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Question: IdeogramTrack and bigWig file errors in Gviz
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4.6 years ago by
Guest User12k
Guest User12k 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: ???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, 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> 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/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.
ADD COMMENTlink modified 4.6 years ago by Robert Ivanek410 • written 4.6 years ago by Guest User12k
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gravatar for Robert Ivanek
4.6 years ago by
Robert Ivanek410
Switzerland
Robert Ivanek410 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 at="" 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: ??~BiocGenerics??T > > The following objects are masked from ??~package:parallel??T: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, > clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, > parSapplyLB > > The following object is masked from ??~package:stats??T: > > xtabs > > The following objects are masked from ??~package:base??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/libgfortran.2.dylib > 0x1004b5000 - 0x1004dffd9 +libreadline.5.2.dylib (5.2) /Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline .5.2.dylib > 0x1005c2000 - 0x1005c9fff +utils.so (0) <8FBF096E-B6CE- 398E-A920-01DE1B245C41> /Library/Frameworks/R.framework/Versions/3.0/R esources/library/utils/libs/utils.so > 0x1005e9000 - 0x1005eefff +methods.so (0) <ab37fbdb-4142-3274-affb-b2fb7fd32fc7> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/methods/libs/methods.so > 0x1005f7000 - 0x1005f9fef +bitops.so (0) <f9843053-e910 -36cf-9df1-f4121020f969=""> /Library/Frameworks/R.framework/Versions/3.0/ Resources/library/bitops/libs/bitops.so > 0x1007f2000 - 0x1007f5fef +parallel.so (0) <e5a82d0c- 98bd-3e65-a7ee-1fab5c8b6264=""> /Library/Frameworks/R.framework/Versions/ 3.0/Resources/library/parallel/libs/parallel.so > 0x1007f9000 - 0x1007fcfff +Biobase.so (0) <68F5403C-3382-31CD-BDAB-4335D037FE5E> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/Biobase/libs/Biobase.so > 0x101194000 - 0x1011cffef +graphics.so (0) <9E6394E4-AF37-3F25-A180-026E82583AF2> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/graphics/libs/graphics.so > 0x1011da000 - 0x1011e3fff +RCurl.so (0) <66E5F530-2EF3-32CB-9373-1A6491E8366A> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/RCurl/libs/RCurl.so > 0x1011ed000 - 0x1011effff +lattice.so (0) <5A52F152 -052E-3C10-B9B3-5B486A910DD7> /Library/Frameworks/R.framework/Versions /3.0/Resources/library/lattice/libs/lattice.so > 0x1011f2000 - 0x1011f3ff7 +plyr.so (0) <eb5cbaa5-f26d- 31d4-a292-f9ac0b2a189e=""> /Library/Frameworks/R.framework/Versions/3.0/R esources/library/plyr/libs/plyr.so > 0x10120f000 - 0x101219fff +GenomicRanges.so (0) <844F62EE-EEF9-3C56-812A-4E75A899CCB2> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/GenomicRanges/libs/GenomicRanges.so > 0x101224000 - 0x101230fff +colorspace.so (0) <0E7C120B- 148E-351A-92A1-C7963AC07174> /Library/Frameworks/R.framework/Versions/ 3.0/Resources/library/colorspace/libs/colorspace.so > 0x10126e000 - 0x10127aff7 +cluster.so (0) <55B40D4D-8432-3FEB-BBB7-8E65C948C17C> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/cluster/libs/cluster.so > 0x10127e000 - 0x10127fff7 +biovizBase.so (0) <45F295A2-1E32-3E5C-96B9-1657114AE545> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/biovizBase/libs/biovizBase.so > 0x101396000 - 0x1013b1fff +grid.so (0) <0A0B45EC-AC1D- 3F33-A57E-6B234CC42505> /Library/Frameworks/R.framework/Versions/3.0/R esources/library/grid/libs/grid.so > 0x1013be000 - 0x1013c3fff +Hmisc.so (0) <45B74820-59DF-3402-9F5C-CB4A0A3E90D4> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/Hmisc/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/tools/libs/tools.so > 0x102e82000 - 0x102ebffff +grDevices.so (0) <f7087219-a4a6-33c3-a0a8-19aaded62431> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/grDevices/libs/grDevices.so > 0x102edb000 - 0x102f65fef +stats.so (0) <99BD4BBA- AE70-38A3-BC7E-ABEF5775D09A> /Library/Frameworks/R.framework/Versions/ 3.0/Resources/library/stats/libs/stats.so > 0x103900000 - 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/Resources/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/Priv ateFrameworks/AppleFSCompression.framework/Versions/A/AppleFSCompressi on > 0x7fff89b5a000 - 0x7fff89bb0fff com.apple.HIServices (1.20 - 417) <a1129272-fec8-350b-ba26-5a97f23c413d> /System/Library/Frameworks /ApplicationServices.framework/Versions/A/Frameworks/HIServices.framew ork/Versions/A/HIServices > 0x7fff89e2f000 - 0x7fff89e5bff7 libRIP.A.dylib (331.0.4) <4B261CE2-524E-3FA9-9437-B70DAC1EAB95> /System/Library/Frameworks/Appl icationServices.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/Acce lerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/lib BLAS.dylib > 0x7fff8a09a000 - 0x7fff8a0f1ff7 com.apple.ScalableUserInterface (1.0 - 1) <f1d43dfb-1796-361b-ad4b- 39f1eed3be19=""> /System/Library/Frameworks/QuartzCore.framework/Versions /A/Frameworks/ScalableUserInterface.framework/Versions/A/ScalableUserI nterface > 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/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/F rameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServi ces.