-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy paththesis.log
1586 lines (1285 loc) · 47.9 KB
/
thesis.log
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012) (format=latex 2012.6.30) 28 OCT 2012 20:56
entering extended mode
restricted \write18 enabled.
%&-line parsing enabled.
**thesis
(./thesis.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2012-05-30, ngerman-x-2012-05-30, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h
ungarian, icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, ma
rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian,
kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk,
polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s
lovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian,
welsh, loaded.
(./ucbthesis.cls
Document Class: ucbthesis 2012/08/06 v3.391 University of California, Berkeley
Thesis Class
(/usr/local/texlive/2012/texmf-dist/tex/latex/memoir/memoir.cls
Document Class: memoir 2011/03/06 v3.6j configurable book, report, article docu
ment class
\onelineskip=\skip41
\lxvchars=\skip42
\xlvchars=\skip43
\@memcnta=\count79
\c@@memmarkcntra=\count80
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/ifpdf.sty
Package: ifpdf 2011/01/30 v2.3 Provides the ifpdf switch (HO)
Package ifpdf Info: pdfTeX in PDF mode is not detected.
)
(/usr/local/texlive/2012/texmf-dist/tex/latex/ifetex/ifetex.sty
Package: ifetex 2011/12/15 v1.2 ifetex
(/usr/local/texlive/2012/texmf-dist/tex/plain/ifetex/ifetex.tex))
(/usr/local/texlive/2012/texmf-dist/tex/generic/ifxetex/ifxetex.sty
Package: ifxetex 2010/09/12 v0.6 Provides ifxetex conditional
)
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/ifluatex.sty
Package: ifluatex 2010/03/01 v1.3 Provides the ifluatex switch (HO)
Package ifluatex Info: LuaTeX not detected.
)
\stockheight=\skip44
\stockwidth=\skip45
\trimtop=\skip46
\trimedge=\skip47
(/usr/local/texlive/2012/texmf-dist/tex/latex/etex-pkg/etex.sty
Package: etex 1998/03/26 v2.0 eTeX basic definition package (PEB)
\et@xins=\count81
)
(/usr/local/texlive/2012/texmf-dist/tex/latex/memoir/mem12.clo
File: mem12.clo 2010/10/19 v0.4b memoir class 12pt size option
)
\binding=\skip48
\spinemargin=\skip49
\foremargin=\skip50
\uppermargin=\skip51
\lowermargin=\skip52
\headdrop=\skip53
\normalrulethickness=\skip54
\mem@maxheadheight=\skip55
\mem@maxfootheight=\skip56
\headwidth=\skip57
\c@storedpagenumber=\count82
\memPD=\dimen102
\m@mabparskip=\skip58
\thanksmarkwidth=\skip59
\thanksmarksep=\skip60
\droptitle=\skip61
\c@book=\count83
\c@part=\count84
\c@chapter=\count85
\c@section=\count86
\c@subsection=\count87
\c@subsubsection=\count88
\c@paragraph=\count89
\c@subparagraph=\count90
\beforechapskip=\skip62
\midchapskip=\skip63
\afterchapskip=\skip64
\chapindent=\skip65
\bottomsectionskip=\skip66
\secindent=\skip67
\beforesecskip=\skip68
\aftersecskip=\skip69
\subsecindent=\skip70
\beforesubsecskip=\skip71
\aftersubsecskip=\skip72
\subsubsecindent=\skip73
\beforesubsubsecskip=\skip74
\aftersubsubsecskip=\skip75
\paraindent=\skip76
\beforeparaskip=\skip77
\afterparaskip=\skip78
\subparaindent=\skip79
\beforesubparaskip=\skip80
\aftersubparaskip=\skip81
\pfbreakskip=\skip82
\c@@ppsavesec=\count91
\c@@ppsaveapp=\count92
\ragrparindent=\dimen103
\everylistparindent=\dimen104
\parsepi=\skip83
\topsepi=\skip84
\itemsepi=\skip85
\parsepii=\skip86
\topsepii=\skip87
\topsepiii=\skip88
\itemsepii=\skip89
\itemsepiii=\skip90
\partopsepii=\skip91
\partopsepiii=\skip92
\m@msavetopsep=\skip93
\m@msavepartopsep=\skip94
\@enLab=\toks14
\abstitleskip=\skip95
\absleftindent=\skip96
\abs@leftindent=\dimen105
\absrightindent=\skip97
\absparindent=\skip98
\absparsep=\skip99
\c@vslineno=\count93
\c@poemline=\count94
\c@modulo@vs=\count95
\c@memfvsline=\count96
\vleftskip=\skip100
\vrightskip=\skip101
\stanzaskip=\skip102
\versewidth=\skip103
\vgap=\skip104
\vindent=\skip105
\vleftmargin=\dimen106
\c@verse=\count97
