You need to use a 64 bit version of R.
Raphael
On 3-Jun-08, at 8:21 AM, Joseph Dhahbi, P.h.D. wrote:
Hello
I need help on how to get around the memory error reported below,
especially when I can not add anymore RAM:
Here is the Hardware Overview:
Model Name: Mac Pro
Model Identifier: MacPro1,1
Processor Name: Dual-Core Intel Xeon
Processor Speed: 2.66 GHz
Number Of Processors: 2
Total Number Of Cores: 4
L2 Cache (per processor): 4 MB
Memory: 20 GB
Bus Speed: 1.33 GHz
Boot ROM Version: MP11.005C.B08
SMC Version: 1.7f10
Serial Number: G87052SGUPZ
NM_seq=readSolexaFastA(NM_fa)
NM_alf=alphabetFrequency(NM_seq, baseOnly=TRUE)
NM_seq_clean = NM_seq[NM_alf[,"other"]==0]
length(NM_seq)
[1] 4820218
length(NM_seq_clean)
[1] 4817537
NM_seq_clean
A DNAStringSet instance of length 4817537
width seq
[1] 36 GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGGAT
[2] 36 GTGGTAATTCATCAGATCTCGGATGGCATTGGTCAT
[3] 36 GGGAGGTCACTAATGGAGACACACAGAAATGTAACA
[4] 36 GGGATTGGTTTTTTGTTACTGATTTGTTTGAGTTCA
[5] 36 GTGGTAATTTTGACTTTTTAGGTTAATTTATTTTTT
[6] 36 GATCGGAAGGAGCTCGTATGCCGTCTTCTGCTTAGA
[7] 36 GGTCAGTTGTGTTCTCCTGAGTAGGTTGTGTGAATG
[8] 36 GGGAGGTCACTAATGGAGACACACAGAAATGTAACA
[9] 36 GGGAGGCTGAGGCAGGAGAATGGCATGAACCTAGAT
... ... ...
[4817529] 36 TTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAG
[4817530] 36 CATCAATGTATCTTAAGGCGTAAATTGTAAGCGTTA
[4817531] 36 CGAGCAGCGACGCATCACCCAGCTAGATCGGAAGAG
[4817532] 36 GCAATGCCACTGGCGCGACAACCGGGACACCATAGG
[4817533] 36 CCTCGCCGGACACGCTGAACTTGTGGCCGTTTTCGT
[4817534] 36 CCATTGTACAACGTATCGACATATCCTCCACCCGCC
[4817535] 36 CCCCCTGAACCTGAAACATAAAATGAATGCAATTGT
[4817536] 36 ACCATGTTGTCCAAGGGCGAATTCTGCAGATATCCA
[4817537] 36 CAGGGGCCGGCGGCTGGCTAGGGCTGCAGCGTTAAA
NM_seq_pDict=PDict(NM_seq_clean)
Error in .PDict(dict, names(dict), tb.start, tb.end, drop.head,
drop.tail, :
alloc_actree_nodes_buf(): failed to alloc actree_nodes_buf
R(433,0xa000d000) malloc: *** vm_allocate(size=4032987136) failed
(error code=3)
R(433,0xa000d000) malloc: *** error: can't allocate region
R(433,0xa000d000) malloc: *** set a breakpoint in szone_error to debug
sessionInfo()
R version 2.7.0 (2008-04-22)
i386-apple-darwin8.10.1
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] tools stats graphics grDevices utils datasets
methods base
other attached packages:
[1] BiostringsCinterfaceDemo_0.1.2 Biostrings_2.8.9
Biobase_2.0.1
Regards,
Joseph
Joseph M. Dhahbi, PhD
Childrens Hospital Oakland Research Institute
5700 Martin Luther King Jr. Way
Oakland, CA 94609
USA
Ph.(510)428-3885 EXT.5743
Cell.(702)335-0795
Fax (510)450-7910
[EMAIL PROTECTED]
The email message (and any attachments) is for the sol...{{dropped:26}}
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