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/Framewor ks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.frame work/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 > 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com.apple.desktopservices (1.7.3 - 1.7.3) <707F77D2-EC0E-3431-840F-B984BD7ABDD6> /System/Library /PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/DesktopSer vicesPriv > 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/PrivateFramewor ks/MultitouchSupport.framework/Versions/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> 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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> /System/Libr ary/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.frame work/Versions/A/vecLib > 0x7fff90634000 - 0x7fff9064bfff com.apple.CFOpenDirectory (10.8 - 151.10) <ffbba538-00b5-334e-ba5b-c8ad6cdcda14> 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<71E771A1-0489-3417-8A4A-56A2C930F80C> /usr/lib/libcups.2.dylib > 0x7fff92c78000 - 0x7fff92d12fff libvMisc.dylib (380.6) <714336EA-1C0E-3735-B31C-19DFDAAF6221> /System/Library/Frameworks/Acce lerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/lib vMisc.dylib > 0x7fff92d13000 - 0x7fff92d64ff7 com.apple.SystemConfiguration (1.12.2 - 1.12.2) <a4341bbd-a330-3a57-8891-e9c1a286a72d> /System/Library/Frameworks/Syst emConfiguration.framework/Versions/A/SystemConfiguration > 0x7fff92dba000 - 0x7fff92ddafff libPng.dylib (849) <f4c23a55 -f17b-3e4f-9e80-bc97f778ba49=""> /System/Library/Frameworks/ImageIO.frame work/Versions/A/Resources/libPng.dylib > 0x7fff92e08000 - 0x7fff92e89fff com.apple.Metadata (10.7.0 - 707.5) <4140B1F6-7D73-33C7-B3F2-4DB349C31AE9> /System/Library/Framewor ks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Ver sions/A/Metadata > 0x7fff93132000 - 0x7fff93134fff libCVMSPluginSupport.dylib (8.7.25) <a45e21e3-4b40-39b0-a8b6-411526a84f47> /System/Library/Framew orks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.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/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/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/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/Frameworks/Appl icationServices.framework/Versions/A/Frameworks/CoreGraphics.framework /Versions/A/Resources/libCGXType.A.dylib > 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/DiskArbitration > 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/Open GL.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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 4.6 years ago by Robert Ivanek410
I am trying to install Gviz using biocLite in R devel and it says it's only available as a source package. I'm a little new at this...how would I install the latest version from source within R? Thx - 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<mailto:miles-pufall@uiowa.edu> On Apr 26, 2013, at 8:00 AM, Robert Ivanek <robert.ivanek@unibas.ch<mailto: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<mailto: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> 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com.apple.GenerationalStorage (1.1 - 132.3) <fd4a84b3-13a8-3c60-a59e-25a361447a17> /System/Library/P rivateFrameworks/GenerationalStorage.framework/Versions/A/Generational Storage 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/SecurityFoundation.framework/Versions/A/SecurityFoundation 0x7fff9431b000 - 0x7fff943b9ff7 com.apple.ink.framework (10.8.2 - 150) <84B9825C-3822-375F-BE58-A753444FBDE2> /System/Library/Framewor ks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/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/Frameworks/Appl icationServices.framework/Versions/A/Frameworks/CoreGraphics.framework /Versions/A/Resources/libCGXType.A.dylib 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/DiskArbitration 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/Open GL.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<http: bioconductor.org="">. _______________________________________________ Bioconductor 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ADD REPLYlink written 4.6 years ago by Pufall, Miles A10
Oops - and here's my sessionInfo: > sessionInfo() R Under development (unstable) (2013-04-26 r62678) 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] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.11.0 loaded via a namespace (and not attached): [1] tools_3.1.0 M On Apr 27, 2013, at 10:08 AM, "Pufall, Miles A" <miles-pufall at="" uiowa.edu=""> wrote: > I am trying to install Gviz using biocLite in R devel and it says it's only available as a source package. I'm a little new at this...how would I install the latest version from source within R? > > Thx - > > 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 at uiowa.edu<mailto:miles-pufall at="" uiowa.edu=""> > > > On Apr 26, 2013, at 8:00 AM, Robert Ivanek <robert.ivanek at="" unibas.ch<mailto:robert.ivanek="" at="" 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 at="" bioconductor.org<mailto:guest="" at="" 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: ??~BiocGenerics??T > > The following objects are masked from ??~package:parallel??T: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, > clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, > parSapplyLB > > The following object is masked from ??~package:stats??T: > > xtabs > > The following objects are masked from ??~package:base??