Question: IdeogramTrack and bigWig file errors in Gviz
0
gravatar for Miles Pufall
6.3 years ago by
Miles Pufall40
Miles Pufall40 wrote:
Hi Michael - I know this is an old thread, but I am still unable to use BigWig files from my ChIPseq data using Gviz on a Mac. When I run it on a linux box everything runs perfectly. Should I still be having this problem, or have I missed a fix along the way. Here are my sessionInfo() and error. Thanks, and, as always, happy to share any files you'd like. M *****************(sessionInfo) > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel grid stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicFeatures_1.13.46 AnnotationDbi_1.23.27 Biobase_2.21.7 GenomicRanges_1.13.51 XVector_0.1.4 IRanges_1.19.38 [7] BiocGenerics_0.7.5 Gviz_1.5.15 loaded via a namespace (and not attached): [1] biomaRt_2.17.3 Biostrings_2.29.19 biovizBase_1.9.4 bitops_1.0-6 BSgenome_1.29.1 cluster_1.14.4 colorspace_1.2-3 [8] DBI_0.2-7 dichromat_2.0-0 Hmisc_3.12-2 labeling_0.2 lattice_0.20-23 latticeExtra_0.6-26 munsell_0.4.2 [15] plyr_1.8 RColorBrewer_1.0-5 RCurl_1.95-4.1 rpart_4.1-3 Rsamtools_1.13.47 RSQLite_0.11.4 rtracklayer_1.21.12 [22] scales_0.2.3 stats4_3.0.2 stringr_0.6.2 tools_3.0.2 XML_3.98-1.1 zlibbioc_1.7.0 *****************(error) library("Gviz") Loading required package: grid library(GenomicFeatures) setwd("/Volumes/Pufall_BD1/ChIPseq/Nalm6/GR/") itrack <- IdeogramTrack(genome = "hg19", cex = 1) gtrack <- GenomeAxisTrack(cex=1) tris_1p<-DataTrack("nalm6_1p_tris_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", col.histogram="blue", fill.histogram ="blue",name ="1% Tris", ylim=c(0,1.5)) tris_05p<-DataTrack("nalm6_05p_tris_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", col.histogram="blue", fill.histogram ="blue",name ="0.5% Tris", ylim=c(0,1.5)) less_Ab<-DataTrack("nalm6_6ugn499_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", col.histogram="blue", fill.histogram ="blue",name ="Less Ab", ylim=c(0,1.5)) standard<-DataTrack("nalm6_05_gly_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", col.histogram="blue", fill.histogram ="blue",name ="Standard", ylim=c(0,1.5)) nalm6_nodex<-D> library(GenomicFeatures) Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: IRanges Loading required package: GenomicRanges setwd("/Volumes/Pufall_BD1/ChIPseq/Nalm6/GR/") itrack <- IdeogramTrack(genome = "hg19", cex = 1) gtrack <- GenomeAxisTrack(cex=1) tris_1p<-DataTrack("nalm6_1p_tris_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", col.histogram="blue", fill.histogram ="blue",name ="1% Tris", ylim=c(0,1.5)) tris_05p<-DataTrack("nalm6_05p_tris_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", col.histogram="blue", fill.histogram ="blue",name ="0.5% Tris", ylim=c(0,1.5)) less_Ab<-DataTrack("nalm6_6ugn499_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", col.histogram="blue", fill.histogram ="blue",name ="Less Ab", ylim=c(0,1.5)) standard<-DataTrack("nalm6_05_gly_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", col.histogram="blue", fill.histogram ="blue",name ="Standard", ylim=c(0,1.5)) nalm6_nodex<-DataTrack("nalnalm6_nly_conLoading required package: XVector Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > setwd("/Volumes/Pufall_BD1/ChIPseq/Nalm6/GR/") > itrack <- IdeogramTrack(genome = "hg19", cex = 1) gtrack <- GenomeAxisTrack(cex=1) tris_1p<-DataTrack("nalm6_1p_tris_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", col.histogram="blue", fill.histogram ="blue",name ="1% Tris", ylim=c(0,1.5)) tris_05p<-DataTrack("nalm6_05p_tris_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", col.histogram="blue", fill.histogram ="blue",name ="0.5% Tris", ylim=c(0,1.5)) less_Ab<-DataTrack("nalm6_6ugn499_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", col.histogram="blue", fill.histogram ="blue",name ="Less Ab", ylim=c(0,1.5)) standard<-DataTrack("nalm6_05_gly_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", col.histogram="blue", fill.histogram ="blue",name ="Standard", ylim=c(0,1.5)) nalm6_nodex<-DataTrack("nalnalm6_nly_control_lambda.bw",genome="hg19", cex.title=0.95, background.title="darkgreen", > gtrack <- GenomeAxisTrack(cex=1) > > tris_1p<-DataTrack("nalm6_1p_tris_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", + col.histogram="blue", fill.histogram ="blue",name ="1% Tris", ylim=c(0,1.5)) > tris_05p<-DataTrack("nalm6_05p_tris_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", col.histogram="blue", fill.histogram ="blue",name ="0.5% Tris", ylim=c(0,1.5)) less_Ab<-DataTrack("nalm6_6ugn499_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", col.histogram="blue", fill.histogram ="blue",name ="Less Ab", ylim=c(0,1.5)) standard<-DataTrack("nalm6_05_gly_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", col.histogram="blue", fill.histogram ="blue",name ="Standard", ylim=c(0,1.5)) nalm6_nodex<-DataTrack("nalnalm6_nly_control_lambda.bw",genome="hg19", cex.title=0.95, background.title="darkgreen", col.histogram="darkgreen", fill.histogram ="darkgreen",name ="No Drug", ylim=c(0,1.5),background.panel = "lightyellow") bcl6.gr<-GeneRegionTrack("bcl6.gtf",name="BCL6",stacking="squish",stac kHeight = 0.2, geneSymbols=TRUE, showId = TRUE, cex=1, cex.title=1.2, background.title="darkgray") plotTracks(list(itrack,gtrack,bcl6.gr, t+ col.histogram="blue", fill.histogram ="blue",name ="0.5% Tris", ylim=c(0,1.5)) > less_Ab<-DataTrack("nalm6_6ugn499_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", + col.histogram="blue", fill.histogram ="blue",name ="Less Ab", ylim=c(0,1.5)) > standard<-DataTrack("nalm6_05_gly_treat_pileup.bw",genome="hg19", cex.title=0.95, background.title="darkgray", + col.histogram="blue", fill.histogram ="blue",name ="Standard", ylim=c(0,1.5)) > nalm6_nodex<-DataTrack("nalnalm6_nly_control_lambda.bw",genome="hg19", cex.title=0.95, background.title="darkgreen", + col.histogram="darkgreen", fill.histogram ="darkgreen",name ="No Drug", ylim=c(0,1.5),background.panel = "lightyellow") bcl6.gr<-GeneRegionTrack("bcl6.gtf",name="BCL6",stacking="squish",stac kHeight = 0.2, geneSymbols=TRUE, showId = TRUE, cex=1, cex.title=1.2, background.title="darkgray") plotTracks(list(itrack,gtrack,bcl6.gr, tris_1p, tris_05p,less_Ab,standard,nalm6_nodex),from=187437000, to=187470000,type="histogram",chromosome="chr3")Error in validObject(.Object) : invalid class “ReferenceDataTrack” object: The referenced file 'nalnalm6_nly_control_lambda.bw' does not exist > > bcl6.gr<-GeneRegionTrack("bcl6.gtf",name="BCL6",stacking="squish",st ackHeight = 0.2, + geneSymbols=TRUE, showId = TRUE, cex=1, cex.title=1.2, background.title="darkgray") > > nalm6_nodex<-DataTrack("nalm6_05_gly_control_lambda.bw",genome="hg19", cex.title=0.95, background.title="darkgreen", + col.histogram="darkgreen", fill.histogram ="darkgreen",name ="No Drug", ylim=c(0,1.5),background.panel = "lightyellow") > > bcl6.gr<-GeneRegionTrack("bcl6.gtf",name="BCL6",stacking="squish",st ackHeight = 0.2, + geneSymbols=TRUE, showId = TRUE, cex=1, cex.title=1.2, background.title="darkgray") > plotTracks(list(itrack,gtrack,bcl6.gr, tris_1p, tris_05p,less_Ab,standard,nalm6_nodex),from=187437000, to=187470000,type="histogram",chromosome="chr3") Abort trap: 6 bash-3.2$ **************************** On May 1, 2013, at 3:58 PM, Michael Lawrence <lawrence.michael@gene.com> wrote: > Thanks for this. I just want to let you know that I am planning on looking into this. But I'll need to find a Mac, get gdb setup on it, etc. My guess is the error is inside Jim Kent's library, so it might be a pain to fix. > > Michael > > > On Mon, Apr 29, 2013 at 5:58 AM, Robert Ivanek <robert.ivanek@unibas.ch> wrote: > Dear Miles, > > Thanks for making the BigWigFile available. > > I can reproduce the error on my MAC (using devel version) and I can also > confirm that it works on my linux system (using both release and devel). > I think that the error is coming from rtraklayer import function, which > is used by Gviz to import the BigWigFile. > > I am sending this email to the BioC list and another one to the Michael > Lawrence (rtraklayer maintainer) together with the link you provided. > > Best > Robert > > ## --------------------------------------------------------------- > ## MAC > > library(Gviz) > gtrack <- GenomeAxisTrack() > b1_dex <- DataTrack("~/nalm6_dex.bw", strand="+",genome ="hg19"); > names(b1_dex)<-"Fkbp5"; > plotTracks(list(gtrack, b1_dex), from = 35540000, to = 35698000, > type="histogram", chromosome="chr6") > > Abort trap: 6 > > sessionInfo() > > ## R Under development (unstable) (2013-04-17 r62600) > ## Platform: x86_64-apple-darwin12.3.0/x86_64 (64-bit) > > ## locale: > ## [1] C/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > ## attached base packages: > ## [1] grid stats graphics grDevices utils datasets > methods base > > ## other attached packages: > ## [1] Gviz_1.5.1 > > ## loaded via a namespace (and not attached): > ## [1] AnnotationDbi_1.23.4 BSgenome_1.29.0 Biobase_2.21.0 > BiocGenerics_0.7.2 Biostrings_2.29.1 > ## [6] DBI_0.2-6 GenomicFeatures_1.13.1 > GenomicRanges_1.13.7 Hmisc_3.10-1 IRanges_1.19.3 > ## [11] RColorBrewer_1.0-5 RCurl_1.95-4.1 RSQLite_0.11.3 > Rsamtools_1.13.5 XML_3.96-1.1 > ## [16] biomaRt_2.17.0 biovizBase_1.9.1 bitops_1.0-5 > cluster_1.14.4 colorspace_1.2-2 > ## [21] compiler_3.1.0 dichromat_2.0-0 labeling_0.1 > lattice_0.20-15 munsell_0.4 > ## [26] parallel_3.1.0 plyr_1.8 rtracklayer_1.21.3 > scales_0.2.3 stats4_3.1.0 > ## [31] stringr_0.6.2 tools_3.1.0 zlibbioc_1.7.0 > > library(rtracklayer) > sessionInfo() > ## R Under development (unstable) (2013-04-17 r62600) > ## Platform: x86_64-apple-darwin12.3.0/x86_64 (64-bit) > > ## locale: > ## [1] C/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > ## attached base packages: > ## [1] parallel stats graphics grDevices utils datasets > methods base > > ## other attached packages: > ## [1] rtracklayer_1.21.3 GenomicRanges_1.13.7 IRanges_1.19.3 > BiocGenerics_0.7.2 > > ## loaded via a namespace (and not attached): > ## [1] BSgenome_1.29.0 Biostrings_2.29.1 RCurl_1.95-4.1 > Rsamtools_1.13.5 XML_3.96-1.1 bitops_1.0-5 > ## [7] stats4_3.1.0 tools_3.1.0 zlibbioc_1.7.0 > > import.bw("nalm6_dex.bw", GRanges("chr6", IRanges(start=35540000, > end=35698000), strand="+")) > > Abort trap: 6 > > > > ## --------------------------------------------------------------- > > ## --------------------------------------------------------------- > ## LINUX > > ## R version 3.0.0 Patched (2013-04-08 r62518) > ## Platform: x86_64-unknown-linux-gnu (64-bit) > > ## locale: > ## [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > LC_TIME=en_GB.UTF-8 > ## [4] LC_COLLATE=C LC_MONETARY=en_US.utf8 > LC_MESSAGES=en_US.utf8 > ## [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C > ## [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 > LC_IDENTIFICATION=C > > ## attached base packages: > ## [1] grid stats graphics grDevices utils datasets > methods base > > ## other attached packages: > ## [1] Gviz_1.4.1 > > ## loaded via a namespace (and not attached): > ## [1] AnnotationDbi_1.22.3 BSgenome_1.28.0 Biobase_2.20.0 > BiocGenerics_0.6.0 > ## [5] Biostrings_2.28.0 DBI_0.2-6 > GenomicFeatures_1.12.1 GenomicRanges_1.13.0 > ## [9] Hmisc_3.10-1 IRanges_1.18.0 RColorBrewer_1.0-5 > RCurl_1.95-4.1 > ## [13] RSQLite_0.11.3 Rsamtools_1.12.2 XML_3.96-1.1 > biomaRt_2.16.0 > ## [17] biovizBase_1.8.0 bitops_1.0-5 cluster_1.14.4 > colorspace_1.2-2 > ## [21] compiler_3.0.0 dichromat_2.0-0 labeling_0.1 > lattice_0.20-15 > ## [25] munsell_0.4 parallel_3.0.0 plyr_1.8 > rtracklayer_1.20.1 > ## [29] scales_0.2.3 stats4_3.0.0 stringr_0.6.2 > tools_3.0.0 > ## [33] zlibbioc_1.6.0 > > > > ## R Under development (unstable) (2013-04-08 r62518) > ## Platform: x86_64-unknown-linux-gnu (64-bit) > > ## locale: > ## [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > LC_TIME=en_GB.UTF-8 > ## [4] LC_COLLATE=C LC_MONETARY=en_US.utf8 > LC_MESSAGES=en_US.utf8 > ## [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C > ## [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 > LC_IDENTIFICATION=C > > ## attached base packages: > ## [1] grid stats graphics grDevices utils datasets > methods base > > ## other attached packages: > ## [1] Gviz_1.5.1 > > ## loaded via a namespace (and not attached): > ## [1] AnnotationDbi_1.23.4 BSgenome_1.29.0 Biobase_2.21.0 > BiocGenerics_0.7.2 > ## [5] Biostrings_2.29.1 DBI_0.2-6 > GenomicFeatures_1.13.1 GenomicRanges_1.13.7 > ## [9] Hmisc_3.10-1 IRanges_1.19.3 RColorBrewer_1.0-5 > RCurl_1.95-4.1 > ## [13] RSQLite_0.11.3 Rsamtools_1.13.5 XML_3.96-1.1 > biomaRt_2.17.0 > ## [17] biovizBase_1.9.1 bitops_1.0-5 cluster_1.14.4 > colorspace_1.2-2 > ## [21] dichromat_2.0-0 labeling_0.1 lattice_0.20-15 > munsell_0.4 > ## [25] parallel_3.1.0 plyr_1.8 rtracklayer_1.21.3 > scales_0.2.3 > ## [29] stats4_3.1.0 stringr_0.6.2 tools_3.1.0 > zlibbioc_1.7.0 > > > On 26/04/13 21:31, Miles Pufall wrote: > > Sure - I'm not sure of the protocol, so I'm sending this large file by replying to you directly. Just to re-emphasize, I was able to work with this file on my Linux box, but not on my mac (rMBP, 16Gb memory). You can grab it from my dropbox here: > > > > > > Let me know if you need anything else. > > > > Miles > > > > Miles Pufall, PhD > > Assistant Professor, Department of Biochemistry > > University of Iowa > > 51 Newton Rd., BSB 4-430 > > Iowa City, IA 52242 > > Office: 319-384-1820 > > Email: miles-pufall@uiowa.edu > > > > > > On Apr 26, 2013, at 8:00 AM, Robert Ivanek <robert.ivanek@unibas.ch> > > wrote: > > > >> Dear Dweebis, > >> > >> Thanks for reporting this issue. The first one is fixed, there was a bug > >> in "chromosome<-" method . Fixed versions 1.4.1 (2.12 branch) and 1.5.1 > >> (devel) should be available in 24 hours. > >> > >> Regarding the crash with BigWig file, would you mind to share it? > >> > >> Best > >> Robert > >> > >> On 26 Apr 2013, at 06:49, "Dweebis [guest]" <guest@bioconductor.org> wrote: > >> > >>> > >>> I'm trying to use Gviz to make figures displaying some ChIPseq data. I'd converted it to bigWig files to display in a genome browser and to store more easily. When I use Gviz on a Linux workstation, it seems to go smoothly, but when I use my MacBook Pro I have a few problems. The first is running some code from the vignette, which gives me the following error: > >>>> library(Gviz) > >>> Loading required package: grid > >>>> ideoTrack <- IdeogramTrack(genome = "hg19", chromosome = "chrX") > >>>> plotTracks(ideoTrack, from = 85000000, to = 129000000) > >>> Error in .normargSeqnames(seqnames) : > >>> supplied 'seqnames' cannot contain NAs or empty strings ("") > >>> > >>> The second is when I try to plot from my bigWig files: > >>>> library("Gviz") > >>> Loading required package: grid > >>>> library(GenomicRanges) > >>> Loading required package: BiocGenerics > >>> Loading required package: parallel > >>> > >>> Attaching package: â?