\c@chrsinstr=\count98
\beforepoemtitleskip=\skip106
\afterpoemtitleskip=\skip107
\c@poem=\count99
\beforePoemTitleskip=\skip108
\midPoemTitleskip=\skip109
\afterPoemTitleskip=\skip110
\col@sep=\dimen107
\extrarowheight=\dimen108
\NC@list=\toks15
\extratabsurround=\skip111
\backup@length=\skip112
\TX@col@width=\dimen109
\TX@old@table=\dimen110
\TX@old@col=\dimen111
\TX@target=\dimen112
\TX@delta=\dimen113
\TX@cols=\count100
\TX@ftn=\toks16
\heavyrulewidth=\dimen114
\lightrulewidth=\dimen115
\cmidrulewidth=\dimen116
\belowrulesep=\dimen117
\belowbottomsep=\dimen118
\aboverulesep=\dimen119
\abovetopsep=\dimen120
\cmidrulesep=\dimen121
\cmidrulekern=\dimen122
\defaultaddspace=\dimen123
\@cmidla=\count101
\@cmidlb=\count102
\@aboverulesep=\dimen124
\@belowrulesep=\dimen125
\@thisruleclass=\count103
\@lastruleclass=\count104
\@thisrulewidth=\dimen126
\ctableftskip=\skip113
\ctabrightskip=\skip114
\abovecolumnspenalty=\count105
\@linestogo=\count106
\@cellstogo=\count107
\@cellsincolumn=\count108
\crtok=\toks17
\@mincolumnwidth=\dimen127
\c@newflo@tctr=\count109
\mem@margin@floatbox=\box26
\@contcwidth=\skip115
\@contindw=\skip116
\abovecaptionskip=\skip117
\belowcaptionskip=\skip118
\subfloattopskip=\skip119
\subfloatcapskip=\skip120
\subfloatcaptopadj=\skip121
\subfloatbottomskip=\skip122
\subfloatlabelskip=\skip123
\subfloatcapmargin=\dimen128
\c@@contsubnum=\count110
\m@mscap@capbox=\box27
\m@mscap@fbox=\box28
\sidecapsep=\dimen129
\sidecapwidth=\dimen130
\m@m@tempdima=\dimen131
\m@mscapraise=\dimen132
\sidecapraise=\dimen133
\m@mscapmainwidth=\dimen134
\m@mscaplkern=\dimen135
\beforeepigraphskip=\skip124
\afterepigraphskip=\skip125
\epigraphwidth=\skip126
\epigraphrule=\skip127
LaTeX Info: Redefining \em on input line 7377.
LaTeX Info: Redefining \emph on input line 7385.
\tocentryskip=\skip128
\tocbaseline=\skip129
\cftparskip=\skip130
\cftbeforebookskip=\skip131
\cftbookindent=\dimen136
\cftbooknumwidth=\dimen137
\cftbeforepartskip=\skip132
\cftpartindent=\skip133
\cftpartnumwidth=\skip134
\cftbeforechapterskip=\skip135
\cftchapterindent=\skip136
\cftchapternumwidth=\skip137
\cftbeforesectionskip=\skip138
\cftsectionindent=\skip139
\cftsectionnumwidth=\skip140
\cftbeforesubsectionskip=\skip141
\cftsubsectionindent=\skip142
\cftsubsectionnumwidth=\skip143
\cftbeforesubsubsectionskip=\skip144
\cftsubsubsectionindent=\skip145
\cftsubsubsectionnumwidth=\skip146
\cftbeforeparagraphskip=\skip147
\cftparagraphindent=\skip148
\cftparagraphnumwidth=\skip149
\cftbeforesubparagraphskip=\skip150
\cftsubparagraphindent=\skip151
\cftsubparagraphnumwidth=\skip152
\prechapterprecisshift=\dimen138
\c@maxsecnumdepth=\count111
\bibindent=\dimen139
\bibitemsep=\skip153
\indexcolsep=\skip154
\indexrule=\skip155
\indexmarkstyle=\toks18
\@indexbox=\insert233
\glossarycolsep=\dimen140
\glossaryrule=\dimen141
\sideparvshift=\skip156
\sideins=\insert232
\sidebartopsep=\skip157
\sidebarhsep=\skip158
\sidebarvsep=\skip159
\sidebarwidth=\skip160
\footmarkwidth=\skip161
\footmarksep=\skip162
\footparindent=\skip163
\footinsdim=\skip164
\footinsv@r=\insert231
\@mpfootinsv@r=\insert230
\m@m@k=\count112
\m@m@h=\dimen142
\m@mipn@skip=\skip165
\sidefootins=\insert229
\sidefootadjust=\skip166
\sidefootheight=\skip167
\sidefoothsep=\skip168
\sidefootvsep=\skip169
\sidefootwidth=\skip170
\m@mdownsf=\skip171
\c@sidefootnote=\count113
\sidefootmarkwidth=\skip172
\sidefootmarksep=\skip173
\sidefootparindent=\skip174
\c@pagenote=\count114
\c@pagenoteshadow=\count115
\mem@pn@lastkern=\skip175
\every@verbatim=\toks19
\afterevery@verbatim=\toks20
\verbatim@line=\toks21
\tab@position=\count116
\verbatim@in@stream=\read1
\verbatimindent=\skip176
\verbatim@out=\write3
\bvboxsep=\skip177
\c@memfbvline=\count117
\c@bvlinectr=\count118
\bvnumlength=\skip178
\fb@frw=\dimen143
\fb@frh=\dimen144
\FrameRule=\dimen145
\FrameSep=\dimen146
\c@cp@cntr=\count119
LaTeX Info: Redefining \: on input line 11807.