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/libgfortran.2.dylib > 0x1004b5000 - 0x1004dffd9 +libreadline.5.2.dylib (5.2) /L ibrary/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5 .2.dylib > 0x1005c2000 - 0x1005c9fff +utils.so (0) <8FBF096E-B6CE- 398E-A920-01DE1B245C41> /Library/Frameworks/R.framework/Versions/3.0/R esources/library/utils/libs/utils.so 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/System/Library/Framewor ks/CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/Ve rsions/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.framew ork/Versions/A/ServiceManagement > 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/Acce lerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vIm age > 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/Acce lerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/lib vMisc.dylib > 0x7fff92d13000 - 0x7fff92d64ff7 com.apple.SystemConfiguration (1.12.2 - 1.12.2) <a4341bbd-a330-3a57-8891-e9c1a286a72d> /System/Libra ry/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfigura tion > 0x7fff92dba000 - 0x7fff92ddafff libPng.dylib (849) <f4c23a55 -f17b-3e4f-9e80-bc97f778ba49=""> /System/Library/Frameworks/ImageIO.frame work/Versions/A/Resources/libPng.dylib > 0x7fff92e08000 - 0x7fff92e89fff com.apple.Metadata (10.7.0 - 707.5) <4140B1F6-7D73-33C7-B3F2-4DB349C31AE9> /System/Library/Framewor ks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Ver sions/A/Metadata > 0x7fff93132000 - 0x7fff93134fff libCVMSPluginSupport.dylib (8.7.25) <a45e21e3-4b40-39b0-a8b6-411526a84f47> /System/Library/Framew orks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.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/Open GL.framework/Versions/A/Libraries/libGLImage.dylib > 0x7fff93536000 - 0x7fff9354dfff com.apple.GenerationalStorage (1.1 - 132.3) <fd4a84b3-13a8-3c60-a59e-25a361447a17> /System/Library/P rivateFrameworks/GenerationalStorage.framework/Versions/A/Generational Storage > 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/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/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/Frameworks/Appl icationServices.framework/Versions/A/Frameworks/CoreGraphics.framework /Versions/A/Resources/libCGXType.A.dylib > 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/DiskArbitration > 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/Open GL.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<http: bioconductor.org="">. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications 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If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. > ________________________________ > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 4.6 years ago by Miles Pufall40
On Sat, Apr 27, 2013 at 8:51 AM, Miles Pufall <miles.pufall at="" gmail.com=""> wrote: > Oops - and here's my sessionInfo: > > >> sessionInfo() > R Under development (unstable) (2013-04-26 r62678) Not sure if this is your problem or not, but both the release (2.12) and devel (2.13) versions of Bioconductor are meant to work with R 3.0.x, not R-devel. Dan > 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] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.11.0 > > loaded via a namespace (and not attached): > [1] tools_3.1.0 > > M > > On Apr 27, 2013, at 10:08 AM, "Pufall, Miles A" <miles-pufall at="" uiowa.edu=""> wrote: > >> I am trying to install Gviz using biocLite in R devel and it says it's only available as a source package. I'm a little new at this...how would I install the latest version from source within R? >> >> Thx - >> >> 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 at uiowa.edu<mailto:miles-pufall at="" uiowa.edu=""> >> >> >> On Apr 26, 2013, at 8:00 AM, Robert Ivanek <robert.ivanek at="" unibas.ch<mailto:robert.ivanek="" at="" 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 at="" bioconductor.org<mailto:guest="" at="" 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: ??~BiocGenerics??T >> >> The following objects are masked from ??~package:parallel??T: >> >> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, >> clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, >> parSapplyLB >> >> The following object is masked from ??~package:stats??T: >> >> xtabs >> >> The following objects are masked from ??~package:base??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/libgfortran.2.dylib >> 0x1004b5000 - 0x1004dffd9 +libreadline.5.2.dylib (5.2) / 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<9E6394E4-AF37-3F25-A180-026E82583AF2> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/graphics/libs/graphics.so >> 0x1011da000 - 0x1011e3fff +RCurl.so (0) <66E5F530-2EF3-32CB-9373-1A6491E8366A> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/RCurl/libs/RCurl.so >> 0x1011ed000 - 0x1011effff +lattice.so (0) <5A52F152 -052E-3C10-B9B3-5B486A910DD7> /Library/Frameworks/R.framework/Versions /3.0/Resources/library/lattice/libs/lattice.so >> 0x1011f2000 - 0x1011f3ff7 +plyr.so (0) <eb5cbaa5-f26d- 31d4-a292-f9ac0b2a189e=""> /Library/Frameworks/R.framework/Versions/3.0/R esources/library/plyr/libs/plyr.so >> 0x10120f000 - 0x101219fff +GenomicRanges.so (0) <844F62EE-EEF9-3C56-812A-4E75A899CCB2> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/GenomicRanges/libs/GenomicRanges.so >> 0x101224000 - 0x101230fff +colorspace.so (0) <0E7C120B- 148E-351A-92A1-C7963AC07174> /Library/Frameworks/R.framework/Versions/ 3.0/Resources/library/colorspace/libs/colorspace.so >> 0x10126e000 - 0x10127aff7 +cluster.so (0) <55B40D4D-8432 -3FEB-BBB7-8E65C948C17C> /Library/Frameworks/R.framework/Versions/3.0/ Resources/library/cluster/libs/cluster.so >> 0x10127e000 - 0x10127fff7 +biovizBase.so (0) <45F295A2-1E32-3E5C-96B9-1657114AE545> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/biovizBase/libs/biovizBase.so >> 0x101396000 - 0x1013b1fff +grid.so (0) <0A0B45EC-AC1D- 3F33-A57E-6B234CC42505> /Library/Frameworks/R.framework/Versions/3.0/R esources/library/grid/libs/grid.so >> 0x1013be000 - 0x1013c3fff +Hmisc.so (0) <45B74820-59DF-3402-9F5C-CB4A0A3E90D4> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/Hmisc/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/tools/libs/tools.so >> 0x102e82000 - 0x102ebffff +grDevices.so (0) <f7087219-a4a6-33c3-a0a8-19aaded62431> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/grDevices/libs/grDevices.so >> 0x102edb000 - 0x102f65fef +stats.so (0) <99BD4BBA- AE70-38A3-BC7E-ABEF5775D09A> /Library/Frameworks/R.framework/Versions/ 3.0/Resources/library/stats/libs/stats.so >> 0x103900000 - 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/Resources/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/Priv ateFrameworks/AppleFSCompression.framework/Versions/A/AppleFSCompressi on >> 0x7fff89b5a000 - 0x7fff89bb0fff com.apple.HIServices (1.20 - 417) <a1129272-fec8-350b-ba26-5a97f23c413d> /System/Library/Frameworks /ApplicationServices.framework/Versions/A/Frameworks/HIServices.framew ork/Versions/A/HIServices >> 0x7fff89e2f000 - 0x7fff89e5bff7 libRIP.A.dylib (331.0.4) <4B261CE2-524E-3FA9-9437-B70DAC1EAB95> /System/Library/Frameworks/Appl icationServices.