~BiocGenericsâ?T > >>> > >>> The following objects are masked from â?~package:parallelâ?T: > >>> > >>> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, > >>> clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, > >>> parSapplyLB > >>> > >>> The following object is masked from â?~package:statsâ?T: > >>> > >>> xtabs > >>> > >>> The following objects are masked from â?~package:baseâ?T: > >>> > >>> anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, Filter, Find, > >>> get, intersect, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, > >>> pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, > >>> setdiff, sort, table, tapply, union, unique, unlist > >>> > >>> Loading required package: IRanges > >>>> setwd("~/Desktop/B1_ChIPseq") > >>>> gtrack <- GenomeAxisTrack() > >>>> b1_dex <- DataTrack("/Volumes/puf_3/Nalm6/nalm6_dex_n499.bw", strand="+",genome ="hg19"); > >>>> names(b1_dex)<-"Fkbp5"; > >>>> plotTracks(list(gtrack, b1_dex), from = 35540000, to = 35698000, type="histogram", chromosome="chr6") > >>> > >>> This crashes R completely with an exit message: Abort trap: 6 > >>> > >>> There is an associated OSX crash report, which I've pasted below. > >>> > >>> Any ideas what's going wrong? > >>> > >>> Thx - > >>> > >>> D > >>> > >>> Process: R [26469] > >>> Path: /Library/Frameworks/R.framework/Resources/bin/exec/R > >>> Identifier: R > >>> Version: ??? > >>> Code Type: X86-64 (Native) > >>> Parent Process: bash [26264] > >>> User ID: 501 > >>> > >>> Date/Time: 2013-04-25 23:24:05.617 -0500 > >>> OS Version: Mac OS X 10.8.3 (12D78) > >>> Report Version: 10 > >>> > >>> Interval Since Last Report: 2714 sec > >>> Crashes Since Last Report: 7 > >>> Per-App Crashes Since Last Report: 1 > >>> Anonymous UUID: 0FFEC26B- 8E19-7735-0F96-8B3430A59ECE > >>> > >>> Crashed Thread: 0 Dispatch queue: com.apple.main-thread > >>> > >>> Exception Type: EXC_CRASH (SIGABRT) > >>> Exception Codes: 0x0000000000000000, 0x0000000000000000 > >>> > >>> Application Specific Information: > >>> [26469] stack overflow > >>> > >>> Thread 0 Crashed:: Dispatch queue: com.apple.main-thread > >>> 0 libsystem_kernel.dylib 0x00007fff8a832212 __pthread_kill + 10 > >>> 1 libsystem_c.dylib 0x00007fff926f0b54 pthread_kill + 90 > >>> 2 libsystem_c.dylib 0x00007fff92734e9e __abort + 159 > >>> 3 libsystem_c.dylib 0x00007fff92735d17 __stack_chk_fail + 195 > >>> 4 rtracklayer.so 0x0000000107427d24 bptFileFind + 212 > >>> 5 rtracklayer.so 0x0000000107429104 bbiOverlappingBlocks + 68 > >>> 6 rtracklayer.so 0x000000010742cb00 bigWigIntervalQuery + 128 > >>> 7 rtracklayer.so 0x0000000107425bc0 BWGFile_query + 448 > >>> 8 libR.dylib 0x0000000100071033 do_dotcall + 547 (dotcode.c:585) > >>> 9 libR.dylib 0x0000000100099d67 Rf_eval + 1335 (eval.c:612) > >>> 10 libR.dylib 0x00000001000a7771 do_set + 369 (eval.c:1863) > >>> 11 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 12 libR.dylib 0x00000001000a7ad0 do_begin + 384 (eval.c:1534) > >>> 13 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 14 libR.dylib 0x00000001000a529e Rf_applyClosure + 1390 (eval.c:980) > >>> 15 libR.dylib 0x0000000100099e05 Rf_eval + 1493 (eval.c:631) > >>> 16 libR.dylib 0x00000001000a7ad0 do_begin + 384 (eval.c:1534) > >>> 17 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 18 libR.dylib 0x00000001000a86a2 R_execMethod + 1410 (eval.c:1076) > >>> 19 methods.so 0x00000001005eb474 R_dispatchGeneric + 1972 > >>> 20 libR.dylib 0x00000001000d6235 do_standardGeneric + 565 (objects.c:1142) > >>> 21 libR.dylib 0x0000000100099da3 Rf_eval + 1395 (eval.c:616) > >>> 22 libR.dylib 0x00000001000a529e Rf_applyClosure + 1390 (eval.c:980) > >>> 23 libR.dylib 0x0000000100099e05 Rf_eval + 1493 (eval.c:631) > >>> 24 libR.dylib 0x00000001000a7ad0 do_begin + 384 (eval.c:1534) > >>> 25 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 26 libR.dylib 0x00000001000a86a2 R_execMethod + 1410 (eval.c:1076) > >>> 27 methods.so 0x00000001005eb474 R_dispatchGeneric + 1972 > >>> 28 libR.dylib 0x00000001000d6235 do_standardGeneric + 565 (objects.c:1142) > >>> 29 libR.dylib 0x0000000100099da3 Rf_eval + 1395 (eval.c:616) > >>> 30 libR.dylib 0x00000001000a529e Rf_applyClosure + 1390 (eval.c:980) > >>> 31 libR.dylib 0x0000000100099e05 Rf_eval + 1493 (eval.c:631) > >>> 32 libR.dylib 0x00000001000a7ad0 do_begin + 384 (eval.c:1534) > >>> 33 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 34 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 35 libR.dylib 0x00000001000a7771 do_set + 369 (eval.c:1863) > >>> 36 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 37 libR.dylib 0x00000001000a7ad0 do_begin + 384 (eval.c:1534) > >>> 38 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 39 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 40 libR.dylib 0x00000001000a7ad0 do_begin + 384 (eval.c:1534) > >>> 41 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 42 libR.dylib 0x00000001000a529e Rf_applyClosure + 1390 (eval.c:980) > >>> 43 libR.dylib 0x0000000100099e05 Rf_eval + 1493 (eval.c:631) > >>> 44 libR.dylib 0x00000001000a7771 do_set + 369 (eval.c:1863) > >>> 45 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 46 libR.dylib 0x00000001000a7ad0 do_begin + 384 (eval.c:1534) > >>> 47 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 48 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 49 libR.dylib 0x00000001000a7ad0 do_begin + 384 (eval.c:1534) > >>> 50 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 51 libR.dylib 0x00000001000a529e Rf_applyClosure + 1390 (eval.c:980) > >>> 52 libR.dylib 0x0000000100099e05 Rf_eval + 1493 (eval.c:631) > >>> 53 libR.dylib 0x00000001000a7ad0 do_begin + 384 (eval.c:1534) > >>> 54 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 55 libR.dylib 0x00000001000a86a2 R_execMethod + 1410 (eval.c:1076) > >>> 56 methods.so 0x00000001005eb474 R_dispatchGeneric + 1972 > >>> 57 libR.dylib 0x00000001000d6235 do_standardGeneric + 565 (objects.c:1142) > >>> 58 libR.dylib 0x0000000100099da3 Rf_eval + 1395 (eval.c:616) > >>> 59 libR.dylib 0x00000001000a529e Rf_applyClosure + 1390 (eval.c:980) > >>> 60 libR.dylib 0x0000000100099e05 Rf_eval + 1493 (eval.c:631) > >>> 61 libR.dylib 0x000000010000eb81 do_lapply + 673 (apply.c:76) > >>> 62 libR.dylib 0x00000001000d3c5a do_internal + 362 (names.c:1168) > >>> 63 libR.dylib 0x000000010009cd1f bcEval + 11791 (eval.c:4583) > >>> 64 libR.dylib 0x000000010009994f Rf_eval + 287 (eval.c:515) > >>> 65 libR.dylib 0x00000001000a86a2 R_execMethod + 1410 (eval.c:1076) > >>> 66 methods.so 0x00000001005eb474 R_dispatchGeneric + 1972 > >>> 67 libR.dylib 0x00000001000d6235 do_standardGeneric + 565 (objects.c:1142) > >>> 68 libR.dylib 0x0000000100099da3 Rf_eval + 1395 (eval.c:616) > >>> 69 libR.dylib 0x00000001000a529e Rf_applyClosure + 1390 (eval.c:980) > >>> 70 libR.dylib 0x0000000100099e05 Rf_eval + 1493 (eval.c:631) > >>> 71 libR.dylib 0x00000001000a7771 do_set + 369 (eval.c:1863) > >>> 72 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 73 libR.dylib 0x00000001000a7ad0 do_begin + 384 (eval.c:1534) > >>> 74 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 75 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 76 libR.dylib 0x00000001000a7ad0 do_begin + 384 (eval.c:1534) > >>> 77 libR.dylib 0x0000000100099bd6 Rf_eval + 934 (eval.c:584) > >>> 78 libR.dylib 0x00000001000a529e Rf_applyClosure + 1390 (eval.c:980) > >>> 79 libR.dylib 0x0000000100099e05 Rf_eval + 1493 (eval.c:631) > >>> 80 libR.dylib 0x00000001000c97df Rf_ReplIteration + 879 (main.c:258) > >>> 81 libR.dylib 0x00000001000c9e63 run_Rmainloop + 211 (main.c:307) > >>> 82 R 0x0000000100000e5b main + 27 > >>> 83 R 0x0000000100000e34 start + 52 > >>> > >>> Thread 1:: Dispatch queue: com.apple.libdispatch-manager > >>> 0 libsystem_kernel.dylib 0x00007fff8a832d16 kevent + 10 > >>> 1 libdispatch.dylib 0x00007fff8affddea _dispatch_mgr_invoke + 883 > >>> 2 libdispatch.dylib 0x00007fff8affd9ee _dispatch_mgr_thread + 54 > >>> > >>> Thread 2: > >>> 0 libsystem_kernel.dylib 0x00007fff8a832322 __select + 10 > >>> 1 grDevices.so 0x0000000102ea8440 -[ELThread eventsThread:] + 176 > >>> 2 com.apple.Foundation 0x00007fff8f55ecd2 __NSThread__main__ + 1345 > >>> 3 libsystem_c.dylib 0x00007fff926ef7a2 _pthread_start + 327 > >>> 4 libsystem_c.dylib 0x00007fff926dc1e1 thread_start + 13 > >>> > >>> Thread 0 crashed with X86 Thread State (64-bit): > >>> rax: 0x0000000000000000 rbx: 0x0000000000000006 rcx: 0x00007fff5fbf83f8 rdx: 0x0000000000000000 > >>> rdi: 0x0000000000000f07 rsi: 0x0000000000000006 rbp: 0x00007fff5fbf8420 rsp: 0x00007fff5fbf83f8 > >>> r8: 0x00007fff7abed278 r9: 0x0000000000000000 r10: 0x0000000020000000 r11: 0x0000000000000206 > >>> r12: 0x00007fff5fbf84f0 r13: 0x0000000000000004 r14: 0x00007fff7abee180 r15: 0x0000000107293010 > >>> rip: 0x00007fff8a832212 rfl: 0x0000000000000206 cr2: 0x00007fff7abe6ff0 > >>> Logical CPU: 0 > >>> > >>> Binary Images: > >>> 0x100000000 - 0x100000ff7 +R (???) <d62f3923-33a9-31e3-8256-72609aff38df> /Library/Frameworks/R.framework/Resources/bin/exec/R > >>> 0x100003000 - 0x10026efff +libR.dylib (3) 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0x103a7efff +libRlapack.dylib (3) <c2dd755e-0f94-37f9-85f2-305e6f3720fb> /Library/Frameworks/R.framework /Versions/3.0/Resources/lib/libRlapack.dylib > >>> 0x103e66000 - 0x103e97ff7 +IRanges.so (0) <65E44E38-96BC- 3AC5-8490-5EDE934749F4> /Library/Frameworks/R.framework/Versions/3.0/R esources/library/IRanges/libs/IRanges.so > >>> 0x103f9a000 - 0x103fd5fef +Rsamtools.so (0) <2ECCAE63-A2CE-3097-8AFF-31E11FB22989> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/Rsamtools/libs/Rsamtools.so > >>> 0x107420000 - 0x107461ff7 +rtracklayer.so (0) <a1b33ecb- 4c97-3d25-a0c1-21609054a3ca=""> /Library/Frameworks/R.framework/Versions/ 3.0/Resources/library/rtracklayer/libs/rtracklayer.so > >>> 0x108000000 - 0x10802aff7 +Biostrings.so (0) <d2594ec2 -693d-3b33-ade7-6cd903626301=""> /Library/Frameworks/R.framework/Versions /3.0/Resources/library/Biostrings/libs/Biostrings.so > >>> 0x10f800000 - 0x10f8c8fff +RSQLite.so (0) <e5afc155-2126-35f7-bb65-9ec27183117a> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/RSQLite/libs/RSQLite.so > >>> 0x7fff619d3000 - 0x7fff61a0793f dyld (210.2.3) <a40597aa-5529-3337-8c09-d8a014eb1578> /usr/lib/dyld > >>> 0x7fff8973b000 - 0x7fff8975aff7 libresolv.9.dylib (51) <0882DC2D-A892-31FF-AD8C-0BB518C48B23> /usr/lib/libresolv.9.dylib > >>> 0x7fff8975b000 - 0x7fff897aaff7 libFontRegistry.dylib (100) <2E03D7DA-9B8F-31BB-8FB5-3D3B6272127F> /System/Library/Frameworks/Appl icationServices.framework/Versions/A/Frameworks/ATS.framework/Versions /A/Resources/libFontRegistry.dylib > >>> 0x7fff89b4c000 - 0x7fff89b59fff com.apple.AppleFSCompression (49 - 1.0) <5508344A- 2A7E-3122-9562-6F363910A80E> /System/Library/PrivateFrameworks/AppleFS Compression.framework/Versions/A/AppleFSCompression > >>> 0x7fff89b5a000 - 0x7fff89bb0fff com.apple.HIServices (1.20 - 417) <a1129272-fec8-350b-ba26-5a97f23c413d> /System/Library/Framewor ks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.fram 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<d15f3fb3-be53-3545-ad37-9a25a597fe3c> /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio > >>> 0x7fff8a3d1000 - 0x7fff8a43afff libstdc++.6.dylib (56) <eaa2b53e-eade-39cf-a0ef-fb9d4940672a> /usr/lib/libstdc++.6.dylib > >>> 0x7fff8a43b000 - 0x7fff8a63bfff libicucore.A.dylib (491.11.2) <fd6282d8-df3f-3842-8c2e-cf478d2b9669> /usr/lib/libicucore.A.dylib > >>> 0x7fff8a63c000 - 0x7fff8a755fff com.apple.ImageIO.framework (3.2.0 - 849) <c52aed41-a7c2-300b-91fa-5af73718d243> /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO > >>> 0x7fff8a789000 - 0x7fff8a798fff