LaTeX Info: Redefining \! on input line 11809.
\c@ism@mctr=\count120
\c@xsm@mctr=\count121
\c@csm@mctr=\count122
\c@ksm@mctr=\count123
\c@xksm@mctr=\count124
\c@cksm@mctr=\count125
\c@msm@mctr=\count126
\c@xmsm@mctr=\count127
\c@cmsm@mctr=\count128
\c@bsm@mctr=\count129
\c@workm@mctr=\count130
\c@sheetsequence=\count131
\c@lastsheet=\count132
\c@lastpage=\count133
\c@figure=\count134
\c@lofdepth=\count135
\cftbeforefigureskip=\skip179
\cftfigureindent=\skip180
\cftfigurenumwidth=\skip181
\c@table=\count136
\c@lotdepth=\count137
\cftbeforetableskip=\skip182
\cfttableindent=\skip183
\cfttablenumwidth=\skip184
Package abstract [2008/07/23] emulated by memoir.
Package appendix [2008/07/23] emulated by memoir.
Package array [2008/07/23] emulated by memoir.
Package booktabs [2008/07/23] emulated by memoir.
Package ccaption [2008/07/23] emulated by memoir.
Package changepage [2008/07/23] emulated by memoir.
Package chngcntr [2008/07/23] emulated by memoir.
Package chngpage [2008/07/23] emulated by memoir.
Package crop emulated by memoir.
Package dcolumn [2008/07/23] emulated by memoir.
Package delarray [2008/07/23] emulated by memoir.
Package enumerate [2008/07/23] emulated by memoir.
Package epigraph [2008/07/23] emulated by memoir.
Package ifmtarg [2008/07/23] emulated by memoir.
Package index [2008/07/23] emulated by memoir.
Package makeidx [2008/07/23] emulated by memoir.
Package moreverb [2008/07/23] emulated by memoir.
Package mparhack [2008/07/23] emulated by memoir.
Package needspace [2008/07/23] emulated by memoir.
Package newfile [2008/07/23] emulated by memoir.
Package nextpage [2008/07/23] emulated by memoir.
Package pagenote [2008/07/23] emulated by memoir.
Package parskip [2008/07/23] emulated by memoir.
Package patchcmd [2008/07/23] emulated by memoir.
Package setspace [2008/07/23] emulated by memoir.
Package shortvrb [2008/07/23] emulated by memoir.
Package showidx [2008/07/23] emulated by memoir.
Package tabularx [2008/07/23] emulated by memoir.
Package titleref [2008/07/23] emulated by memoir.
Package titling [2008/07/23] emulated by memoir.
Package tocbibind [2008/07/23] emulated by memoir.
Package tocloft [2008/07/23] emulated by memoir.
Package tocvsec2 [2008/07/23] emulated by memoir.
Package verbatim [2008/07/23] emulated by memoir.
Package verse [2008/07/23] emulated by memoir.
(/usr/local/texlive/2012/texmf-dist/tex/latex/memoir/mempatch.sty
Package: mempatch 2009/07/24 v6.0f Patches for memoir class v1.6180339
)))
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex.sty
Package: biblatex 2011/11/13 v1.7 programmable bibliographies
(/usr/local/texlive/2012/texmf-dist/tex/latex/etoolbox/etoolbox.sty
Package: etoolbox 2011/01/03 v2.1 e-TeX tools for LaTeX
\etb@tempcnta=\count138
)
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/keyval.sty
Package: keyval 1999/03/16 v1.13 key=value parser (DPC)
\KV@toks@=\toks22
)
(/usr/local/texlive/2012/texmf-dist/tex/latex/logreq/logreq.sty
Package: logreq 2010/08/04 v1.0 xml request logger
\lrq@indent=\count139
(/usr/local/texlive/2012/texmf-dist/tex/latex/logreq/logreq.def
File: logreq.def 2010/08/04 v1.0 logreq spec v1.0
))
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ifthen.sty
Package: ifthen 2001/05/26 v1.1c Standard LaTeX ifthen package (DPC)
)
(/usr/local/texlive/2012/texmf-dist/tex/latex/url/url.sty
\Urlmuskip=\muskip10
Package: url 2006/04/12 ver 3.3 Verb mode for urls, etc.