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/Acce lerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/lib BLAS.dylib >> 0x7fff8a09a000 - 0x7fff8a0f1ff7 com.apple.ScalableUserInterface (1.0 - 1) <f1d43dfb-1796-361b-ad4b- 39f1eed3be19=""> /System/Library/Frameworks/QuartzCore.framework/Versions /A/Frameworks/ScalableUserInterface.framework/Versions/A/ScalableUserI nterface >> 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> 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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/PrivateFramewor ks/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/F rameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServi ces.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/Framewor 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com.apple.CoreServices (57 - 57) <9DD44CB0-C644-35C3-8F57-0B41B3EC147D> /System/Library/Frameworks/ 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/PrivateFr ameworks/CommerceKit.framework/Versions/A/Frameworks/CommerceCore.fram ework/Versions/A/CommerceCore >> 0x7fff8c23a000 - 0x7fff8c631fff libLAPACK.dylib (1073.4) 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<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 - 0x7fff8ccc4fff libRadiance.dylib (849) <f7d9a0fd-1195-34cb-bfe5-79daf3f40ac3> /System/Library/Frameworks/Imag eIO.framework/Versions/A/Resources/libRadiance.dylib >> 0x7fff8cde0000 - 0x7fff8ce3afff com.apple.print.framework.PrintCore (8.3 - 387.2) <5BA0CBED- 4D80-386A-9646-F835C9805B71> /System/Library/Frameworks/ApplicationSer vices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/P rintCore >> 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 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0x7fff8ddb3000 - 0x7fff8df9dff7 com.apple.CoreFoundation (6.8 - 744.18) <a60c3c9b-3764-3291-844c-c487acf77c2c> /System/Library/Frame works/CoreFoundation.framework/Versions/A/CoreFoundation >> 0x7fff8dfde000 - 0x7fff8e014fff com.apple.DebugSymbols (98 - 98) <14E788B1-4EB2-3FD7-934B-849534DFC198> /System/Library/PrivateFram eworks/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/Pr ivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServ ices >> 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 - 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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 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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<http: bioconductor.org="">. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> ________________________________ >> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. >> ________________________________ >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at 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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 4.6 years ago by Dan Tenenbaum ♦♦ 8.2k
On Sat, Apr 27, 2013 at 10:05 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > On Sat, Apr 27, 2013 at 8:51 AM, Miles Pufall <miles.pufall at="" gmail.com=""> wrote: >> Oops - and here's my sessionInfo: >> >> >>> sessionInfo() >> R Under development (unstable) (2013-04-26 r62678) > > Not sure if this is your problem or not, but both the release (2.12) > and devel (2.13) versions of Bioconductor are meant to work with R > 3.0.x, not R-devel. > It appears that there was not a Mac binary of Gviz until today. There is now and I was just able to biocLite("Gviz") on a Mac and Gviz was successfully installed. > I am trying to install Gviz using biocLite in R devel and it says it's only available as a source package. I'm a little new at this...how would I install the latest version from source within R? biocLite("Gviz", type="source") This requires that you have Xcode, the Xcode command-line tools, and MacTeX installed. Dan > Dan > > > >> 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] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.11.0 >> >> loaded via a namespace (and not attached): >> [1] tools_3.1.0 >> >> M >> >> On Apr 27, 2013, at 10:08 AM, "Pufall, Miles A" <miles-pufall at="" uiowa.edu=""> wrote: >> >>> I am trying to install Gviz using biocLite in R devel and it says it's only available as a source package. I'm a little new at this...how would I install the latest version from source within R? >>> >>> Thx - >>> >>> 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 at uiowa.edu<mailto:miles-pufall at="" uiowa.edu=""> >>> >>> >>> On Apr 26, 2013, at 8:00 AM, Robert Ivanek <robert.ivanek at="" unibas.ch<mailto:robert.ivanek="" at="" 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 at="" bioconductor.org<mailto:guest="" at="" 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: ??~BiocGenerics??T >>> >>> The following objects are masked from ??~package:parallel??T: >>> >>> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, >>> clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, >>> parSapplyLB >>> >>> The following object is masked from ??~package:stats??T: >>> >>> xtabs >>> >>> The following objects are masked from ??~package:base??