Hi Joseph
You look like you should have enough RAM on your MacPro. Have you compiled a 64-bit version of R for the Mac? The CRAN binaries are 32-bit and will restrict the available memory.
 
Stephen
 

________________________________

From: bioc-sig-sequencing-bounces@r-project.org on behalf of Joseph Dhahbi, P.h.D.
Sent: Tue 03/06/2008 16:21
To: bioc-sig-sequencing@r-project.org
Cc: bioc-sig-sequencing@r-project.org
Subject: [Bioc-sig-seq] PDict question



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
jdhahbi@chori.org
 The email message (and any attachments) is for the sole...{{dropped:21}}