)
\c@listtotal=\count140
\c@listcount=\count141
\c@liststart=\count142
\c@liststop=\count143
\c@citecount=\count144
\c@citetotal=\count145
\c@multicitecount=\count146
\c@multicitetotal=\count147
\c@instcount=\count148
\c@maxnames=\count149
\c@minnames=\count150
\c@maxitems=\count151
\c@minitems=\count152
\c@citecounter=\count153
\c@savedcitecounter=\count154
\c@uniquelist=\count155
\c@uniquename=\count156
\c@refsection=\count157
\c@refsegment=\count158
\c@maxextrayear=\count159
\c@maxextraalpha=\count160
\c@abbrvpenalty=\count161
\c@highnamepenalty=\count162
\c@lownamepenalty=\count163
\c@maxparens=\count164
\c@parenlevel=\count165
\blx@tempcnta=\count166
\blx@tempcntb=\count167
\blx@tempcntc=\count168
\blx@maxsection=\count169
\blx@maxsegment=\count170
\blx@notetype=\count171
\blx@parenlevel@text=\count172
\blx@parenlevel@foot=\count173
\labelnumberwidth=\skip185
\labelalphawidth=\skip186
\shorthandwidth=\skip187
\biblabelsep=\skip188
\bibnamesep=\skip189
\bibinitsep=\skip190
\bibparsep=\skip191
\bibhang=\skip192
\blx@auxin=\read2
\blx@auxout=\write4
\c@mincomprange=\count174
\c@maxcomprange=\count175
\c@mincompwidth=\count176
\c@labelname=\count177
\c@savedlabelname=\count178
\c@author=\count179
\c@savedauthor=\count180
\c@shortauthor=\count181
\c@savedshortauthor=\count182
\c@editor=\count183
\c@savededitor=\count184
\c@editora=\count185
\c@savededitora=\count186
\c@editorb=\count187
\c@savededitorb=\count188
\c@editorc=\count189
\c@savededitorc=\count190
\c@shorteditor=\count191
\c@savedshorteditor=\count192
\c@bookauthor=\count193
\c@savedbookauthor=\count194
\c@translator=\count195
\c@savedtranslator=\count196
\c@annotator=\count197
\c@savedannotator=\count198
\c@commentator=\count199
\c@savedcommentator=\count200
\c@introduction=\count201
\c@savedintroduction=\count202
\c@foreword=\count203
\c@savedforeword=\count204
\c@afterword=\count205
\c@savedafterword=\count206
\c@holder=\count207
\c@savedholder=\count208
\c@namea=\count209
\c@savednamea=\count210
\c@nameb=\count211
\c@savednameb=\count212
\c@namec=\count213
\c@savednamec=\count214
\c@institution=\count215
\c@savedinstitution=\count216
\c@language=\count217
\c@savedlanguage=\count218
\c@location=\count219
\c@savedlocation=\count220
\c@organization=\count221
\c@savedorganization=\count222
\c@origlocation=\count223
\c@savedoriglocation=\count224
\c@origpublisher=\count225
\c@savedorigpublisher=\count226
\c@pageref=\count227
\c@savedpageref=\count228
Normal \count register pool exhausted, switching to extended pool.
\c@publisher=\count277
\c@savedpublisher=\count278
\c@lista=\count279
\c@savedlista=\count280
\c@listb=\count281
\c@savedlistb=\count282
\c@listc=\count283
\c@savedlistc=\count284
\c@listd=\count285
\c@savedlistd=\count286
\c@liste=\count287
\c@savedliste=\count288
\c@listf=\count289
\c@savedlistf=\count290
Package biblatex Info: Trying to load compatibility code...
Package biblatex Info: ... file 'blx-compat.def' found.
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/blx-compat.def
File: blx-compat.def 2011/11/13 v1.7 biblatex generic compatibility
)
Package biblatex Info: Trying to load generic definitions...
Package biblatex Info: ... file 'biblatex.def' found.
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex.def
File: biblatex.def 2011/11/13 v1.7 biblatex generic definitions
\c@biburlnumpenalty=\count291
\c@biburlucpenalty=\count292
\c@biburllcpenalty=\count293
\c@smartand=\count294
)
Package biblatex Info: Trying to load bibliography style 'numeric'...
Package biblatex Info: ... file 'numeric.bbx' found.
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/bbx/numeric.bbx
File: numeric.bbx 2011/11/13 v1.7 biblatex bibliography style
Package biblatex Info: Trying to load bibliography style 'standard'...
Package biblatex Info: ... file 'standard.bbx' found.