com.apple.opengl (1.8.7 - 1.8.7) <26F7FF79-6BB2-3968-B70D-71D4E07C9551> /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL > >>> 0x7fff8a799000 - 0x7fff8a7c3ff7 com.apple.CoreVideo (1.8 - 99.4) <e5082966-6d81-3973-a05a-38aa5b85f886> /System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo > >>> 0x7fff8a820000 - 0x7fff8a83bff7 libsystem_kernel.dylib (2050.22.13) <5A961E2A-CFB8-362B-BC43-122704AEB047> /usr/lib/system/libsystem_kernel.dylib > >>> 0x7fff8a977000 - 0x7fff8a981fff com.apple.speech.recognition.framework (4.1.5 - 4.1.5) <d803919c-3102-3515-a178-61e9c86c46a1> /System/Library/Frameworks/Carb on.framework/Versions/A/Frameworks/SpeechRecognition.framework/Version s/A/SpeechRecognition > >>> 0x7fff8a991000 - 0x7fff8a9e0ff7 libcorecrypto.dylib (106.2) <ce0c29a3-c420-339b-adaa-52f4683233cc> /usr/lib/system/libcorecrypto.dylib > >>> 0x7fff8a9ed000 - 0x7fff8aa04fff libGL.dylib (8.7.25) <15F5CB64-847B-3D3D-9663-E0523F15F513> /System/Library/Frameworks/Open GL.framework/Versions/A/Libraries/libGL.dylib > >>> 0x7fff8aa16000 - 0x7fff8aa18fff com.apple.TrustEvaluationAgent (2.0 - 23) <a97d348b-32bf- 3e52-8df2-59bfad21e1a3=""> /System/Library/PrivateFrameworks/TrustEvaluat ionAgent.framework/Versions/A/TrustEvaluationAgent > >>> 0x7fff8aa1d000 - 0x7fff8aa2bfff com.apple.Librarian (1.1 - 1) <5AC28666-7642-395F-A923-C6F8A274BBBD> /System/Library/PrivateFrame works/Librarian.framework/Versions/A/Librarian > >>> 0x7fff8aa2c000 - 0x7fff8aa2dff7 libSystem.B.dylib (169.3) <365477AB-D641-389D-B8F4-A1FAE9657EEE> /usr/lib/libSystem.B.dylib > >>> 0x7fff8aa2e000 - 0x7fff8aa50ff7 libxpc.dylib (140.42) <bbe558bd-5e55-35e4-89ed-1aa6b056d05a> /usr/lib/system/libxpc.dylib > >>> 0x7fff8aa51000 - 0x7fff8ab02fff com.apple.LaunchServices (539.7 - 539.7) <da7c602e-5e01-31b8-925d-b45360ca089f> /System/Library /Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchService s.framework/Versions/A/LaunchServices > >>> 0x7fff8ab03000 - 0x7fff8ab0afff com.apple.NetFS (5.0 - 4.0) <82E24B9A-7742-3DA3-9E99-ED267D98C05E> /System/Library/Frameworks/NetFS.framework/Versions/A/NetFS > >>> 0x7fff8ab22000 - 0x7fff8ab34ff7 libz.1.dylib (43) <2A1551E8-A272-3DE5-B692-955974FE1416> /usr/lib/libz.1.dylib > >>> 0x7fff8ab35000 - 0x7fff8ab3bfff libmacho.dylib (829) <bf332ad9-e89f-387e-92a4-6e1ab74bd4d9> /usr/lib/system/libmacho.dylib > >>> 0x7fff8ab3c000 - 0x7fff8ab3cfff libOpenScriptingUtil.dylib (148.3) <f8681222-0969-3b10-8bce-c55a4b9c520c> /usr/lib/libOpenScriptingUtil.dylib > >>> 0x7fff8ade0000 - 0x7fff8ae11ff7 com.apple.DictionaryServices (1.2 - 184.4) <054F2D6F-9CFF- 3EF1-9778-25C551B616C1> /System/Library/Frameworks/CoreServices.framew ork/Versions/A/Frameworks/DictionaryServices.framework/Versions/A/Dict ionaryServices > >>> 0x7fff8ae12000 - 0x7fff8af0ffff libsqlite3.dylib (138.1) <ade9cb98-d77d-300c-a32a-556b7440769f> /usr/lib/libsqlite3.dylib > >>> 0x7fff8af10000 - 0x7fff8afcdff7 com.apple.ColorSync (4.8.0 - 4.8.0) <6CE333AE-EDDB-3768-9598-9DB38041DC55> /System/Library/Framew orks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.fra mework/Versions/A/ColorSync > >>> 0x7fff8aff7000 - 0x7fff8aff8fff libsystem_blocks.dylib (59) <d92dcbc3-541c-37bd-aade-acc75a0c59c8> /usr/lib/system/libsystem_blocks.dylib > >>> 0x7fff8aff9000 - 0x7fff8b00eff7 libdispatch.dylib (228.23) <d26996bf-fc57-39eb-8829-f63585561e09> /usr/lib/system/libdispatch.dylib > >>> 0x7fff8b00f000 - 0x7fff8b016fff libGFXShared.dylib (8.7.25) <869580B2-39CB-30C3-B76E-73BB4894B6B7> /System/Library/Frameworks/Open GL.framework/Versions/A/Libraries/libGFXShared.dylib > >>> 0x7fff8b0d9000 - 0x7fff8b22afff com.apple.audio.toolbox.AudioToolbox (1.8 - 1.8) <c680ee1a-b4ed-3e77 -a08c-dc47922aca33=""> /System/Library/Frameworks/AudioToolbox.framework/ Versions/A/AudioToolbox > >>> 0x7fff8b729000 - 0x7fff8b748ff7 com.apple.ChunkingLibrary (2.0 - 133.3) <8BEC9AFB-DCAA-37E8-A5AB-24422B234ECF> /System/Library/P rivateFrameworks/ChunkingLibrary.framework/Versions/A/ChunkingLibrary > >>> 0x7fff8b749000 - 0x7fff8b749fff com.apple.CoreServices (57 - 57) <9DD44CB0-C644-35C3-8F57-0B41B3EC147D> /System/Library/Framework s/CoreServices.framework/Versions/A/CoreServices > >>> 0x7fff8b7da000 - 0x7fff8b7dcfff libquarantine.dylib (52) <4BE2E642-A14F-340A-B482-5BD2AEFD9C24> /usr/lib/system/libquarantine.dylib > >>> 0x7fff8c093000 - 0x7fff8c19efff libFontParser.dylib (84.6) <96C42E49-79A6-3475-B5E4-6A782599A6DA> /System/Library/Frameworks/Appl icationServices.framework/Versions/A/Frameworks/ATS.framework/Versions /A/Resources/libFontParser.dylib > >>> 0x7fff8c1e3000 - 0x7fff8c1e7ff7 com.apple.TCC (1.0 - 1) <f2f3b753-fc73-3543-8bbe-859fdbb4d6a6> /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC > >>> 0x7fff8c230000 - 0x7fff8c239ff7 com.apple.CommerceCore (1.0 - 26.1) <40A129A8-4E5D-3C7A-B299-8CB203C4C65D> /System/Library/Private Frameworks/CommerceKit.framework/Versions/A/Frameworks/CommerceCore.fr amework/Versions/A/CommerceCore > >>> 0x7fff8c23a000 - 0x7fff8c631fff libLAPACK.dylib (1073.4) <d632ec8b-2ba0-3853-800a-20da00a1091c> /System/Library/Frameworks/Acce lerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/lib LAPACK.dylib > >>> 0x7fff8c652000 - 0x7fff8c661ff7 libxar.1.dylib (105) <370ED355-E516-311E-BAFD-D80633A84BE1> /usr/lib/libxar.1.dylib > >>> 0x7fff8c67c000 - 0x7fff8c690fff com.apple.speech.synthesis.framework (4.1.12 - 4.1.12) <94EDF2AB-809C- 3D15-BED5-7AD45B2A7C16> /System/Library/Frameworks/ApplicationServices .framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/ SpeechSynthesis > >>> 0x7fff8c698000 - 0x7fff8c6a5ff7 com.apple.NetAuth (4.0 - 4.0) <f5bc7d7d-af28-3c83-a674-dada48ff7810> /System/Library/PrivateFrameworks/NetAuth.framework/Versions/A/NetAuth > >>> 0x7fff8c798000 - 0x7fff8c85dff7 com.apple.coreui (2.0 - 181.1) <83D2C92D-6842-3C9D-9289-39D5B4554C3A> /System/Library/PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI > >>> 0x7fff8c85e000 - 0x7fff8c899fff com.apple.LDAPFramework (2.4.28 - 194.5) <67FBDB29-3B9F-309A-BA7C-AA5921D9A4FB> /System/Library/Frameworks/LDAP.framework/Versions/A/LDAP > >>> 0x7fff8c89a000 - 0x7fff8ccb7fff FaceCoreLight (2.4.1) <a34c9575-c4c1-31b1-809b-7751070b4e8b> /System/Library/PrivateFramewor ks/FaceCoreLight.framework/Versions/A/FaceCoreLight > >>> 0x7fff8ccc1000 - 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com.apple.PerformanceAnalysis (1.16 - 16) <e4888388-f41b-313e-9cbb- 5807d077bda9=""> /System/Library/PrivateFrameworks/PerformanceAnalysis.fr amework/Versions/A/PerformanceAnalysis > >>> 0x7fff8ff0d000 - 0x7fff8ff2efff com.apple.Ubiquity (1.2 - 243.15) <c9a7ee77-b637-3676-b667-c0843bbb0409> /System/Library/Private Frameworks/Ubiquity.framework/Versions/A/Ubiquity > >>> 0x7fff901f3000 - 0x7fff901f3fff com.apple.Accelerate (1.8 - Accelerate 1.8) <6AD48543-0864-3D40-80CE-01F184F24B45> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate > >>> 0x7fff901f4000 - 0x7fff9021cfff libJPEG.dylib (849) <5C9052F6-D0B3-39CC-8302-468B43D694D5> /System/Library/Frameworks/Imag eIO.framework/Versions/A/Resources/libJPEG.dylib > >>> 0x7fff90631000 - 0x7fff90632ff7 libremovefile.dylib (23.2) <6763BC8E-18B8-3AD9-8FFA-B43713A7264F> /usr/lib/system/libremovefile.dylib > >>> 0x7fff90633000 - 0x7fff90633fff com.apple.Accelerate.vecLib (3.8 - vecLib 3.8) <b5a18ee8-df81-38dd-acaf-7076b2a26225> 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<0BF1F2D2-3648-36B7-BE4B-551A0173209B> /System/Library/PrivateFrameworks/Bom.framework/Versions/A/Bom > >>> 0x7fff93385000 - 0x7fff9349d92f libobjc.A.dylib (532.2) <90D31928-F48D-3E37-874F-220A51FD9E37> /usr/lib/libobjc.A.dylib > >>> 0x7fff934e7000 - 0x7fff934eaff7 libdyld.dylib (210.2.3) <f59367c9-c110-382b-a695-9035a6dd387e> /usr/lib/system/libdyld.dylib > >>> 0x7fff934eb000 - 0x7fff934ebffd com.apple.audio.units.AudioUnit (1.8 - 1.8) <173346B7-614C-380B- 8E80-9BD1BE501674> /System/Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit > >>> 0x7fff934f8000 - 0x7fff93535fef libGLImage.dylib (8.7.25) <139A9892-A6F2-3F49-87FB-E7AC3F56E003> /System/Library/Frameworks/Open GL.framework/Versions/A/Libraries/libGLImage.dylib > >>> 0x7fff93536000 - 0x7fff9354dfff com.apple.GenerationalStorage (1.1 - 132.3) <fd4a84b3-13a8-3c60-a59e- 25a361447a17=""> /System/Library/PrivateFrameworks/GenerationalStorage.fr amework/Versions/A/GenerationalStorage > >>> 0x7fff935ee000 - 0x7fff935fcff7 libkxld.dylib (2050.22.13) <4AAF0573-8632-3D06-BE32-C5675F77638D> /usr/lib/system/libkxld.dylib > >>> 0x7fff935fd000 - 0x7fff93628fff libxslt.1.dylib (11.3) <441776B8-9130-3893-956F-39C85FFA644F> /usr/lib/libxslt.1.dylib > >>> 0x7fff93629000 - 0x7fff93630fff libcopyfile.dylib (89) <876573D0-E907-3566-A108-577EAD1B6182> /usr/lib/system/libcopyfile.dylib > >>> 0x7fff93e5e000 - 0x7fff93ea6fff libcurl.4.dylib (69.2) <ebdbf42d-e4a6-3d05-a76b-2817d79d59e2> /usr/lib/libcurl.4.dylib > >>> 0x7fff93ea7000 - 0x7fff93f0ffff libvDSP.dylib (380.6) <cd4c5eeb-9e63-30c4-8103-7a5eaea0be60> /System/Library/Frameworks/Acce lerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/lib vDSP.dylib > >>> 0x7fff94062000 - 0x7fff94297ff7 com.apple.CoreData (106.1 - 407.7) <24E0A6B4-9ECA-3D12-B26A-72B9DCF09768> /System/Library/Frameworks/CoreData.framework/Versions/A/CoreData > >>> 0x7fff9429b000 - 0x7fff94319ff7 com.apple.securityfoundation (6.0 - 55115.4) <c5461971-e455-31a6-99b8-af80c4bc26dd> /System/Library/Frameworks/Secu rityFoundation.framework/Versions/A/SecurityFoundation > >>> 0x7fff9431b000 - 0x7fff943b9ff7 com.apple.ink.framework (10.8.2 - 150) <84B9825C-3822-375F-BE58-A753444FBDE2> /System/Library/ Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versio ns/A/Ink > >>> 0x7fff95378000 - 0x7fff9568fff7 com.apple.CoreServices.CarbonCore (1037.5 - 1037.5) <731D8F92-1C52-3613-BA01-EFEA54DADF41> /System/Library/Frameworks/Core Services.framework/Versions/A/Frameworks/CarbonCore.framework/Versions /A/CarbonCore > >>> 0x7fff95690000 - 0x7fff95710ff7 com.apple.ApplicationServices.ATS (332 - 341.1) <bd83b039-ab25-3e3e-9975-a67dae66988b> /System/Library/Frameworks/Appl icationServices.framework/Versions/A/Frameworks/ATS.framework/Versions /A/ATS > >>> 0x7fff95711000 - 0x7fff95715fff libCGXType.A.dylib (331.0.4) <251D4D2D-92B9-3D56-B348-CD67397F71FE> /System/Library/Frame works/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics 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/System/Library/Frameworks/vecLib.framework/Versions/A/vecLib > >>> 0x7fff95fbd000 - 0x7fff95fc1fff com.apple.IOSurface (86.0.4 - 86.0.4) <26F01CD4-B76B-37A3-989D-66E8140542B3> /System/Library/Frameworks/IOSurface.framework/Versions/A/IOSurface > >>> 0x7fff963ff000 - 0x7fff965adfff com.apple.QuartzCore (1.8 - 304.2) <234EABE1-067C-3DAE-BEAC-674526E232C2> /System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore > >>> 0x7fff965ae000 - 0x7fff965bcff7 libsystem_network.dylib (77.10) <0D99F24E-56FE-380F-B81B-4A4C630EE587> /usr/lib/system/libsystem_network.dylib > >>> 0x7fff96622000 - 0x7fff96626fff libCoreVMClient.dylib (32.3) <ad8391d9-56dd-3a78-a294-6a30e6ece1a2> /System/Library/Framewor ks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib > >>> 0x7fff96627000 - 0x7fff96701fff com.apple.backup.framework (1.4.2 - 1.4.2) <0B557393-CD2A-3076-BED2-F28D02E1EC1D> /System/Library/PrivateFrameworks/Backup.framework/Versions/A/Backup > >>> 0x7fff96702000 - 0x7fff9674cff7 libGLU.dylib (8.7.25) <c243c6d3-3384-3db1-bb15-e27b65c87294> /System/Library/Frameworks/Open GL.framework/Versions/A/Libraries/libGLU.dylib > >>> > >>> External Modification Summary: > >>> Calls made by other processes targeting this process: > >>> task_for_pid: 2 > >>> thread_create: 0 > >>> thread_set_state: 0 > >>> Calls made by this process: > >>> task_for_pid: 0 > >>> thread_create: 0 > >>> thread_set_state: 0 > >>> Calls made by all processes on this machine: > >>> task_for_pid: 18259 > >>> thread_create: 2 > >>> thread_set_state: 0 > >>> > >>> VM Region Summary: > >>> ReadOnly portion of Libraries: Total=154.5M resident=91.3M(59%) swapped_out_or_unallocated=63.1M(41%) > >>> Writable regions: Total=445.0M written=272.1M(61%) resident=289.8M(65%) swapped_out=1276K(0%) unallocated=155.2M(35%) > >>> > >>> REGION TYPE VIRTUAL > >>> =========== ======= > >>> ATS (font support) 32.3M > >>> ATS (font support) (reserved) 4K reserved VM address space (unallocated) > >>> CG backing stores 10.3M > >>> CG image 4K > >>> CG raster data 96K > >>> CG shared images 192K > >>> CoreServices 7332K > >>> MALLOC 336.8M > >>> MALLOC guard page 48K > >>> MALLOC_LARGE (reserved) 228K reserved VM address space (unallocated) > >>> Memory tag=242 12K > >>> STACK GUARD 56.0M > >>> Stack 9232K > >>> VM_ALLOCATE 16.1M > >>> __DATA 50.6M > >>> __IMAGE 528K > >>> __LINKEDIT 53.8M > >>> __TEXT 100.6M > >>> __UNICODE 544K > >>> mapped file 59.9M > >>> shared memory 308K > >>> =========== ======= > >>> TOTAL 734.5M > >>> TOTAL, minus reserved VM space 734.3M > >>> > >>> Model: MacBookPro10,1, BootROM MBP101.00EE.B02, 4 processors, Intel Core i7, 2.6 GHz, 16 GB, SMC 2.3f35 > >>> Graphics: Intel HD Graphics 4000, Intel HD Graphics 4000, Built- In, 512 MB > >>> Graphics: NVIDIA GeForce GT 650M, NVIDIA GeForce GT 650M, PCIe, 1024 MB > >>> Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80CE, 0x4D34373142314737334248302D434B302020 > >>> Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80CE, 