This is pdfeTeX, Version 3.141592-1.21a-2.2 (Web2C 7.5.4) (format=pdflatex 2011.8.7) 5 JAN 2012 04:51 entering extended mode **/home/projects/WholeCell/simulation/output/runSimulation/2012_01_03_20_29_11/ summary.tex (/home/projects/WholeCell/simulation/output/runSimulation/2012_01_03_20_29_11/s ummary.tex LaTeX2e <2003/12/01> Babel and hyphenation patterns for american, french, german, ngerman, b ahasa, basque, bulgarian, catalan, croatian, czech, danish, dutch, esperanto, e stonian, finnish, greek, icelandic, irish, italian, latin, magyar, norsk, polis h, portuges, romanian, russian, serbian, slovak, slovene, spanish, swedish, tur kish, ukrainian, nohyphenation, loaded. (/usr/share/texmf/tex/latex/base/article.cls Document Class: article 2004/02/16 v1.4f Standard LaTeX document class (/usr/share/texmf/tex/latex/base/size12.clo File: size12.clo 2004/02/16 v1.4f 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/share/texmf/tex/latex/graphics/graphicx.sty Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR) (/usr/share/texmf/tex/latex/graphics/keyval.sty Package: keyval 1999/03/16 v1.13 key=value parser (DPC) \KV@toks@=\toks14 ) (/usr/share/texmf/tex/latex/graphics/graphics.sty Package: graphics 2001/07/07 v1.0n Standard LaTeX Graphics (DPC,SPQR) (/usr/share/texmf/tex/latex/graphics/trig.sty Package: trig 1999/03/16 v1.09 sin cos tan (DPC) ) (/usr/share/texmf/tex/latex/graphics/graphics.cfg File: graphics.cfg 2005/02/03 v1.3 graphics configuration of teTeX/TeXLive ) Package graphics Info: Driver file: pdftex.def on input line 80. (/usr/share/texmf/tex/latex/graphics/pdftex.def File: pdftex.def 2002/06/19 v0.03k graphics/color for pdftex \Gread@gobject=\count87 )) \Gin@req@height=\dimen103 \Gin@req@width=\dimen104 ) (/usr/share/texmf/tex/latex/hyperref/hyperref.sty Package: hyperref 2003/11/30 v6.74m Hypertext links for LaTeX \@linkdim=\dimen105 \Hy@linkcounter=\count88 \Hy@pagecounter=\count89 (/usr/share/texmf/tex/latex/hyperref/pd1enc.def File: pd1enc.def 2003/11/30 v6.74m Hyperref: PDFDocEncoding definition (HO) ) (/usr/share/texmf/tex/latex/hyperref/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 1880. Package hyperref Info: Link nesting OFF on input line 1885. Package hyperref Info: Hyper index ON on input line 1888. Package hyperref Info: Plain pages ON on input line 1893. Package hyperref Info: Backreferencing OFF on input line 1900. Implicit mode ON; LaTeX internals redefined Package hyperref Info: Bookmarks ON on input line 2004. (/usr/share/texmf/tex/latex/url/url.sty \Urlmuskip=\muskip10 Package: url 2004/03/15 ver 3.1 Verb mode for urls, etc. ) LaTeX Info: Redefining \url on input line 2143. \Fld@menulength=\count90 \Field@Width=\dimen106 \Fld@charsize=\dimen107 \Choice@toks=\toks15 \Field@toks=\toks16 Package hyperref Info: Hyper figures OFF on input line 2618. Package hyperref Info: Link nesting OFF on input line 2623. Package hyperref Info: Hyper index ON on input line 2626. Package hyperref Info: backreferencing OFF on input line 2633. Package hyperref Info: Link coloring OFF on input line 2638. \c@Item=\count91 \c@Hfootnote=\count92 ) *hyperref using default driver hpdftex* (/usr/share/texmf/tex/latex/hyperref/hpdftex.def File: hpdftex.def 2003/11/30 v6.74m Hyperref driver for pdfTeX (/usr/share/texmf/tex/latex/psnfss/pifont.sty Package: pifont 2004/09/15 PSNFSS-v9.2 Pi font support (SPQR) LaTeX Font Info: Try loading font information for U+pzd on input line 63. (/usr/share/texmf/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 64. (/usr/share/texmf/tex/latex/psnfss/upsy.fd File: upsy.fd 2001/06/04 font definitions for U/psy. )) \Fld@listcount=\count93 \@outlinefile=\write3 ) (/usr/share/texmf/tex/latex/fancyhdr/fancyhdr.sty \fancy@headwidth=\skip43 \f@ncyO@elh=\skip44 \f@ncyO@erh=\skip45 \f@ncyO@olh=\skip46 \f@ncyO@orh=\skip47 \f@ncyO@elf=\skip48 \f@ncyO@erf=\skip49 \f@ncyO@olf=\skip50 \f@ncyO@orf=\skip51 ) (/usr/share/texmf/tex/latex/tools/afterpage.sty Package: afterpage 1995/10/27 v1.08 After-Page Package (DPC) \AP@output=\toks17 \AP@partial=\box26 \AP@footins=\box27 ) (/usr/share/texmf/tex/latex/caption/caption.sty Package: caption 2006/01/12 v3.0i Customising captions (AR) (/usr/share/texmf/tex/latex/caption/caption3.sty Package: caption3 2006/01/12 v3.0i caption3 kernel (AR) \captionmargin=\dimen108 \captionmarginx=\dimen109 \captionwidth=\dimen110 \captionindent=\dimen111 \captionparindent=\dimen112 \captionhangindent=\dimen113 ) Package caption Info: hyperref package v6.74m (or newer) detected on input line 292. ) (/usr/share/texmf/tex/latex/base/fontenc.sty Package: fontenc 2004/02/22 v1.99f Standard LaTeX package (/usr/share/texmf/tex/latex/base/t1enc.def File: t1enc.def 2004/02/22 v1.99f Standard LaTeX file LaTeX Font Info: Redeclaring font encoding T1 on input line 43. )) (/usr/share/texmf/tex/latex/lm/lmodern.sty Package: lmodern 2003/07/16 ) (/usr/share/texmf/tex/latex/cmbright/cmbright.sty Package: cmbright 2002/05/25 v7.1 (WaS) LaTeX Font Info: Redeclaring symbol font `operators' on input line 30. LaTeX Font Info: Overwriting symbol font `operators' in version `normal' (Font) OT1/cmr/m/n --> OT1/cmbr/m/n on input line 30. LaTeX Font Info: Overwriting symbol font `operators' in version `bold' (Font) OT1/cmr/bx/n --> OT1/cmbr/m/n on input line 30. LaTeX Font Info: Redeclaring symbol font `letters' on input line 31. LaTeX Font Info: Overwriting symbol font `letters' in version `normal' (Font) OML/cmm/m/it --> OML/cmbrm/m/it on input line 31. LaTeX Font Info: Overwriting symbol font `letters' in version `bold' (Font) OML/cmm/b/it --> OML/cmbrm/m/it on input line 31. LaTeX Font Info: Redeclaring symbol font `symbols' on input line 32. LaTeX Font Info: Overwriting symbol font `symbols' in version `normal' (Font) OMS/cmsy/m/n --> OMS/cmbrs/m/n on input line 32. LaTeX Font Info: Overwriting symbol font `symbols' in version `bold' (Font) OMS/cmsy/b/n --> OMS/cmbrs/m/n on input line 32. LaTeX Font Info: Redeclaring math alphabet \mathit on input line 33. LaTeX Font Info: Overwriting math alphabet `\mathit' in version `normal' (Font) OT1/cmr/m/it --> OT1/cmbr/m/sl on input line 33. LaTeX Font Info: Overwriting math alphabet `\mathit' in version `bold' (Font) OT1/cmr/bx/it --> OT1/cmbr/m/sl on input line 33. LaTeX Font Info: Redeclaring math alphabet \mathbf on input line 34. LaTeX Font Info: Overwriting math alphabet `\mathbf' in version `normal' (Font) OT1/cmr/bx/n --> OT1/cmbr/bx/n on input line 34. LaTeX Font Info: Overwriting math alphabet `\mathbf' in version `bold' (Font) OT1/cmr/bx/n --> OT1/cmbr/bx/n