This is pdfeTeX, Version 3.141592-1.11a-2.1 (Web2C 7.5.2) (format=pdflatex 2003.9.6) 2 JUN 2004 11:35 entering extended mode **comp-out.tex (./comp-out.tex{/usr/local/teTeX/share/texmf.local/pdftex/config/pdftex.cfg} LaTeX2e <2001/06/01> Babel and hyphenation patterns for american, french, german, ngerman, n ohyphenation, loaded. (/usr/local/teTeX/share/texmf.tetex/tex/latex/base/article.cls Document Class: article 2001/04/21 v1.4e Standard LaTeX document class (/usr/local/teTeX/share/texmf.tetex/tex/latex/base/size10.clo File: size10.clo 2001/04/21 v1.4e Standard LaTeX file (size option) ) \c@part=\count79 \c@section=\count80 \c@subsection=\count81 \c@subsubsection=\count82 \c@paragraph=\count83 \c@subparagraph=\count84 \c@figure=\count85 \c@table=\count86 \abovecaptionskip=\skip41 \belowcaptionskip=\skip42 \bibindent=\dimen102 ) (/usr/local/teTeX/share/texmf.tetex/tex/latex/amsfonts/amssymb.sty Package: amssymb 2002/01/22 v2.2d (/usr/local/teTeX/share/texmf.tetex/tex/latex/amsfonts/amsfonts.sty Package: amsfonts 2001/10/25 v2.2f \@emptytoks=\toks14 \symAMSa=\mathgroup4 \symAMSb=\mathgroup5 LaTeX Font Info: Overwriting math alphabet `\mathfrak' in version `bold' (Font) U/euf/m/n --> U/euf/b/n on input line 132. )) (/usr/local/teTeX/share/texmf.tetex/tex/latex/amsmath/amsmath.sty Package: amsmath 2000/07/18 v2.13 AMS math features \@mathmargin=\skip43 For additional information on amsmath, use the `?' option. (/usr/local/teTeX/share/texmf.tetex/tex/latex/amsmath/amstext.sty Package: amstext 2000/06/29 v2.01 (/usr/local/teTeX/share/texmf.tetex/tex/latex/amsmath/amsgen.sty File: amsgen.sty 1999/11/30 v2.0 \@emptytoks=\toks15 \ex@=\dimen103 )) (/usr/local/teTeX/share/texmf.tetex/tex/latex/amsmath/amsbsy.sty Package: amsbsy 1999/11/29 v1.2d \pmbraise@=\dimen104 ) (/usr/local/teTeX/share/texmf.tetex/tex/latex/amsmath/amsopn.sty Package: amsopn 1999/12/14 v2.01 operator names ) \inf@bad=\count87 LaTeX Info: Redefining \frac on input line 211. \uproot@=\count88 \leftroot@=\count89 LaTeX Info: Redefining \overline on input line 307. \classnum@=\count90 \DOTSCASE@=\count91 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@=\box26 \strutbox@=\box27 \big@size=\dimen105 LaTeX Font Info: Redeclaring font encoding OML on input line 567. LaTeX Font Info: Redeclaring font encoding OMS on input line 568. \macc@depth=\count92 \c@MaxMatrixCols=\count93 \dotsspace@=\muskip10 \c@parentequation=\count94 \dspbrk@lvl=\count95 \tag@help=\toks16 \row@=\count96 \column@=\count97 \maxfields@=\count98 \andhelp@=\toks17 \eqnshift@=\dimen106 \alignsep@=\dimen107 \tagshift@=\dimen108 \tagwidth@=\dimen109 \totwidth@=\dimen110 \lineht@=\dimen111 \@envbody=\toks18 \multlinegap=\skip44 \multlinetaggap=\skip45 \mathdisplay@stack=\toks19 LaTeX Info: Redefining \[ on input line 2666. LaTeX Info: Redefining \] on input line 2667. ) (./slide-article-tom.sty (/usr/local/teTeX/share/texmf.tetex/tex/latex/base/sfonts.def File: sfonts.def 1998/06/12 v2.2e Standard LaTeX slide font definitions (/usr/local/teTeX/share/texmf.tetex/tex/latex/base/ot1lcmss.fd File: ot1lcmss.fd 1998/06/12 v2.2e Standard LaTeX slide font definitions )) \c@minutes=\count99 \c@seconds=\count100 \c@mv@invisible=\count101 LaTeX Font Info: Overwriting symbol font `operators' in version `normal' (Font) OT1/cmr/m/n --> OT1/lcmss/m/n on input line 