0x4D34373142314737334248302D434B302020 > >>> AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xEF), Broadcom BCM43xx 1.0 (5.106.98.100.16) > >>> Bluetooth: Version 4.1.3f3 11349, 2 service, 18 devices, 1 incoming serial ports > >>> Network Service: Wi-Fi, AirPort, en0 > >>> Serial ATA Device: APPLE SSD SM512E, 500.28 GB > >>> USB Device: FreeAgent GoFlex, 0x0bc2 (Seagate LLC), 0x5031, 0x14a00000 / 4 > >>> USB Device: hub_device, 0x8087 (Intel Corporation), 0x0024, 0x1a100000 / 2 > >>> USB Device: FaceTime HD Camera (Built-in), apple_vendor_id, 0x8510, 0x1a110000 / 3 > >>> USB Device: hub_device, 0x8087 (Intel Corporation), 0x0024, 0x1d100000 / 2 > >>> USB Device: hub_device, 0x0424 (SMSC), 0x2512, 0x1d180000 / 3 > >>> USB Device: BRCM20702 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x1d181000 / 5 > >>> USB Device: Bluetooth USB Host Controller, apple_vendor_id, 0x8286, 0x1d181300 / 6 > >>> USB Device: Apple Internal Keyboard / Trackpad, apple_vendor_id, 0x0262, 0x1d182000 / 4 > >>> USB Device: hub_device, 0x0424 (SMSC), 0x2514, 0x14100000 / 1 > >>> USB Device: ScanSnap S1500, 0x04c5 (Fujitsu Ltd.), 0x11a2, 0x14140000 / 3 > >>> USB Device: Microsoft Digital Sound System 80, 0x045e (Microsoft Corporation), 0x0014, 0x14120000 / 2 > >>> > >>> > >>> > >>> > >>> > >>> -- output of sessionInfo(): > >>> > >>>> sessionInfo() > >>> R version 3.0.0 (2013-04-03) > >>> Platform: x86_64-apple-darwin10.8.0 (64-bit) > >>> > >>> locale: > >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >>> > >>> attached base packages: > >>> [1] parallel grid stats graphics grDevices utils datasets methods base > >>> > >>> other attached packages: > >>> [1] GenomicRanges_1.12.2 IRanges_1.18.0 BiocGenerics_0.6.0 Gviz_1.4.0 > >>> > >>> loaded via a namespace (and not attached): > >>> [1] AnnotationDbi_1.22.2 Biobase_2.20.0 biomaRt_2.16.0 Biostrings_2.28.0 > >>> [5] biovizBase_1.8.0 bitops_1.0-5 BSgenome_1.28.0 cluster_1.14.4 > >>> [9] colorspace_1.2-2 DBI_0.2-6 dichromat_2.0-0 GenomicFeatures_1.12.0 > >>> [13] Hmisc_3.10-1 labeling_0.1 lattice_0.20-15 munsell_0.4 > >>> [17] plyr_1.8 RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.12.2 > >>> [21] RSQLite_0.11.3 rtracklayer_1.20.1 scales_0.2.3 stats4_3.0.0 > >>> [25] stringr_0.6.2 tools_3.0.0 XML_3.95-0.2 zlibbioc_1.6.0 > >>> > >>> -- > >>> Sent via the guest posting facility at bioconductor.org. > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor@r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.3 years ago by Michael Lawrence11k • written 6.3 years ago by Miles Pufall40
Answer: IdeogramTrack and bigWig file errors in Gviz
0
gravatar for Michael Lawrence
6.3 years ago by
United States
Michael Lawrence11k wrote:
Will elevate this on the TODO list. On Mon, Oct 7, 2013 at 11:36 AM, Miles Pufall <miles.pufall@gmail.com>wrote: > Hi Michael - > > I know this is an old thread, but I am still unable to use BigWig files > from my ChIPseq data using Gviz on a Mac. When I run it on a linux box > everything runs perfectly. Should I still be having this problem, or have > I missed a fix along the way. Here are my sessionInfo() and error. > Thanks, and, as always, happy to share any files you'd like. > > M > > *****************(sessionInfo) > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel grid stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] GenomicFeatures_1.13.46 AnnotationDbi_1.23.27 Biobase_2.21.7 > GenomicRanges_1.13.51 XVector_0.1.4 IRanges_1.19.38 > [7] BiocGenerics_0.7.5 Gviz_1.5.15 > > loaded via a namespace (and not attached): > [1] biomaRt_2.17.3 Biostrings_2.29.19 biovizBase_1.9.4 > bitops_1.0-6 BSgenome_1.29.1 cluster_1.14.4 > colorspace_1.2-3 > [8] DBI_0.2-7 dichromat_2.0-0 Hmisc_3.12-2 > labeling_0.2 lattice_0.20-23 latticeExtra_0.6-26 munsell_0.4.2 > > [15] plyr_1.8 RColorBrewer_1.0-5 RCurl_1.95-4.1 > rpart_4.1-3 Rsamtools_1.13.47 RSQLite_0.11.4 > rtracklayer_1.21.12 > [22] scales_0.2.3 stats4_3.0.2 stringr_0.6.2 > tools_3.0.2 XML_3.98-1.1 zlibbioc_1.7.0 > > *****************(error) > library("Gviz") > Loading required package: grid > library(GenomicFeatures) > setwd("/Volumes/Pufall_BD1/ChIPseq/Nalm6/GR/") > itrack <- IdeogramTrack(genome = "hg19", cex = 1) > gtrack <- GenomeAxisTrack(cex=1) > > tris_1p<-DataTrack("nalm6_1p_tris_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > col.histogram="blue", fill.histogram ="blue",name ="1% > Tris", ylim=c(0,1.5)) > tris_05p<-DataTrack("nalm6_05p_tris_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > col.histogram="blue", fill.histogram ="blue",name > ="0.5% Tris", ylim=c(0,1.5)) > less_Ab<-DataTrack("nalm6_6ugn499_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > col.histogram="blue", fill.histogram ="blue",name > ="Less Ab", ylim=c(0,1.5)) > standard<-DataTrack("nalm6_05_gly_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > col.histogram="blue", fill.histogram ="blue",name > ="Standard", ylim=c(0,1.5)) > nalm6_nodex<-D> library(GenomicFeatures) > Loading required package: BiocGenerics > Loading required package: parallel > > Attaching package: ‘BiocGenerics’ > > The following objects are masked from ‘package:parallel’: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > clusterExport, clusterMap, parApply, parCapply, parLapply, > parLapplyLB, parRapply, parSapply, parSapplyLB > > The following object is masked from ‘package:stats’: > > xtabs > > The following objects are masked from ‘package:base’: > > anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, > duplicated, eval, Filter, Find, get, intersect, lapply, Map, > mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, > Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, > sort, table, tapply, union, unique, unlist > > Loading required package: IRanges > Loading required package: GenomicRanges > setwd("/Volumes/Pufall_BD1/ChIPseq/Nalm6/GR/") > itrack <- IdeogramTrack(genome = "hg19", cex = 1) > gtrack <- GenomeAxisTrack(cex=1) > > tris_1p<-DataTrack("nalm6_1p_tris_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > col.histogram="blue", fill.histogram ="blue",name ="1% > Tris", ylim=c(0,1.5)) > tris_05p<-DataTrack("nalm6_05p_tris_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > col.histogram="blue", fill.histogram ="blue",name > ="0.5% Tris", ylim=c(0,1.5)) > less_Ab<-DataTrack("nalm6_6ugn499_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > col.histogram="blue", fill.histogram ="blue",name > ="Less Ab", ylim=c(0,1.5)) > standard<-DataTrack("nalm6_05_gly_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > col.histogram="blue", fill.histogram ="blue",name > ="Standard", ylim=c(0,1.5)) > nalm6_nodex<-DataTrack("nalnalm6_nly_conLoading required package: XVector > Loading required package: AnnotationDbi > Loading required package: Biobase > Welcome to Bioconductor > > Vignettes contain introductory material; view with > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")', and for packages 'citation("pkgname")'. > > > setwd("/Volumes/Pufall_BD1/ChIPseq/Nalm6/GR/") > > itrack <- IdeogramTrack(genome = "hg19", cex = 1) > gtrack <- GenomeAxisTrack(cex=1) > > tris_1p<-DataTrack("nalm6_1p_tris_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > col.histogram="blue", fill.histogram ="blue",name ="1% > Tris", ylim=c(0,1.5)) > tris_05p<-DataTrack("nalm6_05p_tris_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > col.histogram="blue", fill.histogram ="blue",name > ="0.5% Tris", ylim=c(0,1.5)) > less_Ab<-DataTrack("nalm6_6ugn499_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > col.histogram="blue", fill.histogram ="blue",name > ="Less Ab", ylim=c(0,1.5)) > standard<-DataTrack("nalm6_05_gly_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > col.histogram="blue", fill.histogram ="blue",name > ="Standard", ylim=c(0,1.5)) > nalm6_nodex<-DataTrack("nalnalm6_nly_control_lambda.bw",genome="hg19", > cex.title=0.95, background.title="darkgreen", > > gtrack <- GenomeAxisTrack(cex=1) > > > > tris_1p<-DataTrack("nalm6_1p_tris_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > + col.histogram="blue", fill.histogram ="blue",name > ="1% Tris", ylim=c(0,1.5)) > > tris_05p<-DataTrack("nalm6_05p_tris_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > col.histogram="blue", fill.histogram ="blue",name > ="0.5% Tris", ylim=c(0,1.5)) > less_Ab<-DataTrack("nalm6_6ugn499_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > col.histogram="blue", fill.histogram ="blue",name > ="Less Ab", ylim=c(0,1.5)) > standard<-DataTrack("nalm6_05_gly_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > col.histogram="blue", fill.histogram ="blue",name > ="Standard", ylim=c(0,1.5)) > nalm6_nodex<-DataTrack("nalnalm6_nly_control_lambda.bw",genome="hg19", > cex.title=0.95, background.title="darkgreen", > col.histogram="darkgreen", fill.histogram > ="darkgreen",name ="No Drug", ylim=c(0,1.5),background.panel = > "lightyellow") > > bcl6.gr<-GeneRegionTrack("bcl6.gtf",name="BCL6",stacking="squish",st ackHeight > = 0.2, > geneSymbols=TRUE, showId = TRUE, cex=1, > cex.title=1.2, background.title="darkgray") > > plotTracks(list(itrack,gtrack,bcl6.gr, t+ > col.histogram="blue", fill.histogram ="blue",name ="0.5% Tris", > ylim=c(0,1.5)) > > less_Ab<-DataTrack("nalm6_6ugn499_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > + col.histogram="blue", fill.histogram ="blue",name > ="Less Ab", ylim=c(0,1.5)) > > standard<-DataTrack("nalm6_05_gly_treat_pileup.bw",genome="hg19", > cex.title=0.95, background.title="darkgray", > + col.histogram="blue", fill.histogram ="blue",name > ="Standard", ylim=c(0,1.5)) > > nalm6_nodex<-DataTrack("nalnalm6_nly_control_lambda.bw",genome="hg19", > cex.title=0.95, background.title="darkgreen", > + col.histogram="darkgreen", fill.histogram > ="darkgreen",name ="No Drug", ylim=c(0,1.5),background.panel = > "lightyellow") > > bcl6.gr<-GeneRegionTrack("bcl6.gtf",name="BCL6",stacking="squish",st ackHeight > = 0.2, > geneSymbols=TRUE, showId = TRUE, cex=1, > cex.title=1.2, background.title="darkgray") > > plotTracks(list(itrack,gtrack,bcl6.gr, tris_1p, > tris_05p,less_Ab,standard,nalm6_nodex),from=187437000, > to=187470000,type="histogram",chromosome="chr3")Error in > validObject(.Object) : > invalid class “ReferenceDataTrack” object: The referenced file ' > nalnalm6_nly_control_lambda.bw' does not exist > > > > bcl6.gr<-GeneRegionTrack("bcl6.gtf",name="BCL6",stacking="squish", stackHeight > = 0.2, > + geneSymbols=TRUE, showId = TRUE, cex=1, > cex.title=1.2, background.title="darkgray") > > > > nalm6_nodex<-DataTrack("nalm6_05_gly_control_lambda.bw",genome="hg19", > cex.title=0.95, background.title="darkgreen", > + col.histogram="darkgreen", fill.histogram > ="darkgreen",name ="No Drug", ylim=c(0,1.5),background.panel = > "lightyellow") > > > > bcl6.gr<-GeneRegionTrack("bcl6.gtf",name="BCL6",stacking="squish", stackHeight > = 0.2, > + geneSymbols=TRUE, showId = TRUE, cex=1, > cex.title=1.2, background.title="darkgray") > > plotTracks(list(itrack,gtrack,bcl6.gr, tris_1p, > tris_05p,less_Ab,standard,nalm6_nodex),from=187437000, > to=187470000,type="histogram",chromosome="chr3") > Abort trap: 6 > bash-3.2$ > **************************** > On May 1, 2013, at 3:58 PM, Michael Lawrence <lawrence.michael@gene.com> > wrote: > > Thanks for this. I just want to let you know that I am planning on looking > into this. But I'll need to find a Mac, get gdb setup on it, etc. My guess > is the error is inside Jim Kent's library, so it might be a pain to fix. > > Michael > > > On Mon, Apr 29, 2013 at 5:58 AM, Robert Ivanek <robert.ivanek@unibas.ch>wrote: > >> Dear Miles, >> >> Thanks for making the BigWigFile available. >> >> I can reproduce the error on my MAC (using devel version) and I can also >> confirm that it works on my linux system (using both release and devel). >> I think that the error is coming from rtraklayer import function, which >> is used by Gviz to import the BigWigFile. >> >> I am sending this email to the BioC list and another one to the Michael >> Lawrence (rtraklayer maintainer) together with the link you provided. >> >> Best >> Robert >> >> ## --------------------------------------------------------------- >> ## MAC >> >> library(Gviz) >> gtrack <- GenomeAxisTrack() >> b1_dex <- DataTrack("~/nalm6_dex.bw", strand="+",genome ="hg19"); >> names(b1_dex)<-"Fkbp5"; >> plotTracks(list(gtrack, b1_dex), from = 35540000, to = 35698000, >> type="histogram", chromosome="chr6") >> >> Abort trap: 6 >> >> sessionInfo() >> >> ## R Under development (unstable) (2013-04-17 r62600) >> ## Platform: x86_64-apple-darwin12.3.0/x86_64 (64-bit) >> >> ## locale: >> ## [1] C/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 >> >> ## attached base packages: >> ## [1] grid stats graphics grDevices utils datasets >> methods base >> >> ## other attached packages: >> ## [1] Gviz_1.5.1 >> >> ## loaded via a namespace (and not attached): >> ## [1] AnnotationDbi_1.23.4 BSgenome_1.29.0 Biobase_2.21.0 >> BiocGenerics_0.7.2 Biostrings_2.29.1 >> ## [6] DBI_0.2-6 GenomicFeatures_1.13.1 >> GenomicRanges_1.13.7 Hmisc_3.10-1 IRanges_1.19.3 >> ## [11] RColorBrewer_1.0-5 RCurl_1.95-4.1 RSQLite_0.11.3 >> Rsamtools_1.13.5 XML_3.96-1.1 >> ## [16] biomaRt_2.17.0 biovizBase_1.9.1 bitops_1.0-5 >> cluster_1.14.4 colorspace_1.2-2 >> ## [21] compiler_3.1.0 dichromat_2.0-0 labeling_0.1 >> lattice_0.20-15 munsell_0.4 >> ## [26] parallel_3.1.0 plyr_1.8 rtracklayer_1.21.3 >> scales_0.2.3 stats4_3.1.0 >> ## [31] stringr_0.6.2 tools_3.1.0 zlibbioc_1.7.0 >> >> library(rtracklayer) >> sessionInfo() >> ## R Under development (unstable) (2013-04-17 r62600) >> ## Platform: x86_64-apple-darwin12.3.0/x86_64 (64-bit) >> >> ## locale: >> ## [1] C/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 >> >> ## attached base packages: >> ## [1] parallel stats graphics grDevices utils datasets >> methods base >> >> ## other attached packages: >> ## [1] rtracklayer_1.21.3 GenomicRanges_1.13.7 IRanges_1.19.3 >> BiocGenerics_0.7.2 >> >> ## loaded via a namespace (and not attached): >> ## [1] BSgenome_1.29.0 Biostrings_2.29.1 RCurl_1.95-4.1 >> Rsamtools_1.13.5 XML_3.96-1.1 bitops_1.0-5 >> ## [7] stats4_3.1.0 tools_3.1.0 zlibbioc_1.7.0 >> >> import.bw("nalm6_dex.bw", GRanges("chr6", IRanges(start=35540000, >> end=35698000), strand="+")) >> >> Abort trap: 6 >> >> >> >> ## --------------------------------------------------------------- >> >> ## --------------------------------------------------------------- >> ## LINUX >> >> ## R version 3.0.0 Patched (2013-04-08 r62518) >> ## Platform: x86_64-unknown-linux-gnu (64-bit) >> >> ## locale: >> ## [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C >> LC_TIME=en_GB.UTF-8 >> ## [4] LC_COLLATE=C LC_MONETARY=en_US.utf8 >> LC_MESSAGES=en_US.utf8 >> ## [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C >> ## [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 >> LC_IDENTIFICATION=C >> >> ## attached base packages: >> ## [1] grid stats graphics grDevices utils datasets >> methods base >> >> ## other attached packages: >> ## [1] Gviz_1.4.1 >> >> ## loaded via a namespace (and not attached): >> ## [1] AnnotationDbi_1.22.3 BSgenome_1.28.0 Biobase_2.20.0 >> BiocGenerics_0.6.0 >> ## [5] Biostrings_2.28.0 DBI_0.2-6 >> GenomicFeatures_1.12.1 GenomicRanges_1.13.0 >> ## [9] Hmisc_3.10-1 IRanges_1.18.0 RColorBrewer_1.0-5 >> RCurl_1.95-4.1 >> ## [13] RSQLite_0.11.3 Rsamtools_1.12.2 XML_3.96-1.1 >> biomaRt_2.16.0 >> ## [17] biovizBase_1.8.0 bitops_1.0-5 cluster_1.14.4 >> colorspace_1.2-2 >> ## [21] compiler_3.0.0 dichromat_2.0-0 labeling_0.1 >> lattice_0.20-15 >> ## [25] munsell_0.4 parallel_3.0.0 plyr_1.8 >> rtracklayer_1.20.1 >> ## [29] scales_0.2.3 stats4_3.0.0 stringr_0.6.2 >> tools_3.0.0 >> ## [33] zlibbioc_1.6.0 >> >> >> >> ## R Under development (unstable) (2013-04-08 r62518) >> ## Platform: x86_64-unknown-linux-gnu (64-bit) >> >> ## locale: >> ## [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C >> LC_TIME=en_GB.UTF-8 >> ## [4] LC_COLLATE=C LC_MONETARY=en_US.utf8 >> LC_MESSAGES=en_US.utf8 >> ## [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C >> ## [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 >> LC_IDENTIFICATION=C >> >> ## attached base packages: >> ## [1] grid stats graphics grDevices utils datasets >> methods base >> >> ## other attached packages: >> ## [1] Gviz_1.5.1 >> >> ## loaded via a namespace (and not attached): >> ## [1] AnnotationDbi_1.23.4 BSgenome_1.29.0 Biobase_2.21.0 >> BiocGenerics_0.7.2 >> ## [5] Biostrings_2.29.1 DBI_0.2-6 >> GenomicFeatures_1.13.1 GenomicRanges_1.13.7 >> ## [9] Hmisc_3.10-1 IRanges_1.19.3 RColorBrewer_1.0-5 >> RCurl_1.95-4.1 >> ## [13] RSQLite_0.11.3 Rsamtools_1.13.5 XML_3.96-1.1 >> biomaRt_2.17.0 >> ## [17] biovizBase_1.9.1 bitops_1.0-5 cluster_1.14.4 >> colorspace_1.2-2 >> ## [21] dichromat_2.0-0 labeling_0.1 lattice_0.20-15 >> munsell_0.4 >> ## [25] parallel_3.1.0 plyr_1.8 rtracklayer_1.21.3 >> scales_0.2.3 >> ## [29] stats4_3.1.0 stringr_0.6.2 tools_3.1.0 >> zlibbioc_1.7.0 >> >> >> On 26/04/13 21:31, Miles Pufall wrote: >> > Sure - I'm not sure of the protocol, so I'm sending this large file by >> replying to you directly. Just to re-emphasize, I was able to work with >> this file on my Linux box, but not on my mac (rMBP, 16Gb memory). You can >> grab it from my dropbox here: >> > >> > >> > Let me know if you need anything else. >> > >> > Miles >> > >> > Miles Pufall, PhD >> > Assistant Professor, Department of Biochemistry >> > University of Iowa >> > 51 Newton Rd., BSB 4-430 >> > Iowa City, IA 52242 >> > Office: 319-384-1820 >> > Email: miles-pufall@uiowa.edu >> > >> > >> > On Apr 26, 2013, at 8:00 AM, Robert Ivanek <robert.ivanek@unibas.ch> >> > wrote: >> > >> >> Dear Dweebis, >> >> >> >> Thanks for reporting this issue. The first one is fixed, there was a >> bug >> >> in "chromosome<-" method . Fixed versions 1.4.1 (2.12 branch) and 1.5.1 >> >> (devel) should be available in 24 hours. >> >> >> >> Regarding the crash with BigWig file, would you mind to share it? >> >> >> >> Best >> >> Robert >> >> >> >> On 26 Apr 2013, at 06:49, "Dweebis [guest]" <guest@bioconductor.org> >> wrote: >> >> >> >>> >> >>> I'm trying to use Gviz to make figures displaying some ChIPseq data. >> I'd converted it to bigWig files to display in a genome browser and to >> store more easily. When I use Gviz on a Linux workstation, it seems to go >> smoothly, but when I use my MacBook Pro I have a few problems. The first >> is running some code from the vignette, which gives me the following error: >> >>>> library(Gviz) >> >>> Loading required package: grid >> >>>> ideoTrack <- IdeogramTrack(genome = "hg19", chromosome = "chrX") >> >>>> plotTracks(ideoTrack, from = 85000000, to = 129000000) >> >>> Error in .normargSeqnames(seqnames) : >> >>> supplied 'seqnames' cannot contain NAs or empty strings ("") >> >>> >> >>> The second is when I try to plot from my bigWig files: >> >>>> library("Gviz") >> >>> Loading required package: grid >> >>>> library(GenomicRanges) >> >>> Loading required package: BiocGenerics >> >>> Loading required package: parallel >> >>> >> >>> Attaching package: â?~BiocGenericsâ?T >> >>> >> >>> The following objects are masked from â?~package:parallelâ?T: >> >>> >> >>> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, >> clusterExport, >> >>> clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, >> parSapply, >> >>> parSapplyLB >> >>> >> >>> The following object is masked from â?~package:statsâ?T: >> >>> >> >>> xtabs >> >>> >> >>> The following objects are masked from â?~package:baseâ?T: >> >>> >> >>> anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, >> Filter, Find, >> >>> get, intersect, lapply, Map, mapply, match, mget, order, paste, pmax, >> pmax.int, >> >>> pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, >> sapply, >> >>> setdiff, sort, table, tapply, union, unique, unlist >> >>> >> >>> Loading required package: IRanges >> >>>> setwd("~/Desktop/B1_ChIPseq") >> >>>> gtrack <- GenomeAxisTrack() >> >>>> b1_dex <- DataTrack("/Volumes/puf_3/Nalm6/nalm6_dex_n499.bw", >> strand="+",genome ="hg19"); >> >>>> names(b1_dex)<-"Fkbp5"; >> >>>> plotTracks(list(gtrack, b1_dex), from = 35540000, to = 35698000, >> type="histogram", chromosome="chr6") >> >>> >> >>> This crashes R completely with an exit message: Abort trap: 6 >> >>> >> >>> There is an associated OSX crash report, which I've pasted below. >> >>> >> >>> Any ideas what's going wrong? >> >>> >> >>> Thx - >> >>> >> >>> D >> >>> >> >>> Process: R [26469] >> >>> Path: /Library/Frameworks/R.framework/Resources/bin/exec/R >> >>> Identifier: R >> >>> Version: ??? >> >>> Code Type: X86-64 (Native) >> >>> Parent Process: bash [26264] >> >>> User ID: 501 >> >>> >> >>> Date/Time: 2013-04-25 23:24:05.617 -0500 >> >>> OS Version: Mac OS X 10.8.3 (12D78) >> >>> Report Version: 10 >> >>> >> >>> Interval Since Last Report: 2714 sec >> >>> Crashes Since Last Report: 7 >> >>> Per-App Crashes Since Last Report: 1 >> >>> Anonymous UUID: >> 0FFEC26B-8E19-7735-0F96-8B3430A59ECE >> >>> >> >>> Crashed Thread: 0 Dispatch queue: com.apple.main-thread >> >>> >> >>> Exception Type: EXC_CRASH (SIGABRT) >> >>> Exception Codes: 0x0000000000000000, 0x0000000000000000 >> >>> >> >>> Application Specific Information: >> >>> [26469] stack overflow >> >>> >> >>> Thread 0 Crashed:: Dispatch queue: com.apple.main-thread >> >>> 0 libsystem_kernel.dylib 0x00007fff8a832212 >> __pthread_kill + 10 >> >>> 1 libsystem_c.dylib 0x00007fff926f0b54 pthread_kill >> + 90 >> >>> 2 libsystem_c.dylib 0x00007fff92734e9e __abort + 159 >> >>> 3 libsystem_c.dylib 0x00007fff92735d17 >> __stack_chk_fail + 195 >> >>> 4 rtracklayer.so 0x0000000107427d24 bptFileFind >> + 212 >> >>> 5 rtracklayer.so 0x0000000107429104 >> bbiOverlappingBlocks + 68 >> >>> 6 rtracklayer.so 0x000000010742cb00 >> bigWigIntervalQuery + 128 >> >>> 7 rtracklayer.so 0x0000000107425bc0 >> BWGFile_query + 448 >> >>> 8 libR.dylib 0x0000000100071033 do_dotcall + >> 547 (dotcode.c:585) >> >>> 9 libR.dylib 0x0000000100099d67 Rf_eval + >> 1335 (eval.c:612) >> >>> 10 libR.dylib 0x00000001000a7771 do_set + 369 >> (eval.c:1863) >> >>> 11 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 12 libR.dylib 0x00000001000a7ad0 do_begin + >> 384 (eval.c:1534) >> >>> 13 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 14 libR.dylib 0x00000001000a529e >> Rf_applyClosure + 1390 (eval.c:980) >> >>> 15 libR.dylib 0x0000000100099e05 Rf_eval + >> 1493 (eval.c:631) >> >>> 16 libR.dylib 0x00000001000a7ad0 do_begin + >> 384 (eval.c:1534) >> >>> 17 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 18 libR.dylib 0x00000001000a86a2 R_execMethod >> + 1410 (eval.c:1076) >> >>> 19 methods.so 0x00000001005eb474 >> R_dispatchGeneric + 1972 >> >>> 20 libR.dylib 0x00000001000d6235 >> do_standardGeneric + 565 (objects.c:1142) >> >>> 21 libR.dylib 0x0000000100099da3 Rf_eval + >> 1395 (eval.c:616) >> >>> 22 libR.dylib 0x00000001000a529e >> Rf_applyClosure + 1390 (eval.c:980) >> >>> 23 libR.dylib 0x0000000100099e05 Rf_eval + >> 1493 (eval.c:631) >> >>> 24 libR.dylib 0x00000001000a7ad0 do_begin + >> 384 (eval.c:1534) >> >>> 25 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 26 libR.dylib 0x00000001000a86a2 R_execMethod >> + 1410 (eval.c:1076) >> >>> 27 methods.so 0x00000001005eb474 >> R_dispatchGeneric + 1972 >> >>> 28 libR.dylib 0x00000001000d6235 >> do_standardGeneric + 565 (objects.c:1142) >> >>> 29 libR.dylib 0x0000000100099da3 Rf_eval + >> 1395 (eval.c:616) >> >>> 30 libR.dylib 0x00000001000a529e >> Rf_applyClosure + 1390 (eval.c:980) >> >>> 31 libR.dylib 0x0000000100099e05 Rf_eval + >> 1493 (eval.c:631) >> >>> 32 libR.dylib 0x00000001000a7ad0 do_begin + >> 384 (eval.c:1534) >> >>> 33 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 34 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 35 libR.dylib 0x00000001000a7771 do_set + 369 >> (eval.c:1863) >> >>> 36 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 37 libR.dylib 0x00000001000a7ad0 do_begin + >> 384 (eval.c:1534) >> >>> 38 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 39 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 40 libR.dylib 0x00000001000a7ad0 do_begin + >> 384 (eval.c:1534) >> >>> 41 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 42 libR.dylib 0x00000001000a529e >> Rf_applyClosure + 1390 (eval.c:980) >> >>> 43 libR.dylib 0x0000000100099e05 Rf_eval + >> 1493 (eval.c:631) >> >>> 44 libR.dylib 0x00000001000a7771 do_set + 369 >> (eval.c:1863) >> >>> 45 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 46 libR.dylib 0x00000001000a7ad0 do_begin + >> 384 (eval.c:1534) >> >>> 47 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 48 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 49 libR.dylib 0x00000001000a7ad0 do_begin + >> 384 (eval.c:1534) >> >>> 50 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 51 libR.dylib 0x00000001000a529e >> Rf_applyClosure + 1390 (eval.c:980) >> >>> 52 libR.dylib 0x0000000100099e05 Rf_eval + >> 1493 (eval.c:631) >> >>> 53 libR.dylib 0x00000001000a7ad0 do_begin + >> 384 (eval.c:1534) >> >>> 54 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 55 libR.dylib 0x00000001000a86a2 R_execMethod >> + 1410 (eval.c:1076) >> >>> 56 methods.so 0x00000001005eb474 >> R_dispatchGeneric + 1972 >> >>> 57 libR.dylib 0x00000001000d6235 >> do_standardGeneric + 565 (objects.c:1142) >> >>> 58 libR.dylib 0x0000000100099da3 Rf_eval + >> 1395 (eval.c:616) >> >>> 59 libR.dylib 0x00000001000a529e >> Rf_applyClosure + 1390 (eval.c:980) >> >>> 60 libR.dylib 0x0000000100099e05 Rf_eval + >> 1493 (eval.c:631) >> >>> 61 libR.dylib 0x000000010000eb81 do_lapply + >> 673 (apply.c:76) >> >>> 62 libR.dylib 0x00000001000d3c5a do_internal >> + 362 (names.c:1168) >> >>> 63 libR.dylib 0x000000010009cd1f bcEval + >> 11791 (eval.c:4583) >> >>> 64 libR.dylib 0x000000010009994f Rf_eval + >> 287 (eval.c:515) >> >>> 65 libR.dylib 0x00000001000a86a2 R_execMethod >> + 1410 (eval.c:1076) >> >>> 66 methods.so 0x00000001005eb474 >> R_dispatchGeneric + 1972 >> >>> 67 libR.dylib 0x00000001000d6235 >> do_standardGeneric + 565 (objects.c:1142) >> >>> 68 libR.dylib 0x0000000100099da3 Rf_eval + >> 1395 (eval.c:616) >> >>> 69 libR.dylib 0x00000001000a529e >> Rf_applyClosure + 1390 (eval.c:980) >> >>> 70 libR.dylib 0x0000000100099e05 Rf_eval + >> 1493 (eval.c:631) >> >>> 71 libR.dylib 0x00000001000a7771 do_set + 369 >> (eval.c:1863) >> >>> 72 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 73 libR.dylib 0x00000001000a7ad0 do_begin + >> 384 (eval.c:1534) >> >>> 74 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 75 