This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) (format=pdflatex 2008.8.22) 9 FEB 2009 22:51 entering extended mode %&-line parsing enabled. **fss-v1.tex (./fss-v1.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, german-x-2008-06-18, ngerman-x-2008-06-18, ancientgreek, ibycus, ar abic, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danish, dutc h, esperanto, estonian, farsi, finnish, french, galician, german, ngerman, mono greek, greek, hungarian, icelandic, indonesian, interlingua, irish, italian, la tin, mongolian, mongolian2a, bokmal, nynorsk, polish, portuguese, romanian, rus sian, sanskrit, serbian, slovak, slovenian, spanish, swedish, turkish, ukenglis h, ukrainian, uppersorbian, welsh, loaded. (./sig-alternate.cls (/usr/local/texlive/2008/texmf-dist/tex/latex/graphics/epsfig.sty Package: epsfig 1999/02/16 v1.7a (e)psfig emulation (SPQR) (/usr/local/texlive/2008/texmf-dist/tex/latex/graphics/graphicx.sty Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR) (/usr/local/texlive/2008/texmf-dist/tex/latex/graphics/keyval.sty Package: keyval 1999/03/16 v1.13 key=value parser (DPC) \KV@toks@=\toks14 ) (/usr/local/texlive/2008/texmf-dist/tex/latex/graphics/graphics.sty Package: graphics 2006/02/20 v1.0o Standard LaTeX Graphics (DPC,SPQR) (/usr/local/texlive/2008/texmf-dist/tex/latex/graphics/trig.sty Package: trig 1999/03/16 v1.09 sin cos tan (DPC) ) (/usr/local/texlive/2008/texmf/tex/latex/config/graphics.cfg File: graphics.cfg 2007/01/18 v1.5 graphics configuration of teTeX/TeXLive ) Package graphics Info: Driver file: pdftex.def on input line 90. (/usr/local/texlive/2008/texmf-dist/tex/latex/pdftex-def/pdftex.def File: pdftex.def 2008/07/16 v0.04k Graphics/color for pdfTeX \Gread@gobject=\count79 )) \Gin@req@height=\dimen102 \Gin@req@width=\dimen103 ) \epsfxsize=\dimen104 \epsfysize=\dimen105 ) (/usr/local/texlive/2008/texmf-dist/tex/latex/amsfonts/amssymb.sty Package: amssymb 2002/01/22 v2.2d (/usr/local/texlive/2008/texmf-dist/tex/latex/amsfonts/amsfonts.sty Package: amsfonts 2001/10/25 v2.2f \@emptytoks=\toks15 \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/texlive/2008/texmf-dist/tex/latex/amsmath/amsmath.sty Package: amsmath 2000/07/18 v2.13 AMS math features \@mathmargin=\skip41 For additional information on amsmath, use the `?' option. (/usr/local/texlive/2008/texmf-dist/tex/latex/amsmath/amstext.sty Package: amstext 2000/06/29 v2.01 (/usr/local/texlive/2008/texmf-dist/tex/latex/amsmath/amsgen.sty File: amsgen.sty 1999/11/30 v2.0 \@emptytoks=\toks16 \ex@=\dimen106 )) (/usr/local/texlive/2008/texmf-dist/tex/latex/amsmath/amsbsy.sty Package: amsbsy 1999/11/29 v1.2d \pmbraise@=\dimen107 ) (/usr/local/texlive/2008/texmf-dist/tex/latex/amsmath/amsopn.sty Package: amsopn 1999/12/14 v2.01 operator names ) \inf@bad=\count80 LaTeX Info: Redefining \frac on input line 211. \uproot@=\count81 \leftroot@=\count82 LaTeX Info: Redefining \overline on input line 307. \classnum@=\count83 \DOTSCASE@=\count84 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=\dimen108 LaTeX Font Info: Redeclaring font encoding OML on input line 567. LaTeX Font Info: Redeclaring font encoding OMS on input line 568. \macc@depth=\count85 \c@MaxMatrixCols=\count86 \dotsspace@=\muskip10 \c@parentequation=\count87 \dspbrk@lvl=\count88 \tag@help=\toks17 \row@=\count89 \column@=\count90 \maxfields@=\count91 \andhelp@=\toks18 \eqnshift@=\dimen109 \alignsep@=\dimen110 \tagshift@=\dimen111 \tagwidth@=\dimen112 \totwidth@=\dimen113 \lineht@=\dimen114 \@envbody=\toks19 \multlinegap=\skip42 \multlinetaggap=\skip43 \mathdisplay@stack=\toks20 LaTeX Info: Redefining \[ on input line 2666. LaTeX Info: Redefining \] on input line 2667. ) Document Class 'sig-alternate' <7th. June '07>. Modified by G.K.M. Tobin/Gerry Murray Based in part upon document Style `acmconf' <22 May 89>. Hacked 4/91 by shivers@cs.cmu.edu, 4/93 by theobald@cs.mcgill.ca Excerpts were taken from (Journal Style) 'esub2acm.cls'. ****** Bugs/comments/suggestions/technicalities to Gerry Murray -- murray@hq.ac m.org ****** Questions on the style, SIGS policies, etc. to Adrienne Griscti griscti@acm.org \footheight=\dimen115 \@maxsep=\dimen116 \@dblmaxsep=\dimen117 \aucount=\count92 \originalaucount=\count93 \auwidth=\dimen118 \auskip=\dimen119 \auskipcount=\count94 \auskip=\dimen120 \allauboxes=\dimen121 \addauthors=\toks21 \addauflag=\count95 \subtitletext=\toks22 \savesection=\count96 \sectioncntr=\count97 \c@figure=\count98 \c@table=\count99 \titleboxnotes=\toks23 \titleboxnoteflag=\count100 Document Class: sig-alternate 2007/06/07 - V2.3 - based on acmproc.cls V1.3 (/usr/local/texlive/2008/texmf-dist/tex/latex/base/latexsym.sty Package: latexsym 1998/08/17 v2.2e Standard LaTeX package (lasy symbols) \symlasy=\mathgroup6 LaTeX Font Info: Overwriting symbol font `lasy' in version `bold' (Font) U/lasy/m/n --> U/lasy/b/n on input line 47. ) \@acmtitlebox=\box28 \titlenotecount=\count101 \tntoks=\toks24 \tntokstwo=\toks25 \tntoksthree=\toks26 \tntoksfour=\toks27 \tntoksfive=\toks28 \catcount=\count102 \copyrightnotice=\toks29 \conf=\toks30 \confinfo=\toks31 \c@part=\count103 \c@section=\count104 \c@subsection=\count105 \c@subsubsection=\count106 \c@paragraph=\count107 Using 'Abbrev' bibliography style \bibindent=\dimen122 \colcntr=\count108 \savebox=\box29 \copyrtyr=\toks32 \acmcopyr=\toks33 \boilerplate=\toks34 \copyrightetc=\toks35 (/usr/local/texlive/2008/texmf-dist/tex/latex/base/fontenc.sty Package: fontenc 2005/09/27 v1.99g Standard LaTeX package (/usr/local/texlive/2008/texmf-dist/tex/latex/base/t1enc.def File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file LaTeX Font Info: Redeclaring font encoding T1 on input line 43. ) LaTeX Font Info: Try loading font information for T1+aer on input line 100. (/usr/local/texlive/2008/texmf-dist/tex/latex/ae/t1aer.fd File: t1aer.fd 1997/11/16 Font definitions for T1/aer. ))) (/usr/local/texlive/2008/texmf-dist/tex/latex/base/alltt.sty Package: alltt 1997/06/16 v2.0g defines alltt environment ) (/usr/local/texlive/2008/texmf-dist/tex/latex/psnfss/times.sty Package: times 2005/04/12 PSNFSS-v9.2a (SPQR) ) (/usr/local/texlive/2008/texmf-dist/tex/latex/ltxmisc/url.sty \Urlmuskip=\muskip11 Package: url 2006/04/12 ver 3.3 Verb mode for urls, etc. ) (./dblfloatfix.sty Package: dblfloatfix 2003/11/18 v1.0 (MH) (/usr/local/texlive/2008/texmf-dist/tex/latex/base/fixltx2e.sty Package: fixltx2e 2006/03/24 v1.1n fixes to LaTeX LaTeX Info: Redefining \em on input line 420. LaTeX Info: The control sequence `\[' is already robust on input line 471. LaTeX Info: The control sequence `\]' is