424. LaTeX Font Info: Overwriting symbol font `letters' in version `normal' (Font) OML/cmm/m/it --> OML/lcmm/m/it on input line 427. LaTeX Font Info: Overwriting symbol font `symbols' in version `normal' (Font) OMS/cmsy/m/n --> OMS/lcmsy/m/n on input line 429. LaTeX Font Info: Overwriting symbol font `largesymbols' in version `normal' (Font) OMX/cmex/m/n --> OMX/lcmex/m/n on input line 431. LaTeX Font Info: Overwriting symbol font `operators' in version `invisible' (Font) OT1/cmr/m/n --> OT1/lcmss/m/In on input line 434. LaTeX Font Info: Overwriting symbol font `letters' in version `invisible' (Font) OML/cmm/m/it --> OML/lcmm/m/Iit on input line 436. LaTeX Font Info: Overwriting symbol font `symbols' in version `invisible' (Font) OMS/cmsy/m/n --> OMS/lcmsy/m/In on input line 438. LaTeX Font Info: Overwriting symbol font `largesymbols' in version `invisibl e' (Font) OMX/cmex/m/n --> OMX/lcmex/m/In on input line 440. LaTeX Info: Redefining \rm on input line 526. LaTeX Info: Redefining \sf on input line 527. LaTeX Info: Redefining \tt on input line 528. LaTeX Info: Redefining \bf on input line 529. LaTeX Info: Redefining \it on input line 530. LaTeX Info: Redefining \sl on input line 531. LaTeX Info: Redefining \sc on input line 532. LaTeX Info: Redefining \cal on input line 533. LaTeX Info: Redefining \mit on input line 534. ) (/usr/local/teTeX/share/texmf.tetex/tex/latex/graphics/graphicx.sty Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR) (/usr/local/teTeX/share/texmf.tetex/tex/latex/graphics/keyval.sty Package: keyval 1999/03/16 v1.13 key=value parser (DPC) \KV@toks@=\toks20 ) (/usr/local/teTeX/share/texmf.tetex/tex/latex/graphics/graphics.sty Package: graphics 2001/07/07 v1.0n Standard LaTeX Graphics (DPC,SPQR) (/usr/local/teTeX/share/texmf.tetex/tex/latex/graphics/trig.sty Package: trig 1999/03/16 v1.09 sin cos tan (DPC) ) (/usr/local/teTeX/share/texmf.tetex/tex/latex/config/graphics.cfg File: graphics.cfg 2001/08/31 v1.1 graphics configuration of teTeX/TeXLive ) Package graphics Info: Driver file: pdftex.def on input line 80. (/usr/local/teTeX/share/texmf.tetex/tex/latex/graphics/pdftex.def File: pdftex.def 2002/06/19 v0.03k graphics/color for pdftex \Gread@gobject=\count102 )) \Gin@req@height=\dimen112 \Gin@req@width=\dimen113 ) (/usr/local/teTeX/share/texmf.tetex/tex/latex/hyperref/hyperref.sty Package: hyperref 2003/01/22 v6.73n Hypertext links for LaTeX \@linkdim=\dimen114 \Hy@linkcounter=\count103 \Hy@pagecounter=\count104 (/usr/local/teTeX/share/texmf.tetex/tex/latex/hyperref/pd1enc.def File: pd1enc.def 2003/01/22 v6.73n Hyperref: PDFDocEncoding definition (HO) ) (/usr/local/teTeX/share/texmf.tetex/tex/latex/config/hyperref.cfg File: hyperref.cfg 2002/06/06 v1.2 hyperref configuration of TeXLive and teTeX ) Package hyperref Info: Hyper figures OFF on input line 1792. Package hyperref Info: Link nesting OFF on input line 1797. Package hyperref Info: Hyper index ON on input line 1800. Package hyperref Info: Plain pages ON on input line 1805. Package hyperref Info: Backreferencing OFF on input line 1812. Implicit mode ON; LaTeX internals redefined Package hyperref Info: Bookmarks ON on input line 1916. (/usr/local/teTeX/share/texmf.tetex/tex/latex/misc/url.sty \Urlmuskip=\muskip11 Package: url 1999/03/28 ver 1.5x Verb mode for urls, etc. ) LaTeX Info: Redefining \url on