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 76 libR.dylib 0x00000001000a7ad0 do_begin + >> 384 (eval.c:1534) >> >>> 77 libR.dylib 0x0000000100099bd6 Rf_eval + >> 934 (eval.c:584) >> >>> 78 libR.dylib 0x00000001000a529e >> Rf_applyClosure + 1390 (eval.c:980) >> >>> 79 libR.dylib 0x0000000100099e05 Rf_eval + >> 1493 (eval.c:631) >> >>> 80 libR.dylib 0x00000001000c97df >> Rf_ReplIteration + 879 (main.c:258) >> >>> 81 libR.dylib 0x00000001000c9e63 >> run_Rmainloop + 211 (main.c:307) >> >>> 82 R 0x0000000100000e5b main + 27 >> >>> 83 R 0x0000000100000e34 start + 52 >> >>> >> >>> Thread 1:: Dispatch queue: com.apple.libdispatch-manager >> >>> 0 libsystem_kernel.dylib 0x00007fff8a832d16 kevent + 10 >> >>> 1 libdispatch.dylib 0x00007fff8affddea >> _dispatch_mgr_invoke + 883 >> >>> 2 libdispatch.dylib 0x00007fff8affd9ee >> _dispatch_mgr_thread + 54 >> >>> >> >>> Thread 2: >> >>> 0 libsystem_kernel.dylib 0x00007fff8a832322 __select + 10 >> >>> 1 grDevices.so 0x0000000102ea8440 -[ELThread >> eventsThread:] + 176 >> >>> 2 com.apple.Foundation 0x00007fff8f55ecd2 >> __NSThread__main__ + 1345 >> >>> 3 libsystem_c.dylib 0x00007fff926ef7a2 >> _pthread_start + 327 >> >>> 4 libsystem_c.dylib 0x00007fff926dc1e1 thread_start >> + 13 >> >>> >> >>> Thread 0 crashed with X86 Thread State (64-bit): >> >>> rax: 0x0000000000000000 rbx: 0x0000000000000006 rcx: >> 0x00007fff5fbf83f8 rdx: 0x0000000000000000 >> >>> rdi: 0x0000000000000f07 rsi: 0x0000000000000006 rbp: >> 0x00007fff5fbf8420 rsp: 0x00007fff5fbf83f8 >> >>> r8: 0x00007fff7abed278 r9: 0x0000000000000000 r10: >> 0x0000000020000000 r11: 0x0000000000000206 >> >>> r12: 0x00007fff5fbf84f0 r13: 0x0000000000000004 r14: >> 0x00007fff7abee180 r15: 0x0000000107293010 >> >>> rip: 0x00007fff8a832212 rfl: 0x0000000000000206 cr2: >> 0x00007fff7abe6ff0 >> >>> Logical CPU: 0 >> >>> >> >>> Binary Images: >> >>> 0x100000000 - 0x100000ff7 +R (???) >> <d62f3923-33a9-31e3-8256-72609aff38df> >> /Library/Frameworks/R.framework/Resources/bin/exec/R >> >>> 0x100003000 - 0x10026efff +libR.dylib (3) >> <2FA3EDB5-B755-3972-AFBA-337B24212428> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libR.dylib >> >>> 0x10038c000 - 0x1003b5ff7 +libRblas.dylib (0) >> <869671F9-C174-39EA-8496-9E88B343A3B0> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libRblas .dylib >> >>> 0x1003ba000 - 0x100470fcf +libgfortran.2.dylib (3) >> <acf1816e-ea8a-4db9-a893-a4ef0cefffba> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfort ran.2.dylib >> >>> 0x1004b5000 - 0x1004dffd9 +libreadline.5.2.dylib (5.2) >> /Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadl ine.5.2.dylib >> >>> 0x1005c2000 - 0x1005c9fff +utils.so (0) >> <8FBF096E-B6CE-398E-A920-01DE1B245C41> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/util s/libs/utils.so >> >>> 0x1005e9000 - 0x1005eefff +methods.so (0) >> <ab37fbdb-4142-3274-affb-b2fb7fd32fc7> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/meth ods/libs/methods.so >> >>> 0x1005f7000 - 0x1005f9fef +bitops.so (0) >> <f9843053-e910-36cf-9df1-f4121020f969> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/bito ps/libs/bitops.so >> >>> 0x1007f2000 - 0x1007f5fef +parallel.so (0) >> <e5a82d0c-98bd-3e65-a7ee-1fab5c8b6264> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/para llel/libs/parallel.so >> >>> 0x1007f9000 - 0x1007fcfff +Biobase.so (0) >> <68F5403C-3382-31CD-BDAB-4335D037FE5E> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biob ase/libs/Biobase.so >> >>> 0x101194000 - 0x1011cffef +graphics.so (0) >> <9E6394E4-AF37-3F25-A180-026E82583AF2> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/grap hics/libs/graphics.so >> >>> 0x1011da000 - 0x1011e3fff +RCurl.so (0) >> <66E5F530-2EF3-32CB-9373-1A6491E8366A> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RCur l/libs/RCurl.so >> >>> 0x1011ed000 - 0x1011effff +lattice.so (0) >> <5A52F152-052E-3C10-B9B3-5B486A910DD7> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/latt ice/libs/lattice.so >> >>> 0x1011f2000 - 0x1011f3ff7 +plyr.so (0) >> <eb5cbaa5-f26d-31d4-a292-f9ac0b2a189e> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/plyr /libs/plyr.so >> >>> 0x10120f000 - 0x101219fff +GenomicRanges.so (0) >> <844F62EE-EEF9-3C56-812A-4E75A899CCB2> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Geno micRanges/libs/GenomicRanges.so >> >>> 0x101224000 - 0x101230fff +colorspace.so (0) >> <0E7C120B-148E-351A-92A1-C7963AC07174> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/colo rspace/libs/colorspace.so >> >>> 0x10126e000 - 0x10127aff7 +cluster.so (0) >> <55B40D4D-8432-3FEB-BBB7-8E65C948C17C> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/clus ter/libs/cluster.so >> >>> 0x10127e000 - 0x10127fff7 +biovizBase.so (0) >> <45F295A2-1E32-3E5C-96B9-1657114AE545> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/biov izBase/libs/biovizBase.so >> >>> 0x101396000 - 0x1013b1fff +grid.so (0) >> <0A0B45EC-AC1D-3F33-A57E-6B234CC42505> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/grid /libs/grid.so >> >>> 0x1013be000 - 0x1013c3fff +Hmisc.so (0) >> <45B74820-59DF-3402-9F5C-CB4A0A3E90D4> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Hmis c/libs/Hmisc.so >> >>> 0x101420000 - 0x101436ff7 +XML.so (0) >> <e2b500ca-56d9-35b8-aba5-802c93b67bf3> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/XML/ libs/XML.so >> >>> 0x1029ae000 - 0x1029befff +tools.so (0) >> <cef0dc14-7405-36d1-8696-da60801dca44> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/tool s/libs/tools.so >> >>> 0x102e82000 - 0x102ebffff +grDevices.so (0) >> <f7087219-a4a6-33c3-a0a8-19aaded62431> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/grDe vices/libs/grDevices.so >> >>> 0x102edb000 - 0x102f65fef +stats.so (0) >> <99BD4BBA-AE70-38A3-BC7E-ABEF5775D09A> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/stat s/libs/stats.so >> >>> 0x103900000 - 0x103a7efff +libRlapack.dylib (3) >> <c2dd755e-0f94-37f9-85f2-305e6f3720fb> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libRlapa ck.dylib >> >>> 0x103e66000 - 0x103e97ff7 +IRanges.so (0) >> <65E44E38-96BC-3AC5-8490-5EDE934749F4> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRan ges/libs/IRanges.so >> >>> 0x103f9a000 - 0x103fd5fef +Rsamtools.so (0) >> <2ECCAE63-A2CE-3097-8AFF-31E11FB22989> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsam tools/libs/Rsamtools.so >> >>> 0x107420000 - 0x107461ff7 +rtracklayer.so (0) >> <a1b33ecb-4c97-3d25-a0c1-21609054a3ca> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/rtra cklayer/libs/rtracklayer.so >> >>> 0x108000000 - 0x10802aff7 +Biostrings.so (0) >> <d2594ec2-693d-3b33-ade7-6cd903626301> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Bios trings/libs/Biostrings.so >> >>> 0x10f800000 - 0x10f8c8fff +RSQLite.so (0) >> <e5afc155-2126-35f7-bb65-9ec27183117a> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQL ite/libs/RSQLite.so >> >>> 0x7fff619d3000 - 0x7fff61a0793f dyld (210.2.3) >> <a40597aa-5529-3337-8c09-d8a014eb1578> /usr/lib/dyld >> >>> 0x7fff8973b000 - 0x7fff8975aff7 libresolv.9.dylib (51) >> <0882DC2D-A892-31FF-AD8C-0BB518C48B23> /usr/lib/libresolv.9.dylib >> >>> 0x7fff8975b000 - 0x7fff897aaff7 libFontRegistry.dylib (100) >> <2E03D7DA-9B8F-31BB-8FB5-3D3B6272127F> >> /System/Library/Frameworks/ApplicationServices.framework/Versions/A /Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib >> >>> 0x7fff89b4c000 - 0x7fff89b59fff com.apple.AppleFSCompression (49 >> - 1.0) <5508344A-2A7E-3122-9562-6F363910A80E> >> /System/Library/PrivateFrameworks/AppleFSCompression.framework/Vers ions/A/AppleFSCompression >> >>> 0x7fff89b5a000 - 0x7fff89bb0fff com.apple.HIServices (1.20 - >> 417) <a1129272-fec8-350b-ba26-5a97f23c413d> >> /System/Library/Frameworks/ApplicationServices.framework/Versions/A /Frameworks/HIServices.framework/Versions/A/HIServices >> >>> 0x7fff89e2f000 - 0x7fff89e5bff7 libRIP.A.dylib (331.0.4) >> <4B261CE2-524E-3FA9-9437-B70DAC1EAB95> >> /System/Library/Frameworks/ApplicationServices.framework/Versions/A /Frameworks/CoreGraphics.framework/Versions/A/Resources/libRIP.A.dylib >> >>> 0x7fff89ebc000 - 0x7fff89ec1fff libcompiler_rt.dylib (30) >> <08F8731D-5961-39F1-AD00-4590321D24A9> /usr/lib/system/libcompiler_rt.dylib >> >>> 0x7fff89efd000 - 0x7fff8a083fff libBLAS.dylib (1073.4) >> <c102c0f6-8cb6-3b49-ba6b-2eb61f0b2784> >> /System/Library/Frameworks/Accelerate.framework/Versions/A/Framewor ks/vecLib.framework/Versions/A/libBLAS.dylib >> >>> 0x7fff8a09a000 - 0x7fff8a0f1ff7 com.apple.ScalableUserInterface >> (1.0 - 1) <f1d43dfb-1796-361b-ad4b-39f1eed3be19> >> /System/Library/Frameworks/QuartzCore.framework/Versions/A/Framewor ks/ScalableUserInterface.framework/Versions/A/ScalableUserInterface >> >>> 0x7fff8a373000 - 0x7fff8a3d0ff7 com.apple.audio.CoreAudio (4.1.1 >> - 4.1.1) <d15f3fb3-be53-3545-ad37-9a25a597fe3c> >> /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio >> >>> 0x7fff8a3d1000 - 0x7fff8a43afff libstdc++.6.dylib (56) >> <eaa2b53e-eade-39cf-a0ef-fb9d4940672a> /usr/lib/libstdc++.6.dylib >> >>> 0x7fff8a43b000 - 0x7fff8a63bfff libicucore.A.dylib (491.11.2) >> <fd6282d8-df3f-3842-8c2e-cf478d2b9669> /usr/lib/libicucore.A.dylib >> >>> 0x7fff8a63c000 - 0x7fff8a755fff com.apple.ImageIO.framework >> (3.2.0 - 849) <c52aed41-a7c2-300b-91fa-5af73718d243> >> /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO >> >>> 0x7fff8a789000 - 0x7fff8a798fff com.apple.opengl (1.8.7 - 1.8.7) >> <26F7FF79-6BB2-3968-B70D-71D4E07C9551> >> /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL >> >>> 0x7fff8a799000 - 0x7fff8a7c3ff7 com.apple.CoreVideo (1.8 - 99.4) >> <e5082966-6d81-3973-a05a-38aa5b85f886> >> /System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo >> >>> 0x7fff8a820000 - 0x7fff8a83bff7 libsystem_kernel.dylib >> (2050.22.13) <5A961E2A-CFB8-362B-BC43-122704AEB047> >> /usr/lib/system/libsystem_kernel.dylib >> >>> 0x7fff8a977000 - 0x7fff8a981fff >> com.apple.speech.recognition.framework (4.1.5 - 4.1.5) >> <d803919c-3102-3515-a178-61e9c86c46a1> >> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/S peechRecognition.framework/Versions/A/SpeechRecognition >> >>> 0x7fff8a991000 - 0x7fff8a9e0ff7 libcorecrypto.dylib (106.2) >> <ce0c29a3-c420-339b-adaa-52f4683233cc> /usr/lib/system/libcorecrypto.dylib >> >>> 0x7fff8a9ed000 - 0x7fff8aa04fff libGL.dylib (8.7.25) >> <15F5CB64-847B-3D3D-9663-E0523F15F513> >> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/li bGL.dylib >> >>> 0x7fff8aa16000 - 0x7fff8aa18fff com.apple.TrustEvaluationAgent >> (2.0 - 23) <a97d348b-32bf-3e52-8df2-59bfad21e1a3> >> /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Ve rsions/A/TrustEvaluationAgent >> >>> 0x7fff8aa1d000 - 0x7fff8aa2bfff com.apple.Librarian (1.1 - 1) >> <5AC28666-7642-395F-A923-C6F8A274BBBD> >> /System/Library/PrivateFrameworks/Librarian.framework/Versions/A/Li brarian >> >>> 0x7fff8aa2c000 - 0x7fff8aa2dff7 libSystem.B.dylib (169.3) >> <365477AB-D641-389D-B8F4-A1FAE9657EEE> /usr/lib/libSystem.B.dylib >> >>> 0x7fff8aa2e000 - 0x7fff8aa50ff7 libxpc.dylib (140.42) >> <bbe558bd-5e55-35e4-89ed-1aa6b056d05a> /usr/lib/system/libxpc.dylib >> >>> 0x7fff8aa51000 - 0x7fff8ab02fff com.apple.LaunchServices (539.7 >> - 539.7) <da7c602e-5e01-31b8-925d-b45360ca089f> >> /System/Library/Frameworks/CoreServices.framework/Versions/A/Framew orks/LaunchServices.framework/Versions/A/LaunchServices >> >>> 0x7fff8ab03000 - 0x7fff8ab0afff com.apple.NetFS (5.0 - 4.0) >> <82E24B9A-7742-3DA3-9E99-ED267D98C05E> >> /System/Library/Frameworks/NetFS.framework/Versions/A/NetFS >> >>> 0x7fff8ab22000 - 0x7fff8ab34ff7 libz.1.dylib (43) >> <2A1551E8-A272-3DE5-B692-955974FE1416> /usr/lib/libz.1.dylib >> >>> 0x7fff8ab35000 - 0x7fff8ab3bfff libmacho.dylib (829) >> <bf332ad9-e89f-387e-92a4-6e1ab74bd4d9> /usr/lib/system/libmacho.dylib >> >>> 0x7fff8ab3c000 - 0x7fff8ab3cfff libOpenScriptingUtil.dylib >> (148.3) <f8681222-0969-3b10-8bce-c55a4b9c520c> >> /usr/lib/libOpenScriptingUtil.dylib >> >>> 0x7fff8ade0000 - 0x7fff8ae11ff7 com.apple.DictionaryServices >> (1.2 - 184.4) <054F2D6F-9CFF-3EF1-9778-25C551B616C1> >> /System/Library/Frameworks/CoreServices.framework/Versions/A/Framew orks/DictionaryServices.framework/Versions/A/DictionaryServices >> >>> 0x7fff8ae12000 - 0x7fff8af0ffff libsqlite3.dylib (138.1) >> <ade9cb98-d77d-300c-a32a-556b7440769f> /usr/lib/libsqlite3.dylib >> >>> 0x7fff8af10000 - 0x7fff8afcdff7 com.apple.ColorSync (4.8.0 - >> 4.8.0) <6CE333AE-EDDB-3768-9598-9DB38041DC55> >> /System/Library/Frameworks/ApplicationServices.framework/Versions/A /Frameworks/ColorSync.framework/Versions/A/ColorSync >> >>> 0x7fff8aff7000 - 0x7fff8aff8fff libsystem_blocks.dylib (59) >> <d92dcbc3-541c-37bd-aade-acc75a0c59c8> >> /usr/lib/system/libsystem_blocks.dylib >> >>> 0x7fff8aff9000 - 0x7fff8b00eff7 libdispatch.dylib (228.23) >> <d26996bf-fc57-39eb-8829-f63585561e09> /usr/lib/system/libdispatch.dylib >> >>> 0x7fff8b00f000 - 0x7fff8b016fff libGFXShared.dylib (8.7.25) >> <869580B2-39CB-30C3-B76E-73BB4894B6B7> >> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/li bGFXShared.dylib >> >>> 0x7fff8b0d9000 - 0x7fff8b22afff >> com.apple.audio.toolbox.AudioToolbox (1.8 - 1.8) >> <c680ee1a-b4ed-3e77-a08c-dc47922aca33> >> /System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioT oolbox >> >>> 0x7fff8b729000 - 0x7fff8b748ff7 com.apple.ChunkingLibrary (2.0 - >> 