already robust on input line 472. ) \@dblbotnum=\count109 \c@dblbotnumber=\count110 ) (/usr/local/texlive/2008/texmf-dist/tex/latex/cite/cite.sty LaTeX Info: Redefining \cite on input line 149. LaTeX Info: Redefining \nocite on input line 214. Package: cite 2003/11/04 v 4.01 ) (./fss-v1.aux) \openout1 = `fss-v1.aux'. LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 34. LaTeX Font Info: ... okay on input line 34. LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 34. LaTeX Font Info: ... okay on input line 34. LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 34. LaTeX Font Info: ... okay on input line 34. LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 34. LaTeX Font Info: ... okay on input line 34. LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 34. LaTeX Font Info: ... okay on input line 34. LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 34. LaTeX Font Info: ... okay on input line 34. LaTeX Font Info: Try loading font information for T1+ptm on input line 34. (/usr/local/texlive/2008/texmf-dist/tex/latex/psnfss/t1ptm.fd File: t1ptm.fd 2001/06/04 font definitions for T1/ptm. ) (/usr/local/texlive/2008/texmf-dist/tex/context/base/supp-pdf.tex [Loading MPS to PDF converter (version 2006.09.02).] \scratchcounter=\count111 \scratchdimen=\dimen123 \scratchbox=\box30 \nofMPsegments=\count112 \nofMParguments=\count113 \everyMPshowfont=\toks36 \MPscratchCnt=\count114 \MPscratchDim=\dimen124 \MPnumerator=\count115 \everyMPtoPDFconversion=\toks37 ) LaTeX Font Info: Try loading font information for U+msa on input line 60. (/usr/local/texlive/2008/texmf-dist/tex/latex/amsfonts/umsa.fd File: umsa.fd 2002/01/19 v2.2g AMS font definitions ) LaTeX Font Info: Try loading font information for U+msb on input line 60. (/usr/local/texlive/2008/texmf-dist/tex/latex/amsfonts/umsb.fd File: umsb.fd 2002/01/19 v2.2g AMS font definitions ) LaTeX Font Info: Try loading font information for U+lasy on input line 60. (/usr/local/texlive/2008/texmf-dist/tex/latex/base/ulasy.fd File: ulasy.fd 1998/08/17 v2.2e LaTeX symbol font definitions ) LaTeX Font Info: Font shape `T1/ptm/bx/n' in size <9> not available (Font) Font shape `T1/ptm/b/n' tried instead on input line 79. Overfull \hbox (5.49854pt too wide) in paragraph at lines 79--83 \T1/ptm/m/n/9 Anal-y-sis; G.3 [\T1/ptm/b/n/9 General\T1/ptm/m/n/9 ]: Prob-a-bil -ity and Statis-tics--- \T1/ptm/m/it/9 sta-tis-ti-cal com- [] (./oldresults.tex File: sloccov.pdf Graphic file (type pdf) File: sloctime.pdf Graphic file (type pdf) ) LaTeX Font Info: Try loading font information for T1+pcr on input line 129. (/usr/local/texlive/2008/texmf-dist/tex/latex/psnfss/t1pcr.fd File: t1pcr.fd 2001/06/04 font definitions for T1/pcr. ) Overfull \hbox (2.31297pt too wide) in paragraph at lines 178--199 \T1/ptm/m/n/9 per'' sys-tem that au-to-mates the con-struc-tion of test scripts . Wrapper- [] [1{/usr/local/texlive/2008/texmf-var/fonts/map/pdftex/updmap/pdftex.map} ] Overfull \hbox (1.95435pt too wide) in paragraph at lines 200--205 \T1/ptm/m/it/9 pool \T1/ptm/m/n/9 ap-proach to cov-er-age mod-els, and run-ning over the Java classes [] Overfull \hbox (11.42172pt too wide) in paragraph at lines 207--210 \T1/ptm/m/n/9 ig-nore value pools [19] (mea-sured in terms of con-di-tion/decis ion [] (./related.tex Overfull \hbox (1.35071pt too wide) in paragraph at lines 16--38 \T1/ptm/m/n/9 form-ing tasks re-lated to pro-gram com-pre-hen-sion; for ex-am-p le, Mar- [] [2 <./sloccov.pdf> <./sloctime.pdf>] Overfull \hbox (1.15318pt too wide) in paragraph at lines 56--67 \T1/ptm/m/n/9 ``chunks''. Each chunk is spa-tially in-dexed (e.g. us-ing cover trees [4] [] ) File: xyPlot.pdf Graphic file (type pdf) File: lohiPlot.pdf Graphic file (type pdf) [3 <./xyPlot.pdf> <./lohiPlot.pdf>] Overfull \hbox (5.2209pt too wide) in paragraph at lines 513--520 []\T1/ptm/m/n/9 Here we present a sim-pli-fied de-scrip-tion of Nighthawk's cov erage- [] LaTeX Font Info: Try loading font information for T1+phv on input line 552. (/usr/local/texlive/2008/texmf-dist/tex/latex/psnfss/t1phv.fd File: t1phv.fd 2001/06/04 scalable font definitions for T1/phv. ) Underfull \hbox (badness 10000) in paragraph at lines 551--554 []\T1/ptm/m/n/7 Otherwise, choose an ini-tial-izer method $\OML/cmm/m/it/7 i$ \ T1/ptm/m/n/7 of $\OML/cmm/m/it/7 t$\T1/ptm/m/n/7 , call [] Underfull \hbox (badness 5771) in paragraph at lines 551--554 \T1/phv/m/n/7 tryRunMethod$\OT1/cmr/m/n/7 (\OML/cmm/m/it/7 i; c\OT1/cmr/m/n/7 ) $\T1/ptm/m/n/7 , and place the re-sult in the des-ti-na-tion [] Underfull \vbox (badness 1577) has occurred while \output is active [] [4] Overfull \hbox (17.71309pt too wide) in paragraph at lines 683--690 []\T1/ptm/m/n/9 Here we de-scribe the work that we have done to op-ti-mize Nigh thawk's [] Overfull \hbox (1.96257pt too wide) in paragraph at lines 730--732 []\T1/ptm/m/n/9 Miller has shown that mod-els gen-er-ally con-tain-ing fewer va ri- [] [5] File: Hashtable_rankedByMerit.pdf Graphic file (type pdf) Overfull \hbox (12.94499pt too wide) in paragraph at lines 932--933 [] [] File: Hashtable_rankedByAvgRank.pdf Graphic file (type pdf) Overfull \hbox (12.94499pt too wide) in paragraph at lines 941--942 [] [] [6] Overfull \hbox (2.85374pt too wide) in paragraph at lines 1018--1028 \T1/ptm/m/n/9 cases stud-ied in Fig-ure 1[]a. The cov-er-age is less than one f or columns [] File: timereport.pdf Graphic file (type pdf) Overfull \hbox (23.21167pt too wide) in paragraph at lines 1048--1058 []\T1/ptm/m/n/9 In or-der to de-ter-mine whether elim-i-nat-ing gene types from Nighthawk's [] Overfull \hbox (2.31325pt too wide) in paragraph at lines 1048--1058 \T1/ptm/m/n/9 GA is cost-effective, we must con-sider not only the cov-er-age a chiev- [] [7 <./Hashtable_rankedByMerit.pdf> <./Hashtable_rankedByAvgRank.pdf>] Underfull \vbox (badness 10000) has occurred while \output is active [] [8 <./timereport.pdf>] (./fss-v1.bbl) [9] (./fss-v1.aux) ) Here is how much of TeX's memory you used: 2587 strings out of 493886 31033 string characters out of 1151099 96971 words of memory out of 3000000 5787 multiletter control sequences out of 10000+50000 67185 words of font info for 79 fonts, out of 3000000 for 5000 714 hyphenation exceptions out of 8191 39i,10n,26p,471b,367s stack positions out of 5000i,500n,10000p,200000b,50000s {/usr/local/texlive/ 2008/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on fss-v1.pdf (9 pages, 197408 bytes). PDF statistics: 121 PDF objects out of 1000 (max. 8388607) 0 named destinations out of 1000 (max. 131072) 36 words of extra memory for PDF output out of 10000 (max. 10000000)