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/libgfortran.2.dylib >>> 0x1004b5000 - 0x1004dffd9 +libreadline.5.2.dylib (5.2) /Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline .5.2.dylib >>> 0x1005c2000 - 0x1005c9fff +utils.so (0) <8FBF096E-B6CE- 398E-A920-01DE1B245C41> /Library/Frameworks/R.framework/Versions/3.0/R esources/library/utils/libs/utils.so >>> 0x1005e9000 - 0x1005eefff +methods.so (0) <ab37fbdb-4142-3274-affb-b2fb7fd32fc7> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/methods/libs/methods.so >>> 0x1005f7000 - 0x1005f9fef +bitops.so (0) <f9843053-e910 -36cf-9df1-f4121020f969=""> /Library/Frameworks/R.framework/Versions/3.0/ Resources/library/bitops/libs/bitops.so >>> 0x1007f2000 - 0x1007f5fef +parallel.so (0) <e5a82d0c- 98bd-3e65-a7ee-1fab5c8b6264=""> /Library/Frameworks/R.framework/Versions/ 3.0/Resources/library/parallel/libs/parallel.so >>> 0x1007f9000 - 0x1007fcfff +Biobase.so (0) <68F5403C-3382-31CD-BDAB-4335D037FE5E> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/Biobase/libs/Biobase.so >>> 0x101194000 - 0x1011cffef +graphics.so (0) <9E6394E4-AF37-3F25-A180-026E82583AF2> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/graphics/libs/graphics.so >>> 0x1011da000 - 0x1011e3fff +RCurl.so (0) <66E5F530-2EF3-32CB-9373-1A6491E8366A> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/RCurl/libs/RCurl.so >>> 0x1011ed000 - 0x1011effff +lattice.so (0) <5A52F152 -052E-3C10-B9B3-5B486A910DD7> /Library/Frameworks/R.framework/Versions /3.0/Resources/library/lattice/libs/lattice.so >>> 0x1011f2000 - 0x1011f3ff7 +plyr.so (0) <eb5cbaa5-f26d- 31d4-a292-f9ac0b2a189e=""> /Library/Frameworks/R.framework/Versions/3.0/R esources/library/plyr/libs/plyr.so >>> 0x10120f000 - 0x101219fff +GenomicRanges.so (0) <844F62EE-EEF9-3C56-812A-4E75A899CCB2> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/GenomicRanges/libs/GenomicRanges.so >>> 0x101224000 - 0x101230fff +colorspace.so (0) <0E7C120B- 148E-351A-92A1-C7963AC07174> /Library/Frameworks/R.framework/Versions/ 3.0/Resources/library/colorspace/libs/colorspace.so >>> 0x10126e000 - 0x10127aff7 +cluster.so (0) <55B40D4D-8432-3FEB-BBB7-8E65C948C17C> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/cluster/libs/cluster.so >>> 0x10127e000 - 0x10127fff7 +biovizBase.so (0) <45F295A2-1E32-3E5C-96B9-1657114AE545> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/biovizBase/libs/biovizBase.so >>> 0x101396000 - 0x1013b1fff +grid.so (0) <0A0B45EC-AC1D- 3F33-A57E-6B234CC42505> /Library/Frameworks/R.framework/Versions/3.0/R esources/library/grid/libs/grid.so >>> 0x1013be000 - 0x1013c3fff +Hmisc.so (0) <45B74820-59DF-3402-9F5C-CB4A0A3E90D4> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/Hmisc/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/tools/libs/tools.so >>> 0x102e82000 - 0x102ebffff +grDevices.so (0) <f7087219-a4a6-33c3-a0a8-19aaded62431> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/grDevices/libs/grDevices.so >>> 0x102edb000 - 0x102f65fef +stats.so (0) <99BD4BBA- AE70-38A3-BC7E-ABEF5775D09A> /Library/Frameworks/R.framework/Versions/ 3.0/Resources/library/stats/libs/stats.so >>> 0x103900000 - 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/Resources/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/Priv ateFrameworks/AppleFSCompression.framework/Versions/A/AppleFSCompressi on >>> 0x7fff89b5a000 - 0x7fff89bb0fff com.apple.HIServices (1.20 - 417) <a1129272-fec8-350b-ba26-5a97f23c413d> /System/Library/Frameworks /ApplicationServices.framework/Versions/A/Frameworks/HIServices.framew ork/Versions/A/HIServices >>> 0x7fff89e2f000 - 0x7fff89e5bff7 libRIP.A.dylib (331.0.4) <4B261CE2-524E-3FA9-9437-B70DAC1EAB95> /System/Library/Frameworks/Appl icationServices.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/Acce lerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/lib BLAS.dylib >>> 0x7fff8a09a000 - 0x7fff8a0f1ff7 com.apple.ScalableUserInterface (1.0 - 1) <f1d43dfb-1796-361b-ad4b- 39f1eed3be19=""> /System/Library/Frameworks/QuartzCore.framework/Versions /A/Frameworks/ScalableUserInterface.framework/Versions/A/ScalableUserI nterface >>> 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/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/F rameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServi ces.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/Framewor ks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.frame work/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/Frameworks/ 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 - 0x7fff8ccc4fff libRadiance.dylib (849) <f7d9a0fd-1195-34cb-bfe5-79daf3f40ac3> /System/Library/Frameworks/Imag eIO.framework/Versions/A/Resources/libRadiance.dylib >>> 0x7fff8cde0000 - 0x7fff8ce3afff com.apple.print.framework.PrintCore (8.3 - 387.2) <5BA0CBED- 4D80-386A-9646-F835C9805B71> /System/Library/Frameworks/ApplicationSer vices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/P rintCore >>> 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/Framewor ks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions /A/HIToolbox >>> 0x7fff8d1d4000 - 0x7fff8d478ff7 com.apple.CoreImage (8.2.4 - 1.0.1) <4A6B017F-B9F7-36DA-943D-A95611F147EA> /System/Library/Framewor ks/QuartzCore.framework/Versions/A/Frameworks/CoreImage.framework/Vers ions/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/OpenDirectory >>> 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/CoreFoundation >>> 0x7fff8dfde000 - 0x7fff8e014fff com.apple.DebugSymbols (98 - 98) <14E788B1-4EB2-3FD7-934B-849534DFC198> /System/Library/PrivateFram eworks/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/Pr ivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServ ices >>> 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 (645.6 - 645.6) <44F403C1-660A-3543-AB9C-3902E02F936F> /System/Library/Frameworks/Core Services.