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: [EMAIL PROTECTED] on behalf of Joseph Dhahbi, P.h.D. Sent: Tue 03/06/2008 16:21 To: [email protected] Cc: [email protected] 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 [EMAIL PROTECTED] The email message (and any attachments) is for the sole...{{dropped:21}} _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