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/bbx/standard.bbx
File: standard.bbx 2011/11/13 v1.7 biblatex bibliography style
))
Package biblatex Info: Trying to load citation style 'numeric'...
Package biblatex Info: ... file 'numeric.cbx' found.
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/cbx/numeric.cbx
File: numeric.cbx 2011/11/13 v1.7 biblatex citation style
Package biblatex Info: Redefining '\cite'.
Package biblatex Info: Redefining '\parencite'.
Package biblatex Info: Redefining '\footcite'.
Package biblatex Info: Redefining '\footcitetext'.
Package biblatex Info: Redefining '\smartcite'.
Package biblatex Info: Redefining '\textcite'.
Package biblatex Info: Redefining '\supercite'.
Package biblatex Info: Redefining '\cites'.
Package biblatex Info: Redefining '\parencites'.
Package biblatex Info: Redefining '\smartcites'.
)
Package biblatex Info: Trying to load configuration file...
Package biblatex Info: ... file 'biblatex.cfg' found.
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex.cfg
File: biblatex.cfg
))
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/graphicx.sty
Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR)
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/graphics.sty
Package: graphics 2009/02/05 v1.0o Standard LaTeX Graphics (DPC,SPQR)
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/trig.sty
Package: trig 1999/03/16 v1.09 sin cos tan (DPC)
)
(/usr/local/texlive/2012/texmf-dist/tex/latex/latexconfig/graphics.cfg
File: graphics.cfg 2010/04/23 v1.9 graphics configuration of TeX Live
)
Package graphics Info: Driver file: dvips.def on input line 91.
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/dvips.def
File: dvips.def 1999/02/16 v3.0i Driver-dependant file (DPC,SPQR)
))
\Gin@req@height=\dimen147
\Gin@req@width=\dimen148
)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/textcomp.sty
Package: textcomp 2005/09/27 v1.99g Standard LaTeX package
Package textcomp Info: Sub-encoding information:
(textcomp) 5 = only ISO-Adobe without \textcurrency
(textcomp) 4 = 5 + \texteuro
(textcomp) 3 = 4 + \textohm
(textcomp) 2 = 3 + \textestimated + \textcurrency
(textcomp) 1 = TS1 - \textcircled - \t
(textcomp) 0 = TS1 (full)
(textcomp) Font families with sub-encoding setting implement
(textcomp) only a restricted character set as indicated.
(textcomp) Family '?' is the default used for unknown fonts.
(textcomp) See the documentation for details.
Package textcomp Info: Setting ? sub-encoding to TS1/1 on input line 71.
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1enc.def
File: ts1enc.def 2001/06/05 v3.0e (jk/car/fm) Standard LaTeX file
)
LaTeX Info: Redefining \oldstylenums on input line 266.
Package textcomp Info: Setting cmr sub-encoding to TS1/0 on input line 281.
Package textcomp Info: Setting cmss sub-encoding to TS1/0 on input line 282.
Package textcomp Info: Setting cmtt sub-encoding to TS1/0 on input line 283.
Package textcomp Info: Setting cmvtt sub-encoding to TS1/0 on input line 284.
Package textcomp Info: Setting cmbr sub-encoding to TS1/0 on input line 285.
Package textcomp Info: Setting cmtl sub-encoding to TS1/0 on input line 286.
Package textcomp Info: Setting ccr sub-encoding to TS1/0 on input line 287.
Package textcomp Info: Setting ptm sub-encoding to TS1/4 on input line 288.
Package textcomp Info: Setting pcr sub-encoding to TS1/4 on input line 289.
Package textcomp Info: Setting phv sub-encoding to TS1/4 on input line 290.
Package textcomp Info: Setting ppl sub-encoding to TS1/3 on input line 291.
Package textcomp Info: Setting pag sub-encoding to TS1/4 on input line 292.
Package textcomp Info: Setting pbk sub-encoding to TS1/4 on input line 293.
Package textcomp Info: Setting pnc sub-encoding to TS1/4 on input line 294.
Package textcomp Info: Setting pzc sub-encoding to TS1/4 on input line 295.
Package textcomp Info: Setting bch sub-encoding to TS1/4 on input line 296.
Package textcomp Info: Setting put sub-encoding to TS1/5 on input line 297.
Package textcomp Info: Setting uag sub-encoding to TS1/5 on input line 298.
Package textcomp Info: Setting ugq sub-encoding to TS1/5 on input line 299.
Package textcomp Info: Setting ul8 sub-encoding to TS1/4 on input line 300.
Package textcomp Info: Setting ul9 sub-encoding to TS1/4 on input line 301.
Package textcomp Info: Setting augie sub-encoding to TS1/5 on input line 302.
Package textcomp Info: Setting dayrom sub-encoding to TS1/3 on input line 303.
Package textcomp Info: Setting dayroms sub-encoding to TS1/3 on input line 304.
Package textcomp Info: Setting pxr sub-encoding to TS1/0 on input line 305.