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE >>> 0x7fff8eae4000 - 0x7fff8eae8fff libGIF.dylib (849) <6A664B4D-0A88-33F7-9064-0CD159AB9CE9> /System/Library/Frameworks/Imag eIO.framework/Versions/A/Resources/libGIF.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.fr amework/Versions/A/FamilyControls >>> 0x7fff8edab000 - 0x7fff8eeadfff libJP2.dylib (849) <4EEA33EB-AF9F-365D-A572-F7D11AD1C76F> /System/Library/Frameworks/Imag eIO.framework/Versions/A/Resources/libJP2.dylib >>> 0x7fff8eeae000 - 0x7fff8efcefff com.apple.desktopservices (1.7.3 - 1.7.3) <707F77D2-EC0E-3431-840F-B984BD7ABDD6> /System/Library /PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/DesktopSer vicesPriv >>> 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/PrivateFramewor ks/MultitouchSupport.framework/Versions/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/Appl icationServices.framework/Versions/A/Frameworks/CoreGraphics.framework /Versions/A/Resources/libCSync.A.dylib >>> 0x7fff8f882000 - 0x7fff8f91dfff com.apple.CoreSymbolication (3.0 - 117) <c304fdb8-2ff7-34bc-858a-2b96c2b039d5> /System/Library/Pri vateFrameworks/CoreSymbolication.framework/Versions/A/CoreSymbolicatio n >>> 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/Appl icationServices.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/PrivateFr ameworks/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/V ersions/A/Frameworks/OSServices.framework/Versions/A/OSServices >>> 0x7fff8fe8b000 - 0x7fff8feb2ff7 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> /System/Libr ary/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.frame work/Versions/A/vecLib >>> 0x7fff90634000 - 0x7fff9064bfff com.apple.CFOpenDirectory (10.8 - 151.10) <ffbba538-00b5-334e-ba5b-c8ad6cdcda14> /System/Library /Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirect ory.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/LangAn alysis.framework/Versions/A/LangAnalysis >>> 0x7fff906ab000 - 0x7fff9103b6ff com.apple.CoreGraphics (1.600.0 - 331.0.4) <4953961C-96DC-39D7-ADF5-B767F2A7E4E1> /System/Lib rary/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/Co reGraphics.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/CrashReporterSup port.framework/Versions/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/CoreServicesInter nal.framework/Versions/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/PrivateFra meworks/CommonAuth.framework/Versions/A/CommonAuth >>> 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/P rivateFrameworks/DataDetectorsCore.framework/Versions/A/DataDetectorsC ore >>> 0x7fff92328000 - 0x7fff9237dff7 libTIFF.dylib (849) <c4d0e196-9319-319b-af72-8b63fb5af71b> /System/Library/Frameworks/Imag eIO.framework/Versions/A/Resources/libTIFF.dylib >>> 0x7fff92522000 - 0x7fff925afff7 com.apple.SearchKit (1.4.0 - 1.4.0) <c7f43889-f8bf-3cb9-ad66-11aefcbcede7> /System/Library/Framewor ks/CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/Ve rsions/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.framew ork/Versions/A/ServiceManagement >>> 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/Acce lerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vIm age >>> 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/Acce lerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/lib vMisc.dylib >>> 0x7fff92d13000 - 0x7fff92d64ff7 com.apple.SystemConfiguration (1.12.2 - 1.12.2) <a4341bbd-a330-3a57-8891-e9c1a286a72d> /System/Library/Frameworks/Syst emConfiguration.framework/Versions/A/SystemConfiguration >>> 0x7fff92dba000 - 0x7fff92ddafff libPng.dylib (849) <f4c23a55 -f17b-3e4f-9e80-bc97f778ba49=""> /System/Library/Frameworks/ImageIO.frame work/Versions/A/Resources/libPng.dylib >>> 0x7fff92e08000 - 0x7fff92e89fff com.apple.Metadata (10.7.0 - 707.5) <4140B1F6-7D73-33C7-B3F2-4DB349C31AE9> /System/Library/Framewor ks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Ver sions/A/Metadata >>> 0x7fff93132000 - 0x7fff93134fff libCVMSPluginSupport.dylib (8.7.25) <a45e21e3-4b40-39b0-a8b6-411526a84f47> /System/Library/Framew orks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.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/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/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/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/Frameworks/Appl icationServices.framework/Versions/A/Frameworks/CoreGraphics.framework /Versions/A/Resources/libCGXType.A.dylib >>> 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/DiskArbitration >>> 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/Open GL.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<http: bioconductor.org="">. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> >>> ________________________________ >>> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. >>> ________________________________ >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at 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 at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 4.6 years ago by Dan Tenenbaum ♦♦ 8.2k
0
gravatar for Robert Ivanek
4.6 years ago by
Robert Ivanek410
Switzerland
