGTTAGGGAGCAGGGAGGTTTTGCAAGATTCAGATTTAAGGTCACATTTTATCATCATAATGGAGGACATTAGGAAGGTCAGAAATAACTCCCTTAAGGAAATACTTGACAACACAAGCAAACTAGTAGAAATCTTTTTAAAAGGAAACACAAAAGTATTTTAAAGAATTACAGCAAACCACAACCAAATAGGAGAGGAAATTGAACAAAATCATCCAGGAGTTAAATATGGAAATAGAAACAATGAAGAGAGCACACAGCGAGACAACCCTGGAGATAGAAAATCTAAGGAAGAGATCAGGAGTCATAGATGCAAGCATCACTGACGGACTACATGAGATAGAAGAGAGAATTTTGGGAGCAGAAGATATCATAGAAAACATTGACACAACCTTCAAAGAGAACGTAAATAGGAAAAAGCTCCTAGCCCTAAACATGCAGGAAATCAGGAAACAAATCAAAGATCAAACCTAAATATATCAGGTATAGAAGAGAGTGAAGACTCCCAACATAAAGGGATGGTAAATATCTTCAACAATATAAACAATATAAAGGAAAACATCCCTAACCAAAAGAAATAAATGT!
 
CCATAAATAGACATGAAGCCTGCAGAATTCCAAATAGAATGGACCAGAAAATAAATTCCTCCTGTCACATAATAGTCAAAACACCAAATGCACAAAACAAAGAATGAATATTAAAAGCATTAACGGATAAAGGTCAAGTACATTTAAAGGCAGACATGTCAGAATTACACCAGAATTCTTACCATGGACTATGAAAGCCAGAAGACAGATGT"
> mysDNA = DNAStringSet(myseq) # ok!
> myseq = rep(myseq, 2000000)
> myseq.bs = DNAStringSet(myseq)
Error in .Call("new_SharedRaw_from_STRSXP", x, start(solved_SEW), 
width(solved_SEW),  :

   negative length vectors are not allowed

Enter a frame number, or 0 to exit
1: DNAStringSet(myseq)
2: XStringSet("DNA", x, start = start, end = end, width = width, use.names 

= u
3: XStringSet("DNA", x, start = start, end = end, width = width, use.names 

= u
4: .charToXStringSet(basetype, x, start, end, width, use.names)
5: .charToXString(basetype, x, solved_SEW)

Selection: 0
> 

Strangely the following works ...:

myseq.bs = c(DNAStringSet(myseq[1:1000000]), 
DNAStringSet(myseq[1000001:2000000]))

Somehow there must be an overflow ... .

Here's some more info on my system:

> sessionInfo()
R version 2.11.1 Patched (2010-06-20 r52342) 
x86_64-unknown-linux-gnu 

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C 
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8 
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8 
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C 
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C 

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base 

other attached packages:
[1] BSgenome.Rnorvegicus.UCSC.rn4_1.3.16 BSgenome_1.16.4 
[3] Biostrings_2.16.5                    GenomicRanges_1.0.3 
[5] IRanges_1.6.11 

loaded via a namespace (and not attached):
[1] Biobase_2.8.0 tools_2.11.1 

Linux version 2.6.18-92.el5 (brewbuilder@ls20-bc2-13.build.redhat.com) 
(gcc version 4.1.2 20071124 (Red Hat 4.1.2-41)) #1 SMP Tue Apr 29 13:16:15 

EDT 2008

64 Gb memory

    thanks for your help
    +kind regards,

    Arne

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