This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) (format=pdflatex 2008.10.1) 15 OCT 2008 22:06 entering extended mode %&-line parsing enabled. **summary.tex (./summary.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. 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Package textcomp Info: Setting ptmj sub-encoding to TS1/4 on input line 326. ) (./summary.aux) \openout1 = `summary.aux'. LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 29. LaTeX Font Info: ... okay on input line 29. LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 29. LaTeX Font Info: ... okay on input line 29. LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 29. LaTeX Font Info: ... okay on input line 29. LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 29. LaTeX Font Info: ... okay on input line 29. LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 29. LaTeX Font Info: ... okay on input line 29. LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 29. LaTeX Font Info: ... okay on input line 29. LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 29. LaTeX Font Info: Try loading font information for TS1+cmr on input line 29. (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd File: ts1cmr.fd 1999/05/25 v2.5h Standard LaTeX font definitions ) LaTeX Font Info: ... okay on input line 29. [1 {/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./summary.toc) \tf@toc=\write3 \openout3 = `summary.toc'. [2 ] [3 ] (./timeline/timeline.tex File: timeline/output.pdf Graphic file (type pdf) LaTeX Warning: `h' float specifier changed to `ht'. [4 ] [5 <./timeline/output.pdf pdfTeX warning: pdflatex (file ./timeline/output.pdf): PDF inclusion: Page Grou p detected which pdfTeX can't handle. Ignoring it. >] [6 ] [7] 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! ) [8] (./pavan/eg.tex Overfull \hbox (1.9237pt too wide) in paragraph at lines 3--11 [] \OT1/cmr/m/n/12 The mea-sure-ments are nor-mally dis-tributed with known sta n- [] (./pavan/grove.lisp LaTeX Font Info: Try loading font information for TS1+cmtt on input line 4. (/usr/share/texmf-texlive/tex/latex/base/ts1cmtt.fd File: ts1cmtt.fd 1999/05/25 v2.5h Standard LaTeX font definitions ) Overfull \hbox (44.69916pt too wide) in paragraph at lines 4--5 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (13.19922pt too wide) in paragraph at lines 13--14 [][][][][][][][][][][][][][][][][][][][][][][][][] [] Underfull \hbox (badness 10000) in paragraph at lines 18--19 [][][][][][][][][][][][][][][] [] Overfull \hbox (592.7981pt too wide) in paragraph at lines 23--24 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (63.59912pt too wide) in paragraph at lines 27--28 [][][][][][][][][][][][][][][][][][][][][] [] Underfull \hbox (badness 10000) in paragraph at lines 28--29 [][][][][][][][][][][][][][][] [] ) Overfull \hbox (88.79907pt too wide) in paragraph at lines 37--24 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] (./pavan/grovelr2.lisp Overfull \hbox (13.19922pt too wide) in paragraph at lines 13--14 [][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (13.19922pt too wide) in paragraph at lines 16--17 [][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (0.59924pt too wide) in paragraph at lines 21--22 [][][][][][][][][][][][][] [] Overfull \hbox (25.7992pt too wide) in paragraph at lines 32--33 [][][][][][][][][][][][][] [] Underfull \hbox (badness 10000) in paragraph at lines 35--36 [][][][][][][][][][][][][][][][][][][][][][][][][][][] [] ) LaTeX Warning: Float too large for page by 27.96663pt on input line 25. [9 ] [10] [11] Overfull \hbox (8.52953pt too wide) in paragraph at lines 27--30 \OT1/cmr/m/n/12 from other source.Here p(A/G)=p(A/$[]$)=Pa and p(T/G)= Pt.The [] Underfull \hbox (badness 10000) in paragraph at lines 27--30 [] Underfull \hbox (badness 10000) in paragraph at lines 33--35 [] File: pavan/test1.png Graphic file (type png) File: pavan/test2.png Graphic file (type png) Overfull \hbox (3.81674pt too wide) in paragraph at lines 40--54 \OT1/cmr/m/n/12 be-cause the like-li-hood ra-tion cri-te-ria is high re-sult-in g in the match- [] ) [12] [13 <./pavan/test1.png (PNG copy)>] [14 <./pavan/test2.png (PNG copy)>] (./matt/example.tex [15 ] [16 ] File: matt/filename.png Graphic file (type png) LaTeX Warning: `h' float specifier changed to `ht'. [17 ] [18 <./matt/filename.png (PNG copy)>] File: matt/filename2.png Graphic file (type png) [19 <./matt/filename2.png (PNG copy)>] (./matt/evett94.lisp Overfull \hbox (38.39917pt too wide) in paragraph at lines 15--16 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (38.39917pt too wide) in paragraph at lines 21--22 [][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (38.39917pt too wide) in paragraph at lines 33--34 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] Overfull \hbox (38.39917pt too wide) in paragraph at lines 38--39 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] [] )) [20 ] [21] (./summary.bbl) [22 ] (./summary.aux) ) Here is how much of TeX's memory you used: 3300 strings out of 95086 44341 string characters out of 1183255 139251 words of memory out of 1500000 6426 multiletter control sequences out of 10000+50000 11251 words of font info for 41 fonts, out of 1200000 for 2000 28 hyphenation exceptions out of 8191 29i,7n,32p,463b,1214s stack positions out of 5000i,500n,6000p,200000b,5000s Output written on summary.pdf (22 pages, 177409 bytes). PDF statistics: 163 PDF objects out of 1000 (max. 8388607) 0 named destinations out of 1000 (max. 131072) 26 words of extra memory for PDF output out of 10000 (max. 10000000)