Robert Ivanek410 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 at uiowa.edu > > > On Apr 26, 2013, at 8:00 AM, Robert Ivanek <robert.ivanek at="" 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 at="" 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: ??~BiocGenerics??T >>> >>> The following objects are masked from ??~package:parallel??T: >>> >>> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, >>> clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, >>> parSapplyLB >>> >>> The following object is masked from ??~package:stats??T: >>> >>> xtabs >>> >>> The following objects are masked from ??~package:base??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/libgfortran.2.dylib >>> 0x1004b5000 - 0x1004dffd9 +libreadline.5.2.dylib (5.2) /Lib rary/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2 .dylib >>> 0x1005c2000 - 0x1005c9fff +utils.so (0) <8FBF096E-B6CE- 398E-A920-01DE1B245C41> /Library/Frameworks/R.framework/Versions/3.0/R esources/library/utils/libs/utils.so >>> 0x1005e9000 - 0x1005eefff +methods.so (0) <ab37fbdb-4142-3274-affb-b2fb7fd32fc7> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/methods/libs/methods.so >>> 0x1005f7000 - 0x1005f9fef +bitops.so (0) <f9843053-e910 -36cf-9df1-f4121020f969=""> /Library/Frameworks/R.framework/Versions/3.0/ Resources/library/bitops/libs/bitops.so >>> 0x1007f2000 - 0x1007f5fef +parallel.so (0) <e5a82d0c-98bd- 3e65-a7ee-1fab5c8b6264=""> /Library/Frameworks/R.framework/Versions/3.0/R esources/library/parallel/libs/parallel.so >>> 0x1007f9000 - 0x1007fcfff +Biobase.so (0) <68F5403C-3382 -31CD-BDAB-4335D037FE5E> /Library/Frameworks/R.framework/Versions/3.0/ Resources/library/Biobase/libs/Biobase.so >>> 0x101194000 - 0x1011cffef +graphics.so (0) <9E6394E4-AF37-3F25-A180-026E82583AF2> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/graphics/libs/graphics.so >>> 0x1011da000 - 0x1011e3fff +RCurl.so (0) <66E5F530-2EF3-32CB-9373-1A6491E8366A> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/RCurl/libs/RCurl.so >>> 0x1011ed000 - 0x1011effff +lattice.so (0) <5A52F152-052E- 3C10-B9B3-5B486A910DD7> /Library/Frameworks/R.framework/Versions/3.0/R esources/library/lattice/libs/lattice.so >>> 0x1011f2000 - 0x1011f3ff7 +plyr.so (0) <eb5cbaa5-f26d- 31d4-a292-f9ac0b2a189e=""> /Library/Frameworks/R.framework/Versions/3.0/R esources/library/plyr/libs/plyr.so >>> 0x10120f000 - 0x101219fff +GenomicRanges.so (0) <844F62EE- EEF9-3C56-812A-4E75A899CCB2> /Library/Frameworks/R.framework/Versions/ 3.0/Resources/library/GenomicRanges/libs/GenomicRanges.so >>> 0x101224000 - 0x101230fff +colorspace.so (0) <0E7C120B- 148E-351A-92A1-C7963AC07174> /Library/Frameworks/R.framework/Versions/ 3.0/Resources/library/colorspace/libs/colorspace.so >>> 0x10126e000 - 0x10127aff7 +cluster.so (0) <55B40D4D-8432 -3FEB-BBB7-8E65C948C17C> /Library/Frameworks/R.framework/Versions/3.0/ Resources/library/cluster/libs/cluster.so >>> 0x10127e000 - 0x10127fff7 +biovizBase.so (0) <45F295A2-1E32 -3E5C-96B9-1657114AE545> /Library/Frameworks/R.framework/Versions/3.0/ Resources/library/biovizBase/libs/biovizBase.so >>> 0x101396000 - 0x1013b1fff +grid.so (0) <0A0B45EC-AC1D-3F33 -A57E-6B234CC42505> /Library/Frameworks/R.framework/Versions/3.0/Resou rces/library/grid/libs/grid.so >>> 0x1013be000 - 0x1013c3fff +Hmisc.so (0) <45B74820-59DF-3402 -9F5C-CB4A0A3E90D4> /Library/Frameworks/R.framework/Versions/3.0/Resou rces/library/Hmisc/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/tools/libs/tools.so >>> 0x102e82000 - 0x102ebffff +grDevices.so (0) <f7087219-a4a6-33c3-a0a8-19aaded62431> /Library/Frameworks/R.framework /Versions/3.0/Resources/library/grDevices/libs/grDevices.so >>> 0x102edb000 - 0x102f65fef +stats.so (0) <99BD4BBA-AE70-38A3 -BC7E-ABEF5775D09A> /Library/Frameworks/R.framework/Versions/3.0/Resou rces/library/stats/libs/stats.so >>> 0x103900000 - 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/Priv ateFrameworks/AppleFSCompression.framework/Versions/A/AppleFSCompressi on >>> 0x7fff89b5a000 - 0x7fff89bb0fff com.apple.HIServices (1.20 - 417) <a1129272-fec8-350b-ba26-5a97f23c413d> /System/Library/Frameworks /ApplicationServices.framework/Versions/A/Frameworks/HIServices.framew ork/Versions/A/HIServices >>> 0x7fff89e2f000 - 0x7fff89e5bff7 libRIP.A.dylib (331.0.4) <4B261CE2-524E-3FA9-9437-B70DAC1EAB95> /System/Library/Frameworks/Appl icationServices.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/Acce lerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/lib BLAS.dylib >>> 0x7fff8a09a000 - 0x7fff8a0f1ff7 com.apple.ScalableUserInterface (1.0 - 1) <f1d43dfb-1796-361b-ad4b- 39f1eed3be19=""> /System/Library/Frameworks/QuartzCore.framework/Versions /A/Frameworks/ScalableUserInterface.framework/Versions/A/ScalableUserI nterface >>> 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/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/PrivateFramewor ks/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/F rameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServi ces.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/Framewor ks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.frame work/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/Frameworks/ 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/PrivateFr ameworks/CommerceKit.framework/Versions/A/Frameworks/CommerceCore.fram ework/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 - 0x7fff8ccc4fff libRadiance.dylib (849) <f7d9a0fd-1195-34cb-bfe5-79daf3f40ac3> /System/Library/Frameworks/Imag eIO.framework/Versions/A/Resources/libRadiance.dylib >>> 0x7fff8cde0000 - 0x7fff8ce3afff com.apple.print.framework.PrintCore (8.3 - 387.2) <5BA0CBED- 4D80-386A-9646-F835C9805B71> /System/Library/Frameworks/ApplicationSer vices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/P rintCore >>> 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/Framewor ks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions /A/HIToolbox >>> 0x7fff8d1d4000 - 0x7fff8d478ff7 com.apple.CoreImage (8.2.4 - 1.0.1) <4A6B017F-B9F7-36DA-943D-A95611F147EA> /System/Library/Framewor ks/QuartzCore.framework/Versions/A/Frameworks/CoreImage.framework/Vers ions/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/Frame works/OpenDirectory.framework/Versions/A/OpenDirectory >>> 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/Frame works/CoreFoundation.framework/Versions/A/CoreFoundation >>> 0x7fff8dfde000 - 0x7fff8e014fff com.apple.DebugSymbols (98 - 98) <14E788B1-4EB2-3FD7-934B-849534DFC198> /System/Library/PrivateFram eworks/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/Pr ivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServ ices >>> 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 (645.6 - 645.6) <44F403C1-660A-3543-AB9C-3902E02F936F> /System/Library/Frameworks/Core Services.