133.3) <8BEC9AFB-DCAA-37E8-A5AB-24422B234ECF> >> /System/Library/PrivateFrameworks/ChunkingLibrary.framework/Version s/A/ChunkingLibrary >> >>> 0x7fff8b749000 - 0x7fff8b749fff com.apple.CoreServices (57 - 57) >> <9DD44CB0-C644-35C3-8F57-0B41B3EC147D> >> /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreSe rvices >> >>> 0x7fff8b7da000 - 0x7fff8b7dcfff libquarantine.dylib (52) >> <4BE2E642-A14F-340A-B482-5BD2AEFD9C24> /usr/lib/system/libquarantine.dylib >> >>> 0x7fff8c093000 - 0x7fff8c19efff libFontParser.dylib (84.6) >> <96C42E49-79A6-3475-B5E4-6A782599A6DA> >> /System/Library/Frameworks/ApplicationServices.framework/Versions/A /Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib >> >>> 0x7fff8c1e3000 - 0x7fff8c1e7ff7 com.apple.TCC (1.0 - 1) >> <f2f3b753-fc73-3543-8bbe-859fdbb4d6a6> >> /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC >> >>> 0x7fff8c230000 - 0x7fff8c239ff7 com.apple.CommerceCore (1.0 - >> 26.1) <40A129A8-4E5D-3C7A-B299-8CB203C4C65D> >> /System/Library/PrivateFrameworks/CommerceKit.framework/Versions/A/ Frameworks/CommerceCore.framework/Versions/A/CommerceCore >> >>> 0x7fff8c23a000 - 0x7fff8c631fff libLAPACK.dylib (1073.4) >> <d632ec8b-2ba0-3853-800a-20da00a1091c> >> /System/Library/Frameworks/Accelerate.framework/Versions/A/Framewor ks/vecLib.framework/Versions/A/libLAPACK.dylib >> >>> 0x7fff8c652000 - 0x7fff8c661ff7 libxar.1.dylib (105) >> <370ED355-E516-311E-BAFD-D80633A84BE1> /usr/lib/libxar.1.dylib >> >>> 0x7fff8c67c000 - 0x7fff8c690fff >> com.apple.speech.synthesis.framework (4.1.12 - 4.1.12) >> <94EDF2AB-809C-3D15-BED5-7AD45B2A7C16> >> /System/Library/Frameworks/ApplicationServices.framework/Versions/A /Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis >> >>> 0x7fff8c698000 - 0x7fff8c6a5ff7 com.apple.NetAuth (4.0 - 4.0) >> <f5bc7d7d-af28-3c83-a674-dada48ff7810> >> /System/Library/PrivateFrameworks/NetAuth.framework/Versions/A/NetAuth >> >>> 0x7fff8c798000 - 0x7fff8c85dff7 com.apple.coreui (2.0 - 181.1) >> <83D2C92D-6842-3C9D-9289-39D5B4554C3A> >> /System/Library/PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI >> >>> 0x7fff8c85e000 - 0x7fff8c899fff com.apple.LDAPFramework (2.4.28 >> - 194.5) <67FBDB29-3B9F-309A-BA7C-AA5921D9A4FB> >> /System/Library/Frameworks/LDAP.framework/Versions/A/LDAP >> >>> 0x7fff8c89a000 - 0x7fff8ccb7fff FaceCoreLight (2.4.1) >> <a34c9575-c4c1-31b1-809b-7751070b4e8b> >> /System/Library/PrivateFrameworks/FaceCoreLight.framework/Versions/ A/FaceCoreLight >> >>> 0x7fff8ccc1000 - 0x7fff8ccc4fff libRadiance.dylib (849) >> <f7d9a0fd-1195-34cb-bfe5-79daf3f40ac3> >> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/l ibRadiance.dylib >> >>> 0x7fff8cde0000 - 0x7fff8ce3afff >> com.apple.print.framework.PrintCore (8.3 - 387.2) >> <5BA0CBED-4D80-386A-9646-F835C9805B71> >> /System/Library/Frameworks/ApplicationServices.framework/Versions/A /Frameworks/PrintCore.framework/Versions/A/PrintCore >> >>> 0x7fff8ce3b000 - 0x7fff8ce60ff7 libc++abi.dylib (26) >> <d86169f3-9f31-377a-9af3-db17142052e4> /usr/lib/libc++abi.dylib >> >>> 0x7fff8ce61000 - 0x7fff8ce9bff7 com.apple.GSS (3.0 - 2.0) >> <970CAE00-1437-3F4E-B677-0FDB3714C08C> >> /System/Library/Frameworks/GSS.framework/Versions/A/GSS >> >>> 0x7fff8cea3000 - 0x7fff8d1d3fff com.apple.HIToolbox (2.0 - >> 626.1) <656D08C2-9068-3532-ABDD-32EC5057CCB2> >> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/H IToolbox.framework/Versions/A/HIToolbox >> >>> 0x7fff8d1d4000 - 0x7fff8d478ff7 com.apple.CoreImage (8.2.4 - >> 1.0.1) <4A6B017F-B9F7-36DA-943D-A95611F147EA> >> /System/Library/Frameworks/QuartzCore.framework/Versions/A/Framewor ks/CoreImage.framework/Versions/A/CoreImage >> >>> 0x7fff8d4fd000 - 0x7fff8d4fdfff libkeymgr.dylib (25) >> <cc9e3394-be16-397f-926b-e579b60ee429> /usr/lib/system/libkeymgr.dylib >> >>> 0x7fff8d4fe000 - 0x7fff8d503fff com.apple.OpenDirectory (10.8 - >> 151.10) <cf44120b-9b01-32dd-852e-c9c0e1243fc0> >> /System/Library/Frameworks/OpenDirectory.framework/Versions/A/OpenD irectory >> >>> 0x7fff8d504000 - 0x7fff8d606fff libcrypto.0.9.8.dylib (47) >> <74F165AD-4572-3B26-B0E2-A97477FE59D0> /usr/lib/libcrypto.0.9.8.dylib >> >>> 0x7fff8ddb0000 - 0x7fff8ddb2ff7 libunc.dylib (25) >> <92805328-CD36-34FF-9436-571AB0485072> /usr/lib/system/libunc.dylib >> >>> 0x7fff8ddb3000 - 0x7fff8df9dff7 com.apple.CoreFoundation (6.8 - >> 744.18) <a60c3c9b-3764-3291-844c-c487acf77c2c> >> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/Core Foundation >> >>> 0x7fff8dfde000 - 0x7fff8e014fff com.apple.DebugSymbols (98 - 98) >> <14E788B1-4EB2-3FD7-934B-849534DFC198> >> /System/Library/PrivateFrameworks/DebugSymbols.framework/Versions/A /DebugSymbols >> >>> 0x7fff8e0ca000 - 0x7fff8e0d8fff libcommonCrypto.dylib (60027) >> <baafe0c9-bb86-3ca7-88c0-e3cba98da06f> /usr/lib/system/libcommonCrypto.dylib >> >>> 0x7fff8e0d9000 - 0x7fff8e11cff7 com.apple.RemoteViewServices >> (2.0 - 80.6) <5CFA361D-4853-3ACC-9EFC-A2AC1F43BA4B> >> /System/Library/PrivateFrameworks/RemoteViewServices.framework/Vers ions/A/RemoteViewServices >> >>> 0x7fff8e11d000 - 0x7fff8e11efff liblangid.dylib (116) >> <864C409D-D56B-383E-9B44-A435A47F2346> /usr/lib/liblangid.dylib >> >>> 0x7fff8e480000 - 0x7fff8e4b7ff7 libssl.0.9.8.dylib (47) >> <923945E6-C489-3406-903B-A362410753F8> /usr/lib/libssl.0.9.8.dylib >> >>> 0x7fff8e4b8000 - 0x7fff8e526fff com.apple.framework.IOKit (2.0.1 >> - 755.22.5) <1547DA6F-9793-30A2-8E92-7368DE84D46C> >> /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit >> >>> 0x7fff8e5e0000 - 0x7fff8e662ff7 com.apple.Heimdal (3.0 - 2.0) >> <c94b0c6c-1320-35a1-8143-fe252e7b2a08> >> /System/Library/PrivateFrameworks/Heimdal.framework/Versions/A/Heimdal >> >>> 0x7fff8e663000 - 0x7fff8e6cbff7 libc++.1.dylib (65.1) >> <20E31B90-19B9-3C2A-A9EB-474E08F9FE05> /usr/lib/libc++.1.dylib >> >>> 0x7fff8e6cc000 - 0x7fff8e72bfff com.apple.AE<http: com.apple.ae=""/>(645.6 - 645.6) <44F403C1-660A-3543 -AB9C-3902E02F936F> >> /System/Library/Frameworks/CoreServices.framework/Versions/A/Framew orks/AE.framework/Versions/A/AE >> >>> 0x7fff8eae4000 - 0x7fff8eae8fff libGIF.dylib (849) >> <6A664B4D-0A88-33F7-9064-0CD159AB9CE9> >> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/l ibGIF.dylib >> >>> 0x7fff8eae9000 - 0x7fff8eaf1ff7 libsystem_dnssd.dylib (379.37) >> <616FC901-151E-38BF-B2C4-24A351C5FAAD> /usr/lib/system/libsystem_dnssd.dylib >> >>> 0x7fff8ed83000 - 0x7fff8edaafff >> com.apple.framework.familycontrols (4.1 - 410) >> <50F5A52C-8FB6-300A-977D-5CFDE4D5796B> >> /System/Library/PrivateFrameworks/FamilyControls.framework/Versions /A/FamilyControls >> >>> 0x7fff8edab000 - 0x7fff8eeadfff libJP2.dylib (849) >> <4EEA33EB-AF9F-365D-A572-F7D11AD1C76F> >> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/l ibJP2.dylib >> >>> 0x7fff8eeae000 - 0x7fff8efcefff com.apple.desktopservices (1.7.3 >> - 1.7.3) <707F77D2-EC0E-3431-840F-B984BD7ABDD6> >> /System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Ver sions/A/DesktopServicesPriv >> >>> 0x7fff8f1b8000 - 0x7fff8f1b9fff >> libDiagnosticMessagesClient.dylib (8) >> <8548E0DC-0D2F-30B6-B045-FE8A038E76D8> >> /usr/lib/libDiagnosticMessagesClient.dylib >> >>> 0x7fff8f1ba000 - 0x7fff8f1d0fff >> com.apple.MultitouchSupport.framework (235.29 - 235.29) >> <617EC8F1-BCE7-3553-86DD-F857866E1257> >> /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versi ons/A/MultitouchSupport >> >>> 0x7fff8f343000 - 0x7fff8f371ff7 libsystem_m.dylib (3022.6) >> <b434be5c-25ab-3ebd-baa7-5304b34e3441> /usr/lib/system/libsystem_m.dylib >> >>> 0x7fff8f3a1000 - 0x7fff8f3d7fff libsystem_info.dylib (406.17) >> <4FFCA242-7F04-365F-87A6-D4EFB89503C1> /usr/lib/system/libsystem_info.dylib >> >>> 0x7fff8f4c9000 - 0x7fff8f826ff7 com.apple.Foundation (6.8 - >> 945.16) <89BD68FD-72C8-35C1-94C6-3A07F097C50D> >> /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation >> >>> 0x7fff8f827000 - 0x7fff8f833fff libCSync.A.dylib (331.0.4) >> <c7043bb7-284d-3b9f-a5cb-78ade691b2d4> >> /System/Library/Frameworks/ApplicationServices.framework/Versions/A /Frameworks/CoreGraphics.framework/Versions/A/Resources/libCSync.A.dyl ib >> >>> 0x7fff8f882000 - 0x7fff8f91dfff com.apple.CoreSymbolication (3.0 >> - 117) <c304fdb8-2ff7-34bc-858a-2b96c2b039d5> >> /System/Library/PrivateFrameworks/CoreSymbolication.framework/Versi ons/A/CoreSymbolication >> >>> 0x7fff8f91e000 - 0x7fff8f93fff7 libCRFSuite.dylib (33) >> <736ABE58-8DED-3289-A042-C25AF7AE5B23> /usr/lib/libCRFSuite.dylib >> >>> 0x7fff8f940000 - 0x7fff8f97fff7 com.apple.QD (3.42 - 285) >> <8DF36FCA-C06B-30F4-A631-7BE2FF7E56D1> >> /System/Library/Frameworks/ApplicationServices.framework/Versions/A /Frameworks/QD.framework/Versions/A/QD >> >>> 0x7fff8f9ad000 - 0x7fff8fa07ff7 com.apple.opencl (2.2.18 - >> 2.2.18) <4A78E53C-17B0-3B2D-A9EA-EF8720FE4134> >> /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL >> >>> 0x7fff8fa08000 - 0x7fff8fa09ff7 libdnsinfo.dylib (453.19) >> <14202FFB-C3CA-3FCC-94B0-14611BF8692D> /usr/lib/system/libdnsinfo.dylib >> >>> 0x7fff8fa56000 - 0x7fff8fa67ff7 libsasl2.2.dylib (166) >> <649CAE0E-8FFE-3C60-A849-BE6300E4B726> /usr/lib/libsasl2.2.dylib >> >>> 0x7fff8fa68000 - 0x7fff8fac4ff7 com.apple.Symbolication (1.3 - >> 93) <f2c7e0b6-b241-3020-b30a-0636d0fa3378> >> /System/Library/PrivateFrameworks/Symbolication.framework/Versions/ A/Symbolication >> >>> 0x7fff8fc32000 - 0x7fff8fcd8ff7 >> com.apple.CoreServices.OSServices (557.6 - 557.6) >> <1BDB5456-0CE9-301C-99C1-8EFD0D2BFCCD> >> /System/Library/Frameworks/CoreServices.framework/Versions/A/Framew orks/OSServices.framework/Versions/A/OSServices >> >>> 0x7fff8fe8b000 - 0x7fff8feb2ff7 com.apple.PerformanceAnalysis >> (1.16 - 16) <e4888388-f41b-313e-9cbb-5807d077bda9> >> /System/Library/PrivateFrameworks/PerformanceAnalysis.framework/Ver sions/A/PerformanceAnalysis >> >>> 0x7fff8ff0d000 - 0x7fff8ff2efff com.apple.Ubiquity (1.2 - >> 243.15) <c9a7ee77-b637-3676-b667-c0843bbb0409> >> /System/Library/PrivateFrameworks/Ubiquity.framework/Versions/A/Ubi quity >> >>> 0x7fff901f3000 - 0x7fff901f3fff com.apple.Accelerate (1.8 - >> Accelerate 1.8) <6AD48543-0864-3D40-80CE-01F184F24B45> >> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate >> >>> 0x7fff901f4000 - 0x7fff9021cfff libJPEG.dylib (849) >> <5C9052F6-D0B3-39CC-8302-468B43D694D5> >> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/l ibJPEG.dylib >> >>> 0x7fff90631000 - 0x7fff90632ff7 libremovefile.dylib (23.2) >> <6763BC8E-18B8-3AD9-8FFA-B43713A7264F> /usr/lib/system/libremovefile.dylib >> >>> 0x7fff90633000 - 0x7fff90633fff com.apple.Accelerate.vecLib (3.8 >> - vecLib 3.8) <b5a18ee8-df81-38dd-acaf-7076b2a26225> >> /System/Library/Frameworks/Accelerate.framework/Versions/A/Framewor ks/vecLib.framework/Versions/A/vecLib >> >>> 0x7fff90634000 - 0x7fff9064bfff com.apple.CFOpenDirectory (10.8 >> - 151.10) <ffbba538-00b5-334e-ba5b-c8ad6cdcda14> >> /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frame works/CFOpenDirectory.framework/Versions/A/CFOpenDirectory >> >>> 0x7fff9068e000 - 0x7fff90696fff liblaunch.dylib (442.26.2) >> <2F71CAF8-6524-329E-AC56-C506658B4C0C> /usr/lib/system/liblaunch.dylib >> >>> 0x7fff90697000 - 0x7fff906aaff7 com.apple.LangAnalysis (1.7.0 - >> 1.7.0) <2F2694E9-A7BC-33C7-B4CF-8EC907DF0FEB> >> /System/Library/Frameworks/ApplicationServices.framework/Versions/A /Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis >> >>> 0x7fff906ab000 - 0x7fff9103b6ff com.apple.CoreGraphics (1.600.0 >> - 331.0.4) <4953961C-96DC-39D7-ADF5-B767F2A7E4E1> >> /System/Library/Frameworks/ApplicationServices.framework/Versions/A /Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics >> >>> 0x7fff910ad000 - 0x7fff910c0ff7 libbsm.0.dylib (32) >> <f497d3ce-40d9-3551-84b4-3d5e39600737> /usr/lib/libbsm.0.dylib >> >>> 0x7fff910f5000 - 0x7fff91d22ff7 com.apple.AppKit (6.8 - 1187.37) >> <faea8b77-210f-3c0f-b9cf-85a7595cca26> >> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit >> >>> 0x7fff91ffb000 - 0x7fff920f0fff libiconv.2.dylib (34) >> <fee8b996-eb44-37fa-b96e-d379664defe1> /usr/lib/libiconv.2.dylib >> >>> 0x7fff920f1000 - 0x7fff920fcfff libsystem_notify.dylib (98.5) >> <c49275cc-835a-3207-afba-8c01374927b6> >> /usr/lib/system/libsystem_notify.dylib >> >>> 0x7fff920fd000 - 0x7fff92109fff com.apple.CrashReporterSupport >> (10.8.3 - 417) <48EDDDF3-5720-39D6-B51F-D9AFB93327B3> >> /System/Library/PrivateFrameworks/CrashReporterSupport.framework/Ve rsions/A/CrashReporterSupport >> >>> 0x7fff92184000 - 0x7fff921a6ff7 com.apple.Kerberos (2.0 - 1) >> <c49b8820-34ed-39d7-a407-a3e854153556> >> /System/Library/Frameworks/Kerberos.framework/Versions/A/Kerberos >> >>> 0x7fff921a7000 - 0x7fff921d5fff com.apple.CoreServicesInternal >> (154.2 - 154.2) <3E6196E6-F3B4-316F-9E1F-13B6B9694C7E> >> /System/Library/PrivateFrameworks/CoreServicesInternal.framework/Ve rsions/A/CoreServicesInternal >> >>> 0x7fff921d6000 - 0x7fff922a8ff7 com.apple.CoreText (260.0 - >> 275.16) <5BFC1D67-6A6F-38BC-9D90-9C712684EDAC> >> /System/Library/Frameworks/CoreText.framework/Versions/A/CoreText >> >>> 0x7fff922a9000 - 0x7fff922b4fff com.apple.CommonAuth (3.0 - 2.0) >> <7A953C1F-8B18-3E46-9BEA-26D9B5B7745D> >> /System/Library/PrivateFrameworks/CommonAuth.framework/Versions/A/C ommonAuth >> >>> 0x7fff922b5000 - 0x7fff922b5fff com.apple.ApplicationServices >> (45 - 45) <a3abf20b-ed3a-32b5-830e-b37831a45a80> >> /System/Library/Frameworks/ApplicationServices.framework/Versions/A /ApplicationServices >> >>> 0x7fff922b6000 - 0x7fff92323ff7 com.apple.datadetectorscore (4.1 >> - 269.2) <4FD4A7CE-BB00-3AAB-B7AA-AE395D5400EC> >> /System/Library/PrivateFrameworks/DataDetectorsCore.framework/Versi ons/A/DataDetectorsCore >> >>> 0x7fff92328000 - 0x7fff9237dff7 libTIFF.dylib (849) >> <c4d0e196-9319-319b-af72-8b63fb5af71b> >> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/l ibTIFF.dylib >> >>> 0x7fff92522000 - 0x7fff925afff7 com.apple.SearchKit (1.4.0 - >> 1.4.0) <c7f43889-f8bf-3cb9-ad66-11aefcbcede7> >> /System/Library/Frameworks/CoreServices.framework/Versions/A/Framew orks/SearchKit.framework/Versions/A/SearchKit >> >>> 0x7fff925b0000 - 0x7fff925b1ff7 libsystem_sandbox.dylib (220.2) >> <6838A6FD-8626-3356-BB4F-BB4787216207> >> /usr/lib/system/libsystem_sandbox.dylib >> >>> 0x7fff925b2000 - 0x7fff925bdff7 com.apple.bsd.ServiceManagement >> (2.0 - 2.0) <c12962d5-85fb-349e-aa56-64f4f487f219> >> /System/Library/Frameworks/ServiceManagement.framework/Versions/A/S erviceManagement >> >>> 0x7fff92611000 - 0x7fff92649fff libncurses.5.4.dylib (37.3) >> <68D5B5F5-8252-3F1E-AFF1-C6AFE145DBC1> /usr/lib/libncurses.5.4.dylib >> >>> 0x7fff926db000 - 0x7fff927a7ff7 libsystem_c.dylib (825.26) >> <4C9EB006-FE1F-3F8F-8074-DFD94CF2CE7B> /usr/lib/system/libsystem_c.dylib >> >>> 0x7fff927a8000 - 0x7fff92943fef com.apple.vImage (6.0 - 6.0) >> <fae13169-295a-33a5-8e6b-7c2cc1407fa7> >> /System/Library/Frameworks/Accelerate.framework/Versions/A/Framewor ks/vImage.framework/Versions/A/vImage >> >>> 0x7fff92c33000 - 0x7fff92c77fff libcups.2.dylib (327.3) >> <71E771A1-0489-3417-8A4A-56A2C930F80C> /usr/lib/libcups.2.dylib >> >>> 0x7fff92c78000 - 0x7fff92d12fff libvMisc.dylib (380.6) >> <714336EA-1C0E-3735-B31C-19DFDAAF6221> >> /System/Library/Frameworks/Accelerate.framework/Versions/A/Framewor ks/vecLib.framework/Versions/A/libvMisc.dylib >> >>> 0x7fff92d13000 - 0x7fff92d64ff7 com.apple.SystemConfiguration >> (1.12.2 - 1.12.2) <a4341bbd-a330-3a57-8891-e9c1a286a72d> >> /System/Library/Frameworks/SystemConfiguration.framework/Versions/A /SystemConfiguration >> >>> 0x7fff92dba000 - 0x7fff92ddafff libPng.dylib (849) >> <f4c23a55-f17b-3e4f-9e80-bc97f778ba49> >> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/l ibPng.dylib >> >>> 0x7fff92e08000 - 0x7fff92e89fff com.apple.Metadata (10.7.0 - >> 707.5) <4140B1F6-7D73-33C7-B3F2-4DB349C31AE9> >> /System/Library/Frameworks/CoreServices.framework/Versions/A/Framew orks/Metadata.framework/Versions/A/Metadata >> >>> 0x7fff93132000 - 0x7fff93134fff libCVMSPluginSupport.dylib >> (8.7.25) <a45e21e3-4b40-39b0-a8b6-411526a84f47> >> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/li bCVMSPluginSupport.dylib >> >>> 0x7fff93135000 - 0x7fff93181ff7 libauto.dylib (185.1) >> <73CDC482-16E3-3FC7-9BB4-FBA2DA44DBC2> /usr/lib/libauto.dylib >> >>> 0x7fff93184000 - 0x7fff93189fff libcache.dylib (57) >> <65187C6E-3FBF-3EB8-A1AA-389445E2984D> /usr/lib/system/libcache.dylib >> >>> 0x7fff931e5000 - 0x7fff931ebff7 libunwind.dylib (35.1) >> <21703D36-2DAB-3D8B-8442-EAAB23C060D3> /usr/lib/system/libunwind.dylib >> >>> 0x7fff931ec000 - 0x7fff932e9ff7 libxml2.2.dylib (22.3) >> <47B09CB2-C636-3024-8B55-6040F7829B4C> /usr/lib/libxml2.2.dylib >> >>> 0x7fff932ea000 - 0x7fff9332dff7 com.apple.bom (12.0 - 192) >> <0BF1F2D2-3648-36B7-BE4B-551A0173209B> >> /System/Library/PrivateFrameworks/Bom.framework/Versions/A/Bom >> >>> 0x7fff93385000 - 0x7fff9349d92f libobjc.A.dylib (532.2) >> <90D31928-F48D-3E37-874F-220A51FD9E37> /usr/lib/libobjc.A.dylib >> >>> 0x7fff934e7000 - 0x7fff934eaff7 libdyld.dylib (210.2.3) >> <f59367c9-c110-382b-a695-9035a6dd387e> /usr/lib/system/libdyld.dylib >> >>> 0x7fff934eb000 - 0x7fff934ebffd com.apple.audio.units.AudioUnit >> (1.8 - 1.8) <173346B7-614C-380B-8E80-9BD1BE501674> >> /System/Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit >> >>> 0x7fff934f8000 - 0x7fff93535fef libGLImage.dylib (8.7.25) >> <139A9892-A6F2-3F49-87FB-E7AC3F56E003> >> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/li bGLImage.dylib >> >>> 0x7fff93536000 - 0x7fff9354dfff com.apple.GenerationalStorage >> (1.1 - 132.3) <fd4a84b3-13a8-3c60-a59e-25a361447a17> >> /System/Library/PrivateFrameworks/GenerationalStorage.framework/Ver sions/A/GenerationalStorage >> >>> 0x7fff935ee000 - 0x7fff935fcff7 libkxld.dylib (2050.22.13) >> <4AAF0573-8632-3D06-BE32-C5675F77638D> /usr/lib/system/libkxld.dylib >> >>> 0x7fff935fd000 - 0x7fff93628fff libxslt.1.dylib (11.3) >> <441776B8-9130-3893-956F-39C85FFA644F> /usr/lib/libxslt.1.dylib >> >>> 0x7fff93629000 - 0x7fff93630fff libcopyfile.dylib (89) >> <876573D0-E907-3566-A108-577EAD1B6182> /usr/lib/system/libcopyfile.dylib >> >>> 0x7fff93e5e000 - 0x7fff93ea6fff libcurl.4.dylib (69.2) >> <ebdbf42d-e4a6-3d05-a76b-2817d79d59e2> /usr/lib/libcurl.4.dylib >> >>> 0x7fff93ea7000 - 0x7fff93f0ffff libvDSP.dylib (380.6) >> <cd4c5eeb-9e63-30c4-8103-7a5eaea0be60> >> /System/Library/Frameworks/Accelerate.framework/Versions/A/Framewor ks/vecLib.framework/Versions/A/libvDSP.dylib >> >>> 0x7fff94062000 - 0x7fff94297ff7 com.apple.CoreData (106.1 - >> 407.7) <24E0A6B4-9ECA-3D12-B26A-72B9DCF09768> >> /System/Library/Frameworks/CoreData.framework/Versions/A/CoreData >> >>> 0x7fff9429b000 - 0x7fff94319ff7 com.apple.securityfoundation >> (6.0 - 55115.4) <c5461971-e455-31a6-99b8-af80c4bc26dd> >> /System/Library/Frameworks/SecurityFoundation.framework/Versions/A/ SecurityFoundation >> >>> 0x7fff9431b000 - 0x7fff943b9ff7 com.apple.ink.framework (10.8.2 >> - 150) <84B9825C-3822-375F-BE58-A753444FBDE2> >> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/I nk.framework/Versions/A/Ink >> >>> 0x7fff95378000 - 0x7fff9568fff7 >> com.apple.CoreServices.CarbonCore (1037.5 - 1037.5) >> <731D8F92-1C52-3613-BA01-EFEA54DADF41> >> /System/Library/Frameworks/CoreServices.framework/Versions/A/Framew orks/CarbonCore.framework/Versions/A/CarbonCore >> >>> 0x7fff95690000 - 0x7fff95710ff7 >> com.apple.ApplicationServices.ATS (332 - 341.1) >> <bd83b039-ab25-3e3e-9975-a67dae66988b> >> /System/Library/Frameworks/ApplicationServices.framework/Versions/A /Frameworks/ATS.framework/Versions/A/ATS >> >>> 0x7fff95711000 - 0x7fff95715fff libCGXType.A.dylib (331.0.4) >> <251D4D2D-92B9-3D56-B348-CD67397F71FE> >> /System/Library/Frameworks/ApplicationServices.framework/Versions/A /Frameworks/CoreGraphics.framework/Versions/A/Resources/libCGXType.A.d ylib >> >>> 0x7fff9595f000 - 0x7fff95c30ff7 com.apple.security (7.0 - >> 55179.11) <73958084-5BBC-3597-A751-7370B0C247E5> >> /System/Library/Frameworks/Security.framework/Versions/A/Security >> >>> 0x7fff95c4d000 - 0x7fff95c51fff libpam.2.dylib (20) >> <c8f45864-5b58-3237-87e1-2c258a1d73b8> /usr/lib/libpam.2.dylib >> >>> 0x7fff95ccf000 - 0x7fff95e44fff com.apple.CFNetwork (596.3.3 - >> 596.3.3) <3739DC8D-8610-3740-80EC-43E130779CB8> >> /System/Library/Frameworks/CFNetwork.framework/Versions/A/CFNetwork >> >>> 0x7fff95e45000 - 0x7fff95e52fff libbz2.1.0.dylib (29) >> <ce9785e8-b535-3504-b392-82f0064d9af2> /usr/lib/libbz2.1.0.dylib >> >>> 0x7fff95e53000 - 0x7fff95e59fff com.apple.DiskArbitration (2.5.2 >> - 2.5.2) <c713a35a-360e-36ce-ac0a-25c86a3f50ca> >> /System/Library/Frameworks/DiskArbitration.framework/Versions/A/Dis kArbitration >> >>> 0x7fff95e5a000 - 0x7fff95e5afff com.apple.vecLib (3.8 - vecLib >> 3.8) <794317C7-4E38-338A-A874-5E18001C8503> >> /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib >> >>> 0x7fff95fbd000 - 0x7fff95fc1fff com.apple.IOSurface (86.0.4 - >> 86.0.4) <26F01CD4-B76B-37A3-989D-66E8140542B3> >> /System/Library/Frameworks/IOSurface.framework/Versions/A/IOSurface >> >>> 0x7fff963ff000 - 0x7fff965adfff com.apple.QuartzCore (1.8 - >> 304.2) <234EABE1-067C-3DAE-BEAC-674526E232C2> >> /System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore >> >>> 0x7fff965ae000 - 0x7fff965bcff7 libsystem_network.dylib (77.10) >> <0D99F24E-56FE-380F-B81B-4A4C630EE587> >> /usr/lib/system/libsystem_network.dylib >> >>> 0x7fff96622000 - 0x7fff96626fff libCoreVMClient.dylib (32.3) >> <ad8391d9-56dd-3a78-a294-6a30e6ece1a2> >> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/li bCoreVMClient.dylib >> >>> 0x7fff96627000 - 0x7fff96701fff com.apple.backup.framework >> (1.4.2 - 1.4.2) <0B557393-CD2A-3076-BED2-F28D02E1EC1D> >> /System/Library/PrivateFrameworks/Backup.framework/Versions/A/Backup >> >>> 0x7fff96702000 - 0x7fff9674cff7 libGLU.dylib (8.7.25) >> <c243c6d3-3384-3db1-bb15-e27b65c87294> >> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/li bGLU.dylib >> >>> >> >>> External Modification Summary: >> >>> Calls made by other processes targeting this process: >> >>> task_for_pid: 2 >> >>> thread_create: 0 >> >>> thread_set_state: 0 >> >>> Calls made by this process: >> >>> task_for_pid: 0 >> >>> thread_create: 0 >> >>> thread_set_state: 0 >> >>> Calls made by all processes on this machine: >> >>> task_for_pid: 18259 >> >>> thread_create: 2 >> >>> thread_set_state: 0 >> >>> >> >>> VM Region Summary: >> >>> ReadOnly portion of Libraries: Total=154.5M resident=91.3M(59%) >> swapped_out_or_unallocated=63.1M(41%) >> >>> Writable regions: Total=445.0M written=272.1M(61%) >> resident=289.8M(65%) swapped_out=1276K(0%) unallocated=155.2M(35%) >> >>> >> >>> REGION TYPE VIRTUAL >> >>> =========== ======= >> >>> ATS (font support) 32.3M >> >>> ATS (font support) (reserved) 4K reserved VM address >> space (unallocated) >> >>> CG backing stores 10.3M >> >>> CG image 4K >> >>> CG raster data 96K >> >>> CG shared images 192K >> >>> CoreServices 7332K >> >>> MALLOC 336.8M >> >>> MALLOC guard page 48K >> >>> MALLOC_LARGE (reserved) 228K reserved VM address >> space (unallocated) >> >>> Memory tag=242 12K >> >>> STACK GUARD 56.0M >> >>> Stack 9232K >> >>> VM_ALLOCATE 16.1M >> >>> __DATA 50.6M >> >>> __IMAGE 528K >> >>> __LINKEDIT 53.8M >> >>> __TEXT 100.6M >> >>> __UNICODE 544K >> >>> mapped file 59.9M >> >>> shared memory 308K >> >>> =========== ======= >> >>> TOTAL 734.5M >> >>> TOTAL, minus reserved VM space 734.3M >> >>> >> >>> Model: MacBookPro10,1, BootROM MBP101.00EE.B02, 4 processors, Intel >> Core i7, 2.6 GHz, 16 GB, SMC 2.3f35 >> >>> Graphics: Intel HD Graphics 4000, Intel HD Graphics 4000, Built-In, >> 512 MB >> >>> Graphics: NVIDIA GeForce GT 650M, NVIDIA GeForce GT 650M, PCIe, 1024 >> MB >> >>> Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80CE, >> 0x4D34373142314737334248302D434B302020 >> >>> Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80CE, >> 0x4D34373142314737334248302D434B302020 >> >>> AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xEF), >> Broadcom BCM43xx 1.0 (5.106.98.100.16) >> >>> Bluetooth: Version 4.1.3f3 11349, 2 service, 18 devices, 1 incoming >> serial ports >> >>> Network Service: Wi-Fi, AirPort, en0 >> >>> Serial ATA Device: APPLE SSD SM512E, 500.28 GB >> >>> USB Device: FreeAgent GoFlex, 0x0bc2 (Seagate LLC), 0x5031, >> 0x14a00000 / 4 >> >>> USB Device: hub_device, 0x8087 (Intel Corporation), 0x0024, >> 0x1a100000 / 2 >> >>> USB Device: FaceTime HD Camera (Built-in), apple_vendor_id, 0x8510, >> 0x1a110000 / 3 >> >>> USB Device: hub_device, 0x8087 (Intel Corporation), 0x0024, >> 0x1d100000 / 2 >> >>> USB Device: hub_device, 0x0424 (SMSC), 0x2512, 0x1d180000 / 3 >> >>> USB Device: BRCM20702 Hub, 0x0a5c (Broadcom Corp.), 0x4500, >> 0x1d181000 / 5 >> >>> USB Device: Bluetooth USB Host Controller, apple_vendor_id, 0x8286, >> 0x1d181300 / 6 >> >>> USB Device: Apple Internal Keyboard / Trackpad, apple_vendor_id, >> 0x0262, 0x1d182000 / 4 >> >>> USB Device: hub_device, 0x0424 (SMSC), 0x2514, 0x14100000 / 1 >> >>> USB Device: ScanSnap S1500, 0x04c5 (Fujitsu Ltd.), 0x11a2, >> 0x14140000 / 3 >> >>> USB Device: Microsoft Digital Sound System 80, 0x045e (Microsoft >> Corporation), 0x0014, 0x14120000 / 2 >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> -- output of sessionInfo(): >> >>> >> >>>> sessionInfo() >> >>> R version 3.0.0 (2013-04-03) >> >>> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >>> >> >>> locale: >> >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >>> >> >>> attached base packages: >> >>> [1] parallel grid stats graphics grDevices utils >> datasets methods base >> >>> >> >>> other attached packages: >> >>> [1] GenomicRanges_1.12.2 IRanges_1.18.0 BiocGenerics_0.6.0 >> Gviz_1.4.0 >> >>> >> >>> loaded via a namespace (and not attached): >> >>> [1] AnnotationDbi_1.22.2 Biobase_2.20.0 biomaRt_2.16.0 >> Biostrings_2.28.0 >> >>> [5] biovizBase_1.8.0 bitops_1.0-5 BSgenome_1.28.0 >> cluster_1.14.4 >> >>> [9] colorspace_1.2-2 DBI_0.2-6 dichromat_2.0-0 >> GenomicFeatures_1.12.0 >> >>> [13] Hmisc_3.10-1 labeling_0.1 lattice_0.20-15 >> munsell_0.4 >> >>> [17] plyr_1.8 RColorBrewer_1.0-5 RCurl_1.95-4.1 >> Rsamtools_1.12.2 >> >>> [21] RSQLite_0.11.3 rtracklayer_1.20.1 scales_0.2.3 >> stats4_3.0.0 >> >>> [25] stringr_0.6.2 tools_3.0.0 XML_3.95-0.2 >> zlibbioc_1.6.0 >> >>> >> >>> -- >> >>> Sent via the guest posting facility at bioconductor.org. >> >>> >> >>> _______________________________________________ >> >>> Bioconductor mailing list >> >>> Bioconductor@r-project.org >> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >>> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > [[alternative HTML version deleted]]
ADD COMMENTlink written 6.3 years ago by Michael Lawrence11k
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