on input line 34. LaTeX Font Info: Redeclaring math alphabet \mathtt on input line 35. LaTeX Font Info: Overwriting math alphabet `\mathtt' in version `normal' (Font) OT1/cmtt/m/n --> OT1/cmtl/m/n on input line 35. LaTeX Font Info: Overwriting math alphabet `\mathtt' in version `bold' (Font) OT1/cmtt/m/n --> OT1/cmtl/m/n on input line 35. LaTeX Font Info: Redeclaring math symbol \alpha on input line 37. LaTeX Font Info: Redeclaring math symbol \beta on input line 38. LaTeX Font Info: Redeclaring math symbol \gamma on input line 39. LaTeX Font Info: Redeclaring math symbol \delta on input line 40. LaTeX Font Info: Redeclaring math symbol \epsilon on input line 41. LaTeX Font Info: Redeclaring math symbol \zeta on input line 42. LaTeX Font Info: Redeclaring math symbol \Gamma on input line 43. LaTeX Font Info: Redeclaring math symbol \eta on input line 44. LaTeX Font Info: Redeclaring math symbol \theta on input line 45. LaTeX Font Info: Redeclaring math symbol \iota on input line 46. LaTeX Font Info: Redeclaring math symbol \kappa on input line 47. LaTeX Font Info: Redeclaring math symbol \lambda on input line 48. LaTeX Font Info: Redeclaring math symbol \mu on input line 49. LaTeX Font Info: Redeclaring math symbol \nu on input line 50. LaTeX Font Info: Redeclaring math symbol \xi on input line 51. LaTeX Font Info: Redeclaring math symbol \pi on input line 52. LaTeX Font Info: Redeclaring math symbol \rho on input line 53. LaTeX Font Info: Redeclaring math symbol \sigma on input line 54. LaTeX Font Info: Redeclaring math symbol \tau on input line 55. LaTeX Font Info: Redeclaring math symbol \upsilon on input line 56. LaTeX Font Info: Redeclaring math symbol \phi on input line 57. LaTeX Font Info: Redeclaring math symbol \chi on input line 58. LaTeX Font Info: Redeclaring math symbol \psi on input line 59. LaTeX Font Info: Redeclaring math symbol \omega on input line 60. LaTeX Font Info: Redeclaring math symbol \varepsilon on input line 61. LaTeX Font Info: Redeclaring math symbol \vartheta on input line 62. LaTeX Font Info: Redeclaring math symbol \varpi on input line 63. LaTeX Font Info: Redeclaring math symbol \varrho on input line 64. LaTeX Font Info: Redeclaring math symbol \varsigma on input line 65. LaTeX Font Info: Redeclaring math symbol \varphi on input line 66. LaTeX Font Info: Try loading font information for T1+cmbr on input line 131. (/usr/share/texmf/tex/latex/cmbright/t1cmbr.fd File: t1cmbr.fd 1999/05/12 v7.3 (WaS) )) (/usr/share/texmf/tex/latex/pdfpages/pdfpages.sty Package: pdfpages 2004/01/31 v0.3e Insert pages of external PDF documents (AM) (/usr/share/texmf/tex/latex/base/ifthen.sty Package: ifthen 2001/05/26 v1.1c Standard LaTeX ifthen package (DPC) ) (/usr/share/texmf/tex/latex/tools/calc.sty Package: calc 1998/07/07 v4.1b Infix arithmetic (KKT,FJ) \calc@Acount=\count94 \calc@Bcount=\count95 \calc@Adimen=\dimen114 \calc@Bdimen=\dimen115 \calc@Askip=\skip52 \calc@Bskip=\skip53 LaTeX Info: Redefining \setlength on input line 59. LaTeX Info: Redefining \addtolength on input line 60. \calc@denominator=\count96 ) (/usr/share/texmf/tex/latex/eso-pic/eso-pic.sty Package: eso-pic 2002/11/16 v1.1b eso-pic (RN) (/usr/share/texmf/tex/latex/ms/everyshi.sty Package: everyshi 2001/05/15 v3.00 EveryShipout