input line 2055. \Fld@menulength=\count105 \Field@Width=\dimen115 \Fld@charsize=\dimen116 \Choice@toks=\toks21 \Field@toks=\toks22 Package hyperref Info: Hyper figures OFF on input line 2513. Package hyperref Info: Link nesting OFF on input line 2518. Package hyperref Info: Hyper index ON on input line 2521. Package hyperref Info: backreferencing OFF on input line 2528. Package hyperref Info: Link coloring OFF on input line 2533. \c@Item=\count106 \c@Hfootnote=\count107 ) *hyperref using default driver hpdftex* (/usr/local/teTeX/share/texmf.tetex/tex/latex/hyperref/hpdftex.def File: hpdftex.def 2003/01/22 v6.73n Hyperref driver for pdfTeX (/usr/local/teTeX/share/texmf.tetex/tex/latex/psnfss/pifont.sty Package: pifont 2002/09/08 PSNFSS-v9.0a Pi font support (SPQR) LaTeX Font Info: Try loading font information for U+pzd on input line 62. (/usr/local/teTeX/share/texmf.tetex/tex/latex/psnfss/upzd.fd File: upzd.fd 2001/06/04 font definitions for U/pzd. ) LaTeX Font Info: Try loading font information for U+psy on input line 63. (/usr/local/teTeX/share/texmf.tetex/tex/latex/psnfss/upsy.fd File: upsy.fd 2001/06/04 font definitions for U/psy. )) \Fld@listcount=\count108 \@outlinefile=\write3 ) Package hyperref Info: Option `colorlinks' set `true' on input line 19. (./comp-out.aux) \openout1 = `comp-out.aux'. LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 52. LaTeX Font Info: ... okay on input line 52. LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 52. LaTeX Font Info: ... okay on input line 52. LaTeX Font Info: Checking defaults for OT1/lcmss/m/n on input line 52. LaTeX Font Info: ... okay on input line 52. LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 52. LaTeX Font Info: ... okay on input line 52. LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 52. LaTeX Font Info: ... okay on input line 52. LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 52. LaTeX Font Info: ... okay on input line 52. LaTeX Font Info: Checking defaults for PD1/pdf/m/n on input line 52. LaTeX Font Info: ... okay on input line 52. (/usr/local/teTeX/share/texmf.tetex/tex/context/base/supp-pdf.tex (/usr/local/teTeX/share/texmf.tetex/tex/context/base/supp-mis.tex loading : Context Support Macros / Missing \protectiondepth=\count109 \scratchcounter=\count110 \scratchtoks=\toks23 \scratchdimen=\dimen117 \scratchskip=\skip46 \scratchmuskip=\muskip12 \scratchbox=\box28 \scratchread=\read1 \scratchwrite=\write4 \zeropoint=\dimen118 \minusone=\count111 \thousandpoint=\dimen119 \emptytoks=\toks24 \nextbox=\box29 \nextdepth=\dimen120 \everyline=\toks25 \!!counta=\count112 \!!countb=\count113 \recursecounter=\count114 ) loading : Context Support Macros / PDF \nofMPsegments=\count115 \nofMParguments=\count116 \everyMPtoPDFconversion=\toks26 ) (/usr/local/teTeX/share/texmf.tetex/tex/latex/graphics/color.sty Package: color 1999/02/16 v1.0i Standard LaTeX Color (DPC) LaTeX Info: Redefining \color on input line 71. (/usr/local/teTeX/share/texmf.tetex/tex/latex/config/color.cfg File: color.cfg 2001/08/31 v1.1 color configuration of teTeX/TeXLive ) Package color Info: Driver file: pdftex.def on input line 125. ) Package hyperref Info: Link coloring ON on input line 52. (/usr/local/teTeX/share/texmf.tetex/tex/latex/hyperref/nameref.sty Package: nameref 2001/01/27 v2.19 Cross-referencing by name of