Package textcomp Info: Setting pxss sub-encoding to TS1/0 on input line 306.
Package textcomp Info: Setting pxtt sub-encoding to TS1/0 on input line 307.
Package textcomp Info: Setting txr sub-encoding to TS1/0 on input line 308.
Package textcomp Info: Setting txss sub-encoding to TS1/0 on input line 309.
Package textcomp Info: Setting txtt sub-encoding to TS1/0 on input line 310.
Package textcomp Info: Setting lmr sub-encoding to TS1/0 on input line 311.
Package textcomp Info: Setting lmdh sub-encoding to TS1/0 on input line 312.
Package textcomp Info: Setting lmss sub-encoding to TS1/0 on input line 313.
Package textcomp Info: Setting lmssq sub-encoding to TS1/0 on input line 314.
Package textcomp Info: Setting lmvtt sub-encoding to TS1/0 on input line 315.
Package textcomp Info: Setting qhv sub-encoding to TS1/0 on input line 316.
Package textcomp Info: Setting qag sub-encoding to TS1/0 on input line 317.
Package textcomp Info: Setting qbk sub-encoding to TS1/0 on input line 318.
Package textcomp Info: Setting qcr sub-encoding to TS1/0 on input line 319.
Package textcomp Info: Setting qcs sub-encoding to TS1/0 on input line 320.
Package textcomp Info: Setting qpl sub-encoding to TS1/0 on input line 321.
Package textcomp Info: Setting qtm sub-encoding to TS1/0 on input line 322.
Package textcomp Info: Setting qzc sub-encoding to TS1/0 on input line 323.
Package textcomp Info: Setting qhvc sub-encoding to TS1/0 on input line 324.
Package textcomp Info: Setting futs sub-encoding to TS1/4 on input line 325.
Package textcomp Info: Setting futx sub-encoding to TS1/4 on input line 326.
Package textcomp Info: Setting futj sub-encoding to TS1/4 on input line 327.
Package textcomp Info: Setting hlh sub-encoding to TS1/3 on input line 328.
Package textcomp Info: Setting hls sub-encoding to TS1/3 on input line 329.
Package textcomp Info: Setting hlst sub-encoding to TS1/3 on input line 330.
Package textcomp Info: Setting hlct sub-encoding to TS1/5 on input line 331.
Package textcomp Info: Setting hlx sub-encoding to TS1/5 on input line 332.
Package textcomp Info: Setting hlce sub-encoding to TS1/5 on input line 333.
Package textcomp Info: Setting hlcn sub-encoding to TS1/5 on input line 334.
Package textcomp Info: Setting hlcw sub-encoding to TS1/5 on input line 335.
Package textcomp Info: Setting hlcf sub-encoding to TS1/5 on input line 336.
Package textcomp Info: Setting pplx sub-encoding to TS1/3 on input line 337.
Package textcomp Info: Setting pplj sub-encoding to TS1/3 on input line 338.
Package textcomp Info: Setting ptmx sub-encoding to TS1/4 on input line 339.
Package textcomp Info: Setting ptmj sub-encoding to TS1/4 on input line 340.
)
(/usr/local/texlive/2012/texmf-dist/tex/latex/mh/mathtools.sty
Package: mathtools 2012/04/24 v1.12 mathematical typesetting tools
(/usr/local/texlive/2012/texmf-dist/tex/latex/tools/calc.sty
Package: calc 2007/08/22 v4.3 Infix arithmetic (KKT,FJ)
\calc@Acount=\count295
\calc@Bcount=\count296
\calc@Adimen=\dimen149
\calc@Bdimen=\dimen150
\calc@Askip=\skip193
\calc@Bskip=\skip194
LaTeX Info: Redefining \setlength on input line 76.
LaTeX Info: Redefining \addtolength on input line 77.
\calc@Ccount=\count297
\calc@Cskip=\skip195
)
(/usr/local/texlive/2012/texmf-dist/tex/latex/mh/mhsetup.sty
Package: mhsetup 2010/01/21 v1.2a programming setup (MH)
)
(/usr/local/texlive/2012/texmf-dist/tex/latex/amsmath/amsmath.sty
Package: amsmath 2000/07/18 v2.13 AMS math features
\@mathmargin=\skip196
For additional information on amsmath, use the `?' option.
(/usr/local/texlive/2012/texmf-dist/tex/latex/amsmath/amstext.sty
Package: amstext 2000/06/29 v2.01
(/usr/local/texlive/2012/texmf-dist/tex/latex/amsmath/amsgen.sty
File: amsgen.sty 1999/11/30 v2.0
\@emptytoks=\toks23
\ex@=\dimen151
))
(/usr/local/texlive/2012/texmf-dist/tex/latex/amsmath/amsbsy.sty
Package: amsbsy 1999/11/29 v1.2d
\pmbraise@=\dimen152
)
(/usr/local/texlive/2012/texmf-dist/tex/latex/amsmath/amsopn.sty
Package: amsopn 1999/12/14 v2.01 operator names
)
\inf@bad=\count298
LaTeX Info: Redefining \frac on input line 211.
