This is pdfTeX, Version 3.14159-13d (Web2C 7.3.1) (format=pdflatex 2002.9.12) 5 FEB 2003 14:49 **lesson1 (lesson1.tex[/usr/athena/share/texmf/pdftex/config/pdftex.cfg] LaTeX2e <1998/12/01> patch level 1 Babel and hyphenation patterns for american, french, german, ngerman, n ohyphenation, loaded. (/usr/athena/share/texmf/tex/latex/base/slides.cls Document Class: slides 1997/08/15 v2.3z Standard LaTeX document class (/usr/athena/share/texmf/tex/latex/base/slides.def File: slides.def 1997/08/15 v2.3z SLiTeX definitions hacks, slides, \c@page=\count79 picture, mods, \@smashboxa=\box26 \@smashboxb=\box27 \@smashboxc=\box28 output, init) (/usr/athena/share/texmf/tex/latex/base/sfonts.def File: sfonts.def 1998/06/12 v2.2e Standard LaTeX slide font definitions (/usr/athena/share/texmf/tex/latex/base/ot1lcmss.fd File: ot1lcmss.fd 1998/06/12 v2.2e Standard LaTeX slide font definitions )) \c@minutes=\count80 \c@seconds=\count81 \c@mv@invisible=\count82 LaTeX Font Info: Overwriting symbol font `operators' in version `normal' (Font) OT1/cmr/m/n --> OT1/lcmss/m/n on input line 351. LaTeX Font Info: Overwriting symbol font `letters' in version `normal' (Font) OML/cmm/m/it --> OML/lcmm/m/it on input line 354. 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LaTeX Font Info: Overwriting symbol font `largesymbols' in version `invisibl e' (Font) OMX/cmex/m/n --> OMX/lcmex/m/In on input line 367. ) (/usr/athena/share/texmf/tex/latex/graphics/graphicx.sty Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR) (/usr/athena/share/texmf/tex/latex/graphics/keyval.sty Package: keyval 1999/03/16 v1.13 key=value parser (DPC) \KV@toks@=\toks14 ) (/usr/athena/share/texmf/tex/latex/graphics/graphics.sty Package: graphics 1999/02/16 v1.0l Standard LaTeX Graphics (DPC,SPQR) (/usr/athena/share/texmf/tex/latex/graphics/trig.sty Package: trig 1999/03/16 v1.09 sin cos tan (DPC) ) (/usr/athena/share/texmf/tex/latex/config/graphics.cfg) Package graphics Info: Driver file: pdftex.def on input line 80. 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LaTeX Font Info: ... okay on input line 6. LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 6. LaTeX Font Info: ... okay on input line 6. (/usr/athena/share/texmf/tex/context/base/supp-pdf.tex (/usr/athena/share/texmf/tex/context/base/supp-mis.tex loading : Context Support Macros / Missing \protectiondepth=\count84 \scratchcounter=\count85 \scratchdimen=\dimen104 \scratchskip=\skip41 \scratchmuskip=\muskip10 \scratchbox=\box29 \scratchread=\read2 \scratchwrite=\write3 \nextbox=\box30 \nextdepth=\dimen105 \everyline=\toks17 \!!counta=\count86 \!!countb=\count87 \recursecounter=\count88 ) loading : Context Support Macros / PDF \nofMPsegments=\count89 \nofMParguments=\count90 ) LaTeX Font Info: Try loading font information for OML+lcmm on input line 17. (/usr/athena/share/texmf/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 17 . 