section \c@section@level=\count117 ) LaTeX Info: Redefining \ref on input line 52. LaTeX Info: Redefining \pageref on input line 52. (./comp-out.out) (./comp-out.out) \openout3 = `comp-out.out'. [1 {/usr/local/teTeX/share/texmf.local/dvips/config/pdftex.map}{/usr/local/teTeX/s hare/texmf.gwtex/dvips/config/Ttbbold.map}] LaTeX Font Info: Try loading font information for OML+lcmm on input line 81. (/usr/local/teTeX/share/texmf.tetex/tex/latex/base/omllcmm.fd File: omllcmm.fd 1998/06/12 v2.2e Standard LaTeX slide font definitions ) LaTeX Font Info: Try loading font information for OMS+lcmsy on input line 81 . (/usr/local/teTeX/share/texmf.tetex/tex/latex/base/omslcmsy.fd File: omslcmsy.fd 1998/06/12 v2.2e Standard LaTeX slide font definitions ) LaTeX Font Info: Try loading font information for OMX+lcmex on input line 81 . (/usr/local/teTeX/share/texmf.tetex/tex/latex/base/omxlcmex.fd File: omxlcmex.fd 1998/06/12 v2.2e Standard LaTeX slide font definitions ) LaTeX Font Info: External font `cmex10 at17.28pt' loaded for size (Font) <34.4> on input line 81. LaTeX Font Info: External font `cmex10 at17.28pt' loaded for size (Font) <28.66> on input line 81. LaTeX Font Info: External font `cmex10 at17.28pt' loaded for size (Font) <23.89> on input line 81. LaTeX Font Info: Try loading font information for U+msa on input line 81. (/usr/local/teTeX/share/texmf.tetex/tex/latex/amsfonts/umsa.fd File: umsa.fd 2002/01/19 v2.2g AMS font definitions ) LaTeX Font Warning: Font shape `U/msa/m/n' in size <34.4> not available (Font) size <24.88> substituted on input line 81. LaTeX Font Warning: Font shape `U/msa/m/n' in size <28.66> not available (Font) size <24.88> substituted on input line 81. LaTeX Font Warning: Font shape `U/msa/m/n' in size <23.89> not available (Font) size <24.88> substituted on input line 81. LaTeX Font Info: Try loading font information for U+msb on input line 81. (/usr/local/teTeX/share/texmf.tetex/tex/latex/amsfonts/umsb.fd File: umsb.fd 2002/01/19 v2.2g AMS font definitions ) LaTeX Font Warning: Font shape `U/msb/m/n' in size <34.4> not available (Font) size <24.88> substituted on input line 81. LaTeX Font Warning: Font shape `U/msb/m/n' in size <28.66> not available (Font) size <24.88> substituted on input line 81. LaTeX Font Warning: Font shape `U/msb/m/n' in size <23.89> not available (Font) size <24.88> substituted on input line 81. LaTeX Font Info: External font `cmex10 at17.28pt' loaded for size (Font) <19.907> on input line 85. LaTeX Font Info: External font `cmex10 at17.28pt' loaded for size (Font) <16.59> on input line 85. LaTeX Font Info: External font `cmex10 at17.28pt' loaded for size (Font) <13.82> on input line 85. LaTeX Font Warning: Font shape `U/msa/m/n' in size <19.907> not available (Font) size <20.74> substituted on input line 85. LaTeX Font Warning: Font shape `U/msa/m/n' in size <16.59> not available (Font) size <17.28> substituted on input line 85. LaTeX Font Warning: Font shape `U/msa/m/n' in size <13.82> not available (Font) size <14.4> substituted on input line 85. LaTeX Font Warning: Font shape `U/msb/m/n' in size <19.907> not available (Font) size <20.74> substituted on input line 85. LaTeX Font Warning: Font shape `U/msb/m/n' in size <16.59> not available (Font) size <17.28> substituted on input line 85. LaTeX Font Warning: Font shape `U/msb/m/n' in