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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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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.
