[BioC] IdeogramTrack and bigWig file errors in Gviz
Miles Pufall
miles.pufall at gmail.com
Sat Apr 27 17:51:07 CEST 2013
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: 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:
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> 0x10038c000 - 0x1003b5ff7 +libRblas.dylib (0) <869671F9-C174-39EA-8496-9E88B343A3B0> /Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libRblas.dylib
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> 0x7fff8a63c000 - 0x7fff8a755fff com.apple.ImageIO.framework (3.2.0 - 849) <C52AED41-A7C2-300B-91FA-5AF73718D243> /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
> 0x7fff8a789000 - 0x7fff8a798fff com.apple.opengl (1.8.7 - 1.8.7) <26F7FF79-6BB2-3968-B70D-71D4E07C9551> /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
> 0x7fff8a799000 - 0x7fff8a7c3ff7 com.apple.CoreVideo (1.8 - 99.4) <E5082966-6D81-3973-A05A-38AA5B85F886> /System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo
> 0x7fff8a820000 - 0x7fff8a83bff7 libsystem_kernel.dylib (2050.22.13) <5A961E2A-CFB8-362B-BC43-122704AEB047> /usr/lib/system/libsystem_kernel.dylib
> 0x7fff8a977000 - 0x7fff8a981fff com.apple.speech.recognition.framework (4.1.5 - 4.1.5) <D803919C-3102-3515-A178-61E9C86C46A1> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SpeechRecognition.framework/Versions/A/SpeechRecognition
> 0x7fff8a991000 - 0x7fff8a9e0ff7 libcorecrypto.dylib (106.2) <CE0C29A3-C420-339B-ADAA-52F4683233CC> /usr/lib/system/libcorecrypto.dylib
> 0x7fff8a9ed000 - 0x7fff8aa04fff libGL.dylib (8.7.25) <15F5CB64-847B-3D3D-9663-E0523F15F513> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
> 0x7fff8aa16000 - 0x7fff8aa18fff com.apple.TrustEvaluationAgent (2.0 - 23) <A97D348B-32BF-3E52-8DF2-59BFAD21E1A3> /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
> 0x7fff8aa1d000 - 0x7fff8aa2bfff com.apple.Librarian (1.1 - 1) <5AC28666-7642-395F-A923-C6F8A274BBBD> /System/Library/PrivateFrameworks/Librarian.framework/Versions/A/Librarian
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> 0x7fff8aa51000 - 0x7fff8ab02fff com.apple.LaunchServices (539.7 - 539.7) <DA7C602E-5E01-31B8-925D-B45360CA089F> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices
> 0x7fff8ab03000 - 0x7fff8ab0afff com.apple.NetFS (5.0 - 4.0) <82E24B9A-7742-3DA3-9E99-ED267D98C05E> /System/Library/Frameworks/NetFS.framework/Versions/A/NetFS
> 0x7fff8ab22000 - 0x7fff8ab34ff7 libz.1.dylib (43) <2A1551E8-A272-3DE5-B692-955974FE1416> /usr/lib/libz.1.dylib
> 0x7fff8ab35000 - 0x7fff8ab3bfff libmacho.dylib (829) <BF332AD9-E89F-387E-92A4-6E1AB74BD4D9> /usr/lib/system/libmacho.dylib
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> 0x7fff8af10000 - 0x7fff8afcdff7 com.apple.ColorSync (4.8.0 - 4.8.0) <6CE333AE-EDDB-3768-9598-9DB38041DC55> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync
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> 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/PrivateFrameworks/ChunkingLibrary.framework/Versions/A/ChunkingLibrary
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> 0x7fff8b7da000 - 0x7fff8b7dcfff libquarantine.dylib (52) <4BE2E642-A14F-340A-B482-5BD2AEFD9C24> /usr/lib/system/libquarantine.dylib
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> 0x7fff8c230000 - 0x7fff8c239ff7 com.apple.CommerceCore (1.0 - 26.1) <40A129A8-4E5D-3C7A-B299-8CB203C4C65D> /System/Library/PrivateFrameworks/CommerceKit.framework/Versions/A/Frameworks/CommerceCore.framework/Versions/A/CommerceCore
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> 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
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> 0x7fff8c89a000 - 0x7fff8ccb7fff FaceCoreLight (2.4.1) <A34C9575-C4C1-31B1-809B-7751070B4E8B> /System/Library/PrivateFrameworks/FaceCoreLight.framework/Versions/A/FaceCoreLight
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> 0x7fff8ce3b000 - 0x7fff8ce60ff7 libc++abi.dylib (26) <D86169F3-9F31-377A-9AF3-DB17142052E4> /usr/lib/libc++abi.dylib
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> 0x7fff8cea3000 - 0x7fff8d1d3fff com.apple.HIToolbox (2.0 - 626.1) <656D08C2-9068-3532-ABDD-32EC5057CCB2> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox
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> 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/PrivateFrameworks/DebugSymbols.framework/Versions/A/DebugSymbols
> 0x7fff8e0ca000 - 0x7fff8e0d8fff libcommonCrypto.dylib (60027) <BAAFE0C9-BB86-3CA7-88C0-E3CBA98DA06F> /usr/lib/system/libcommonCrypto.dylib
> 0x7fff8e0d9000 - 0x7fff8e11cff7 com.apple.RemoteViewServices (2.0 - 80.6) <5CFA361D-4853-3ACC-9EFC-A2AC1F43BA4B> /System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices
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> 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
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> 0x7fff8e6cc000 - 0x7fff8e72bfff com.apple.AE (645.6 - 645.6) <44F403C1-660A-3543-AB9C-3902E02F936F> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE
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> 0x7fff8f1ba000 - 0x7fff8f1d0fff com.apple.MultitouchSupport.framework (235.29 - 235.29) <617EC8F1-BCE7-3553-86DD-F857866E1257> /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport
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> 0x7fff922a9000 - 0x7fff922b4fff com.apple.CommonAuth (3.0 - 2.0) <7A953C1F-8B18-3E46-9BEA-26D9B5B7745D> /System/Library/PrivateFrameworks/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/PrivateFrameworks/DataDetectorsCore.framework/Versions/A/DataDetectorsCore
> 0x7fff92328000 - 0x7fff9237dff7 libTIFF.dylib (849) <C4D0E196-9319-319B-AF72-8B63FB5AF71B> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
> 0x7fff92522000 - 0x7fff925afff7 com.apple.SearchKit (1.4.0 - 1.4.0) <C7F43889-F8BF-3CB9-AD66-11AEFCBCEDE7> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/Versions/A/SearchKit
> 0x7fff925b0000 - 0x7fff925b1ff7 libsystem_sandbox.dylib (220.2) <6838A6FD-8626-3356-BB4F-BB4787216207> /usr/lib/system/libsystem_sandbox.dylib
> 0x7fff925b2000 - 0x7fff925bdff7 com.apple.bsd.ServiceManagement (2.0 - 2.0) <C12962D5-85FB-349E-AA56-64F4F487F219> /System/Library/Frameworks/ServiceManagement.framework/Versions/A/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/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
> 0x7fff92c33000 - 0x7fff92c77fff libcups.2.dylib (327.3) <71E771A1-0489-3417-8A4A-56A2C930F80C> /usr/lib/libcups.2.dylib
> 0x7fff92c78000 - 0x7fff92d12fff libvMisc.dylib (380.6) <714336EA-1C0E-3735-B31C-19DFDAAF6221> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
> 0x7fff92d13000 - 0x7fff92d64ff7 com.apple.SystemConfiguration (1.12.2 - 1.12.2) <A4341BBD-A330-3A57-8891-E9C1A286A72D> /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
> 0x7fff92dba000 - 0x7fff92ddafff libPng.dylib (849) <F4C23A55-F17B-3E4F-9E80-BC97F778BA49> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib
> 0x7fff92e08000 - 0x7fff92e89fff com.apple.Metadata (10.7.0 - 707.5) <4140B1F6-7D73-33C7-B3F2-4DB349C31AE9> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata
> 0x7fff93132000 - 0x7fff93134fff libCVMSPluginSupport.dylib (8.7.25) <A45E21E3-4B40-39B0-A8B6-411526A84F47> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/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/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
> 0x7fff93536000 - 0x7fff9354dfff com.apple.GenerationalStorage (1.1 - 132.3) <FD4A84B3-13A8-3C60-A59E-25A361447A17> /System/Library/PrivateFrameworks/GenerationalStorage.framework/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/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
> 0x7fff94062000 - 0x7fff94297ff7 com.apple.CoreData (106.1 - 407.7) <24E0A6B4-9ECA-3D12-B26A-72B9DCF09768> /System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
> 0x7fff9429b000 - 0x7fff94319ff7 com.apple.securityfoundation (6.0 - 55115.4) <C5461971-E455-31A6-99B8-AF80C4BC26DD> /System/Library/Frameworks/SecurityFoundation.framework/Versions/A/SecurityFoundation
> 0x7fff9431b000 - 0x7fff943b9ff7 com.apple.ink.framework (10.8.2 - 150) <84B9825C-3822-375F-BE58-A753444FBDE2> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink
> 0x7fff95378000 - 0x7fff9568fff7 com.apple.CoreServices.CarbonCore (1037.5 - 1037.5) <731D8F92-1C52-3613-BA01-EFEA54DADF41> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
> 0x7fff95690000 - 0x7fff95710ff7 com.apple.ApplicationServices.ATS (332 - 341.1) <BD83B039-AB25-3E3E-9975-A67DAE66988B> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS
> 0x7fff95711000 - 0x7fff95715fff libCGXType.A.dylib (331.0.4) <251D4D2D-92B9-3D56-B348-CD67397F71FE> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCGXType.A.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/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
> 0x7fff96627000 - 0x7fff96701fff com.apple.backup.framework (1.4.2 - 1.4.2) <0B557393-CD2A-3076-BED2-F28D02E1EC1D> /System/Library/PrivateFrameworks/Backup.framework/Versions/A/Backup
> 0x7fff96702000 - 0x7fff9674cff7 libGLU.dylib (8.7.25) <C243C6D3-3384-3DB1-BB15-E27B65C87294> /System/Library/Frameworks/OpenGL.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>.
>
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>
>
>
> ________________________________
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