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE >>> 0x7fff8eae4000 - 0x7fff8eae8fff libGIF.dylib (849) <6A664B4D- 0A88-33F7-9064-0CD159AB9CE9> /System/Library/Frameworks/ImageIO.framew ork/Versions/A/Resources/libGIF.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.fr amework/Versions/A/FamilyControls >>> 0x7fff8edab000 - 0x7fff8eeadfff libJP2.dylib (849) <4EEA33EB- AF9F-365D-A572-F7D11AD1C76F> /System/Library/Frameworks/ImageIO.framew ork/Versions/A/Resources/libJP2.dylib >>> 0x7fff8eeae000 - 0x7fff8efcefff com.apple.desktopservices (1.7.3 - 1.7.3) <707F77D2-EC0E-3431-840F-B984BD7ABDD6> /System/Library /PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/DesktopSer vicesPriv >>> 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/PrivateFramewor ks/MultitouchSupport.framework/Versions/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/Appl icationServices.framework/Versions/A/Frameworks/CoreGraphics.framework /Versions/A/Resources/libCSync.A.dylib >>> 0x7fff8f882000 - 0x7fff8f91dfff com.apple.CoreSymbolication (3.0 - 117) <c304fdb8-2ff7-34bc-858a-2b96c2b039d5> /System/Library/Pri vateFrameworks/CoreSymbolication.framework/Versions/A/CoreSymbolicatio n >>> 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/Appl icationServices.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/PrivateFr ameworks/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/V ersions/A/Frameworks/OSServices.framework/Versions/A/OSServices >>> 0x7fff8fe8b000 - 0x7fff8feb2ff7 com.apple.PerformanceAnalysis (1.16 - 16) <e4888388-f41b-313e-9cbb-5807d077bda9> /System/Library/Pri vateFrameworks/PerformanceAnalysis.framework/Versions/A/PerformanceAna lysis >>> 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> /System/Libr ary/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.frame work/Versions/A/vecLib >>> 0x7fff90634000 - 0x7fff9064bfff com.apple.CFOpenDirectory (10.8 - 151.10) <ffbba538-00b5-334e-ba5b-c8ad6cdcda14> /System/Library /Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirect ory.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/Framew orks/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/Lib rary/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/Co reGraphics.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/CrashReporterSup port.framework/Versions/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/CoreServicesInter nal.framework/Versions/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/PrivateFra meworks/CommonAuth.framework/Versions/A/CommonAuth >>> 0x7fff922b5000 - 0x7fff922b5fff com.apple.ApplicationServices (45 - 45) <a3abf20b-ed3a-32b5-830e-b37831a45a80> /System/Library/Frame works/ApplicationServices.framework/Versions/A/ApplicationServices >>> 0x7fff922b6000 - 0x7fff92323ff7 com.apple.datadetectorscore (4.1 - 269.2) <4FD4A7CE-BB00-3AAB-B7AA-AE395D5400EC> /System/Library/P rivateFrameworks/DataDetectorsCore.framework/Versions/A/DataDetectorsC ore >>> 0x7fff92328000 - 0x7fff9237dff7 libTIFF.dylib (849) <c4d0e196-9319-319b-af72-8b63fb5af71b> /System/Library/Frameworks/Imag eIO.framework/Versions/A/Resources/libTIFF.dylib >>> 0x7fff92522000 - 0x7fff925afff7 com.apple.SearchKit (1.4.0 - 1.4.0) <c7f43889-f8bf-3cb9-ad66-11aefcbcede7> /System/Library/Framewor ks/CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/Ve rsions/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.framew ork/Versions/A/ServiceManagement >>> 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/Acce lerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vIm age >>> 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/Acce lerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/lib vMisc.dylib >>> 0x7fff92d13000 - 0x7fff92d64ff7 com.apple.SystemConfiguration (1.12.2 - 1.12.2) <a4341bbd-a330-3a57-8891-e9c1a286a72d> /System/Libra ry/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfigura tion >>> 0x7fff92dba000 - 0x7fff92ddafff libPng.dylib (849) <f4c23a55 -f17b-3e4f-9e80-bc97f778ba49=""> /System/Library/Frameworks/ImageIO.frame work/Versions/A/Resources/libPng.dylib >>> 0x7fff92e08000 - 0x7fff92e89fff com.apple.Metadata (10.7.0 - 707.5) <4140B1F6-7D73-33C7-B3F2-4DB349C31AE9> /System/Library/Framewor ks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Ver sions/A/Metadata >>> 0x7fff93132000 - 0x7fff93134fff libCVMSPluginSupport.dylib (8.7.25) <a45e21e3-4b40-39b0-a8b6-411526a84f47> /System/Library/Framew orks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.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/Open GL.framework/Versions/A/Libraries/libGLImage.dylib >>> 0x7fff93536000 - 0x7fff9354dfff com.apple.GenerationalStorage (1.1 - 132.3) <fd4a84b3-13a8-3c60-a59e-25a361447a17> /System/Library/P rivateFrameworks/GenerationalStorage.framework/Versions/A/Generational Storage >>> 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/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/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/Frameworks/Appl icationServices.framework/Versions/A/Frameworks/CoreGraphics.framework /Versions/A/Resources/libCGXType.A.dylib >>> 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/DiskArbitration >>> 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/Open GL.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 at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 4.6 years ago by Robert Ivanek410
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