\uproot@=\count299
\leftroot@=\count300
LaTeX Info: Redefining \overline on input line 307.
\classnum@=\count301
\DOTSCASE@=\count302
LaTeX Info: Redefining \ldots on input line 379.
LaTeX Info: Redefining \dots on input line 382.
LaTeX Info: Redefining \cdots on input line 467.
\Mathstrutbox@=\box29
\strutbox@=\box30
\big@size=\dimen153
LaTeX Font Info: Redeclaring font encoding OML on input line 567.
LaTeX Font Info: Redeclaring font encoding OMS on input line 568.
\macc@depth=\count303
\c@MaxMatrixCols=\count304
\dotsspace@=\muskip11
\c@parentequation=\count305
\dspbrk@lvl=\count306
\tag@help=\toks24
\row@=\count307
\column@=\count308
\maxfields@=\count309
\andhelp@=\toks25
\eqnshift@=\dimen154
\alignsep@=\dimen155
\tagshift@=\dimen156
\tagwidth@=\dimen157
\totwidth@=\dimen158
\lineht@=\dimen159
\@envbody=\toks26
\multlinegap=\skip197
\multlinetaggap=\skip198
\mathdisplay@stack=\toks27
LaTeX Info: Redefining \[ on input line 2666.
LaTeX Info: Redefining \] on input line 2667.
)
\g_MT_multlinerow_int=\count310
\l_MT_multwidth_dim=\dimen160
\origjot=\skip199
\l_MT_shortvdotswithinadjustabove_dim=\dimen161
\l_MT_shortvdotswithinadjustbelow_dim=\dimen162
\l_MT_above_intertext_dim=\dimen163
\l_MT_below_intertext_dim=\dimen164
\l_MT_above_shortintertext_dim=\dimen165
\l_MT_below_shortintertext_dim=\dimen166
)
(/usr/local/texlive/2012/texmf-dist/tex/latex/acronym/acronym.sty
Package: acronym 2010/09/08 v1.36 Support for acronyms (Tobias Oetiker)
(/usr/local/texlive/2012/texmf-dist/tex/latex/bigfoot/suffix.sty
Package: suffix 2006/07/15 1.5 Variant command support
)
\AC@clearlist=\toks28
)
\c@theorem=\count311
Package biblatex Info: Trying to load language 'english'...
Package biblatex Info: ... file 'english.lbx' found.
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/lbx/english.lbx
File: english.lbx 2011/11/13 v1.7 biblatex localization
)
\@quotelevel=\count312
\@quotereset=\count313
(./thesis.aux (./abstract.aux) (./acronyms.aux) (./chap1.aux) (./chap2.aux)
(./chap3.aux) (./chap4.aux) (./concl.aux))
\openout1 = `thesis.aux'.
LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 32.
LaTeX Font Info: ... okay on input line 32.
LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 32.
LaTeX Font Info: ... okay on input line 32.
LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 32.
LaTeX Font Info: ... okay on input line 32.
LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 32.
LaTeX Font Info: ... okay on input line 32.
LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 32.
LaTeX Font Info: ... okay on input line 32.
LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 32.
LaTeX Font Info: ... okay on input line 32.
LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 32.
LaTeX Font Info: Try loading font information for TS1+cmr on input line 32.
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1cmr.fd
File: ts1cmr.fd 1999/05/25 v2.5h Standard LaTeX font definitions
)
LaTeX Font Info: ... okay on input line 32.
******************************************************
Stock height and width: 794.96999pt by 614.295pt
Top and edge trims: 0pt and 0pt
Page height and width: 794.96999pt by 614.295pt
Text height and width: 606.5pt by 469pt
Spine and edge margins: 72.26999pt and 72.26999pt
Upper and lower margins: 111.76999pt and 76.7pt
Headheight and headsep: 14.5pt and 19.8738pt
Footskip: 30pt
Columnsep and columnseprule: 10pt and 0pt
Marginparsep and marginparwidth: 7pt and 50pt
Sidecapsep and sidecapwidth: 7pt and 50pt
Sidebarhsep and sidebarwidth: 7pt and 50pt
Sidebarvsep and sidebartopsep: 14.5pt and 0pt
Sidebarheight: 546.64995pt
Sidefoothsep and sidefootwidth: 7pt and 50pt
Sidefootvsep and sidefootheight: 14.5pt and 546.64995pt
******************************************************
Package biblatex Info: No input encoding detected.
(biblatex) Assuming 'ascii'.
Package biblatex Info: Automatic encoding selection.
(biblatex) Assuming data encoding 'ascii'.