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(/usr/athena/share/texmf/tex/latex/base/ot1lcmtt.fd File: ot1lcmtt.fd 1998/06/12 v2.2e Standard LaTeX slide font definitions ) [2] [3] Overfull \hbox (10.1523pt too wide) in paragraph at lines 88--93 \OT1/lcmss/m/n/19.907 ma-chines, let me know, and I'll straighten things [] Overfull \hbox (28.05928pt too wide) in paragraph at lines 94--100 \OT1/lcmtt/m/n/19.907 http://www.activestate.com/Products/ActivePerl/ [] [4] [5] [6] [7] Overfull \hbox (49.4667pt too wide) in paragraph at lines 184--186 []\OT1/lcmss/m/sl/19.907 Always \OT1/lcmss/m/n/19.907 be-gin your pro-grams wit h ``\OT1/lcmtt/m/n/19.907 use strict;\OT1/lcmss/m/n/19.907 ''. [] [8] [9] [10] File: bptranslate.pl (verbatim) [11] Overfull \hbox (0.29802pt too wide) in paragraph at lines 275--280 \OT1/lcmss/m/n/19.907 with ``\OT1/lcmtt/m/n/19.907 my\OT1/lcmss/m/n/19.907 ''. This is due to the ``\OT1/lcmtt/m/n/19.907 use strict;\OT1/lcmss/m/n/19.907 '' [] [12] Overfull \hbox (22.86667pt too wide) in paragraph at lines 305--311 []\OT1/lcmss/m/n/19.907 The \OT1/lcmtt/m/n/19.907 read[]sequence \OT1/lcmss/m/n /19.907 func-tion re-turns a \OT1/lcmtt/m/n/19.907 Bio::Seq [] Overfull \hbox (3.49991pt too wide) in paragraph at lines 305--311 \OT1/lcmss/m/sl/19.907 ob-ject\OT1/lcmss/m/n/19.907 , which we as-sign to the v ari-able \OT1/lcmtt/m/n/19.907 $seq\OT1/lcmss/m/n/19.907 . [] Overfull \hbox (3.91508pt too wide) in paragraph at lines 305--311 \OT1/lcmss/m/n/19.907 func-tion which re-turns an-other \OT1/lcmtt/m/n/19.907 B io::Seq \OT1/lcmss/m/n/19.907 ob- [] Overfull \hbox (11.51761pt too wide) in paragraph at lines 305--311 \OT1/lcmss/m/n/19.907 This ob-ject is con-verted into an ac-tual \OT1/lcmss/m/s l/19.907 string [] Overfull \hbox (37.16194pt too wide) in paragraph at lines 305--311 \OT1/lcmss/m/n/19.907 (se-quence of char-ac-ters) us-ing the \OT1/lcmtt/m/n/19. 907 seq \OT1/lcmss/m/n/19.907 method. [] [13] Overfull \hbox (40.23505pt too wide) in paragraph at lines 325--328 []\OT1/lcmss/m/n/19.907 In \OT1/lcmtt/m/n/19.907 /mit/seven/7.91/perl[]module/t ranslate.pl\OT1/lcmss/m/n/19.907 , there [] Overfull \hbox (6.90782pt too wide) in paragraph at lines 336--336 [] \OT1/lcmtt/m/n/19.907 $codon = substr($sequence, $seqidx, 3);[] [] Overfull \hbox (38.63501pt too wide) in paragraph at lines 338--338 [] \OT1/lcmtt/m/n/19.907 push(@codon_list, $codons{$codon}||'X');[] [] [14] [15] [16] Overfull \hbox (1.0599pt too wide) in paragraph at lines 394--400 \OT1/lcmtt/m/n/19.907 "acgactagcaattcaca"\OT1/lcmss/m/n/19.907 . Within \OT1/lc mtt/m/n/19.907 translate\OT1/lcmss/m/n/19.907 , the [] [17] Overfull \hbox (26.37927pt too wide) in paragraph at lines 425--427 []\OT1/lcmss/m/n/19.907 The \OT1/lcmtt/m/n/19.907 @codons \OT1/lcmss/m/n/19.907 list stores the trans-lated residues. [] Overfull \hbox (0.47032pt too wide) in paragraph at lines 429--431 []\OT1/lcmss/m/n/19.907 The list of residues in \OT1/lcmtt/m/n/19.907 %codon[]l ist \OT1/lcmss/m/n/19.907 are joined [] [18] (lesson1.aux) ) Here is how much of TeX's memory you used: 837 strings out of 10631 10811 string characters out of 67877 55589 words of memory out of 263001 3839 multiletter control sequences out of 10000+0 8207 words of font info for 30 fonts, out of 400000 for 1000 14 hyphenation exceptions out of 1000 25i,6n,19p,201b,249s stack positions out of 300i,100n,500p,50000b,4000s Output written on lesson1.pdf (18 pages, 71709 bytes).