[BioC] IdeogramTrack and bigWig file errors in Gviz

Dweebis [guest] guest at bioconductor.org
Fri Apr 26 06:46:47 CEST 2013


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:
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    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        

--
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