\openout4 = `thesis-blx.bib'.
Package biblatex Info: Trying to load bibliographic data...
Package biblatex Info: ... file 'thesis.bbl' found.
(./thesis.bbl)
Package biblatex Info: Reference section=0 on input line 32.
Package biblatex Info: Reference segment=0 on input line 32.
[1
]
Class ucbthesis Warning: The final submitted version should not have an approva
l page on input line 54.
[2] [3]
\openout2 = `abstract.aux'.
(./abstract.tex
Missing character: There is no â in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no in font cmr12!
[1
] [2]) [1
] (./thesis.toc [2]) [3] (./thesis.lof
[4
]) [5]
\openout2 = `acronyms.aux'.
(./acronyms.tex [6
]) [7]
Underfull \hbox (badness 10000) in paragraph at lines 76--81
[]
[8
] [9]
\openout2 = `chap1.aux'.
(./chap1.tex [1
]
Missing character: There is no â in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no â in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no in font cmr12!
File: ../Ch1_figs/Fig1.1.eps Graphic file (type eps)
<../Ch1_figs/Fig1.1.eps>
File: ../Ch1_figs/Fig1.5b.eps Graphic file (type eps)
<../Ch1_figs/Fig1.5b.eps>
File: ../Ch1_figs/Fig1.3.eps Graphic file (type eps)
<../Ch1_figs/Fig1.3.eps>
File: ../Ch1_figs/Fig1.4.eps Graphic file (type eps)
<../Ch1_figs/Fig1.4.eps> [2] [3] [4] [5] [6] [7]
File: ../Ch1_figs/Enhancers4.eps Graphic file (type eps)
<../Ch1_figs/Enhancers4.eps>
Underfull \hbox (badness 10000) in paragraph at lines 47--56
[]
[8]
File: ../Ch1_figs/TFIID_compare.eps Graphic file (type eps)
<../Ch1_figs/TFIID_compare.eps>
Underfull \hbox (badness 10000) in paragraph at lines 59--70
[]
[9] [10]
Underfull \hbox (badness 10000) in paragraph at lines 73--75
[]
[11]) [12]
\openout2 = `chap2.aux'.
(./chap2.tex
File: ../Ch2_figs/Fig2.1.eps Graphic file (type eps)
<../Ch2_figs/Fig2.1.eps>
File: ../Ch2_figs/Fig2.2.eps Graphic file (type eps)
<../Ch2_figs/Fig2.2.eps>
File: ../Ch2_figs/Fig2.3.eps Graphic file (type eps)
<../Ch2_figs/Fig2.3.eps>
File: ../Ch2_figs/Fig2.4.eps Graphic file (type eps)
<../Ch2_figs/Fig2.4.eps>
Missing character: There is no â in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no â in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no â in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no â in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no â in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no â in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no â in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no â in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no â in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no â in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no in font cmr12!
[13
]
Class memoir Warning: The material used in the headers is too large
(28.99998pt) for the given head height (14.5pt), it is recommended to
either increase the head height or redesign the header
(in both cases you will find help in the memoir manual). on input line 33.
Overfull \vbox (14.49998pt too high) has occurred while \output is active []
[14]
Overfull \vbox (14.49998pt too high) has occurred while \output is active []
[15]
File: ../Ch2_figs/Fig2.5.eps Graphic file (type eps)
<../Ch2_figs/Fig2.5.eps>
Missing character: There is no â in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no â in font cmr12!
Missing character: There is no in font cmr12!
Missing character: There is no in font cmr12!
File: ../Ch2_figs/Fig2.6.eps Graphic file (type eps)
<../Ch2_figs/Fig2.6.eps>
Overfull \vbox (14.49998pt too high) has occurred while \output is active []
[16]
Overfull \vbox (14.49998pt too high) has occurred while \output is active []
[17]
Overfull \vbox (14.49998pt too high) has occurred while \output is active []
[18]
Overfull \vbox (14.49998pt too high) has occurred while \output is active []
[19]
Underfull \hbox (badness 10000) in paragraph at lines 50--52
[]
Overfull \vbox (14.49998pt too high) has occurred while \output is active []
[20]
Overfull \vbox (14.49998pt too high) has occurred while \output is active []
[21]
File: ../Ch2_figs/Fig2.7.eps Graphic file (type eps)
<../Ch2_figs/Fig2.7.eps>
LaTeX Font Info: Try loading font information for OML+cmr on input line 64.
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/omlcmr.fd
File: omlcmr.fd 1999/05/25 v2.5h Standard LaTeX font definitions
)
LaTeX Font Info: Font shape `OML/cmr/m/n' in size <12> not available
(Font) Font shape `OML/cmm/m/it' tried instead on input line 64.
)
Underfull \hbox (badness 10000) in paragraph at lines 57--90
[]
Overfull \vbox (14.49998pt too high) has occurred while \output is active []