size <13.82> not available (Font) size <14.4> substituted on input line 85. [2] [3] LaTeX Font Info: Try loading font information for OMS+lcmss on input line 18 9. LaTeX Font Info: No file OMSlcmss.fd. on input line 189. LaTeX Font Warning: Font shape `OMS/lcmss/m/n' undefined (Font) using `OMS/cmsy/m/n' instead (Font) for symbol `textbraceleft' on input line 189. LaTeX Font Warning: Font shape `OMS/cmsy/m/n' in size <19.907> not available (Font) size <20.74> substituted on input line 189. LaTeX Font Warning: Font shape `OMS/lcmss/m/n' in size <19.907> not available (Font) size <20.74> substituted on input line 189. [4] [5] [6] [7] LaTeX Font Warning: Font shape `OT1/cmr/m/it' in size <19.907> not available (Font) size <20.74> substituted on input line 276. LaTeX Font Warning: Font shape `OT1/cmr/m/it' in size <16.59> not available (Font) size <17.28> substituted on input line 276. LaTeX Font Warning: Font shape `OT1/cmr/m/it' in size <13.82> not available (Font) size <14.4> substituted on input line 276. [8] [9] [10] [11] LaTeX Font Warning: Font shape `OT1/cmr/m/it' in size <34.4> not available (Font) size <24.88> substituted on input line 360. LaTeX Font Warning: Font shape `OT1/cmr/m/it' in size <28.66> not available (Font) size <24.88> substituted on input line 360. LaTeX Font Warning: Font shape `OT1/cmr/m/it' in size <23.89> not available (Font) size <24.88> substituted on input line 360. [12] [13] [14] [15] [16] File: DFA-even-odd.jpg Graphic file (type jpg) [17 <./DFA-even-odd.jpg>] [18] [19] File: RNP-1-motif.jpg Graphic file (type jpg) [20 <./RNP-1-motif.jpg>] [21] [22] [23] [24] File: ACGT-Markov.jpg Graphic file (type jpg) File: Pairwise-align-HMM.jpg Graphic file (type jpg) [25 <./ACGT-Markov.jpg> <./Pairwise-align-HMM.jpg> ] [26] [27] [28] [29] [30] File: yeast-tRNA-Phe.jpg Graphic file (type jpg) Overfull \hbox (38.0pt too wide) in paragraph at lines 735--741 [] [] [31 <./yeast-tRNA-Phe.jpg>] Overfull \hbox (29.2616pt too wide) in alignment at lines 761--766 [][][] [] [] [32] [33] [34] [35] [36] Overfull \hbox (38.0pt too wide) in paragraph at lines 827--830 [] [] Overfull \hbox (38.0pt too wide) in paragraph at lines 827--830 [] [] [37] [38] [39] [40] [41] [42] [43] [44] LaTeX Font Info: External font `cmex10 at17.28pt' loaded for size (Font) <12> on input line 888. LaTeX Font Info: External font `cmex10 at17.28pt' loaded for size (Font) <7> on input line 888. [45] [46] [47] [48] (./comp-out.aux) LaTeX Font Warning: Size substitutions with differences (Font) up to 9.51999pt have occurred. LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) Here is how much of TeX's memory you used: 3727 strings out of 95314 49604 string characters out of 1187312 98572 words of memory out of 1000001 6620 multiletter control sequences out of 10000+50000 18594 words of font info for 66 fonts, out of 500000 for 1000 14 hyphenation exceptions out of 1000 27i,9n,24p,576b,370s stack positions out of 1500i,500n,5000p,200000b,5000s 354 PDF objects out of 300000 124 named destinations out of 131072 42 words of extra memory for PDF output out of 65536 {/usr/local/teTeX/share/texmf.tetex/dvips/tetex/74afc74c.enc}{/usr/local/teTeX/share/texmf.tetex/dv ips/tetex/aae443f0.enc}{/usr/local/teTeX/share/texmf.tetex/dvips/tetex/bbad153f.enc} Output written on comp-out.pdf (48 pages, 821106 bytes).