Package (MS) )) (/usr/share/texmf/tex/latex/pdfpages/pppdftex.def File: pppdftex.def 2004/01/31 v0.3e Pdfpages driver for pdfTeX (AM) ) \AM@pagebox=\box28 \AM@toc@title=\toks18 \c@AM@survey=\count97 ) (/usr/share/texmf/tex/latex/tocloft/tocloft.sty Package: tocloft 2003/09/26 v2.3c parameterised ToC, etc., typesetting Package tocloft Note: The document has section divisions. \cftparskip=\skip54 \cftbeforetoctitleskip=\skip55 \cftaftertoctitleskip=\skip56 \cftbeforepartskip=\skip57 \cftpartnumwidth=\skip58 \cftpartindent=\skip59 \cftbeforesecskip=\skip60 \cftsecindent=\skip61 \cftsecnumwidth=\skip62 \cftbeforesubsecskip=\skip63 \cftsubsecindent=\skip64 \cftsubsecnumwidth=\skip65 \cftbeforesubsubsecskip=\skip66 \cftsubsubsecindent=\skip67 \cftsubsubsecnumwidth=\skip68 \cftbeforeparaskip=\skip69 \cftparaindent=\skip70 \cftparanumwidth=\skip71 \cftbeforesubparaskip=\skip72 \cftsubparaindent=\skip73 \cftsubparanumwidth=\skip74 \cftbeforeloftitleskip=\skip75 \cftafterloftitleskip=\skip76 \cftbeforefigskip=\skip77 \cftfigindent=\skip78 \cftfignumwidth=\skip79 \c@lofdepth=\count98 \c@lotdepth=\count99 \cftbeforelottitleskip=\skip80 \cftafterlottitleskip=\skip81 \cftbeforetabskip=\skip82 \cfttabindent=\skip83 \cfttabnumwidth=\skip84 ) (/usr/share/texmf/tex/latex/xcolor/xcolor.sty Package: xcolor 2004/07/04 v2.00 LaTeX color extensions (UK) (/usr/share/texmf/tex/latex/graphics/color.cfg File: color.cfg 2005/02/03 v1.3 color configuration of teTeX/TeXLive ) Package xcolor Info: Driver file: pdftex.def on input line 136. Package xcolor Info: Color model `cmy' added on input line 972. Package xcolor Info: Color model `hsb' added on input line 980. Package xcolor Info: Color model `HTML' added on input line 1000. Package xcolor Info: Color model `HSB' added on input line 1006. Package xcolor Info: Color model `Gray' added on input line 1012. ) (/usr/share/texmf/tex/latex/chngpage/chngpage.sty Package: chngpage 2003/08/10 v1.2 change page layout \c@cp@cnt=\count100 \c@cp@tempcnt=\count101 ) (/usr/share/texmf/tex/latex/sectsty/sectsty.sty Package: sectsty 2002/02/25 v2.0.2 Commands to change all sectional heading sty les ) (/usr/share/texmf/tex/latex/rotating/rotating.sty Package: rotating 1997/09/26 v2.13 Rotation package \c@r@tfl@t=\count102 \rot@float@box=\box29 ) (/home/projects/WholeCell/simulation/output/runSimulation/2012_01_03_20_29_11/s ummary.aux) \openout1 = `summary.aux'. LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 41. LaTeX Font Info: ... okay on input line 41. LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 41. LaTeX Font Info: ... okay on input line 41. LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 41. LaTeX Font Info: ... okay on input line 41. LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 41. LaTeX Font Info: ... okay on input line 41. LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 41. LaTeX Font Info: ... okay on input line 41. LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 41. LaTeX Font Info: ... okay on input line 41. LaTeX Font Info: Checking defaults for PD1/pdf/m/n on input line 41. LaTeX Font Info: ... okay on input line 41. (/usr/share/texmf/tex/context/base/supp-pdf.tex (/usr/share/texmf/tex/context/base/supp-mis.tex loading : Context Support Macros / Miscellaneous (2004.10.26) \protectiondepth=\count103 \scratchcounter=\count104 \scratchtoks=\toks19 \scratchdimen=\dimen116 \scratchskip=\skip85 \scratchmuskip=\muskip11 \scratchbox=\box30 \scratchread=\read1 \scratchwrite=\write4 \zeropoint=\dimen117 \onepoint=\dimen118 \onebasepoint=\dimen119 \minusone=\count105 \thousandpoint=\dimen120 \onerealpoint=\dimen121 \emptytoks=\toks20 \nextbox=\box31 \nextdepth=\dimen122 \everyline=\toks21 \!!counta=\count106 \!!countb=\count107 \recursecounter=\count108 ) loading : Context Support Macros / PDF (2004.03.26) \nofMPsegments=\count109 \nofMParguments=\count110 \MPscratchCnt=\count111 \MPscratchDim=\dimen123 \MPnumerator=\count112 \everyMPtoPDFconversion=\toks22 ) Package hyperref Info: Link coloring OFF on input line 41. (/usr/share/texmf/tex/latex/hyperref/nameref.sty Package: nameref 2003/12/03 v2.21 Cross-referencing by name of section \c@section@level=\count113 ) LaTeX Info: Redefining \ref on input line 41. LaTeX Info: Redefining \pageref on input line 41. (/home/projects/WholeCell/simulation/output/runSimulation/2012_01_03_20_29_11/s ummary.out) (/home/projects/WholeCell/simulation/output/runSimulation/2012_01_03_20_29_11/s ummary.out) \openout3 = `summary.out'. (/usr/share/texmf/tex/latex/ms/ragged2e.sty Package: ragged2e 2003/03/25 v2.04 ragged2e Package (MS) (/usr/share/texmf/tex/latex/ms/everysel.sty Package: everysel 1999/06/08 v1.03 EverySelectfont Package (MS) LaTeX Info: Redefining \selectfont on input line 125. ) \CenteringLeftskip=\skip86 \RaggedLeftLeftskip=\skip87 \RaggedRightLeftskip=\skip88 \CenteringRightskip=\skip89 \RaggedLeftRightskip=\skip90 \RaggedRightRightskip=\skip91 \CenteringParfillskip=\skip92 \RaggedLeftParfillskip=\skip93 \RaggedRightParfillskip=\skip94 \JustifyingParfillskip=\skip95 \CenteringParindent=\skip96 \RaggedLeftParindent=\skip97 \RaggedRightParindent=\skip98 \JustifyingParindent=\skip99 ) Package caption Info: rotating package v2.0 (or newer) detected on input line 4 1. ABD: EveryShipout initializing macros File: data/summaryCoverPage.pdf Graphic file (type pdf) File: data/summaryCoverPage.pdf Graphic file (type pdf) File: data/summaryCoverPage.pdf Graphic file (type pdf) File: data/summaryCoverPage.pdf Graphic file (type pdf) File: data/summaryCoverPage.pdf Graphic file (type pdf) [1 <./data/summaryCoverPage.pdf Warning: pdflatex (file ./data/summaryCoverPage.pdf): pdf inclusion: Page Group detected which pdfTeX can't handle. Ignoring it. {/usr/share/texmf-var/fonts/map/pdftex/updmap/pdftex.map}>] LaTeX Font Warning: Font shape `T1/cmbr/bx/it' undefined (Font) using `T1/cmbr/bx/n' instead on input line 59. (/home/projects/WholeCell/simulation/output/runSimulation/2012_01_03_20_29_11/s ummary.toc) \tf@toc=\write5 \openout5 = `summary.toc'. [2] (/home/projects/WholeCell/simulation/output/runSimulation/2012_01_03_20_29_11/s ummary.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) Here is how much of TeX's memory you used: 4806 strings out of 94500 68063 string characters out of 1176767 125453 words of memory out of 1000000 7902 multiletter control sequences out of 10000+50000 9155 words of font info for 23 fonts, out of 500000 for 2000 580 hyphenation exceptions out of 1000 35i,16n,43p,320b,393s stack positions out of 1500i,500n,5000p,200000b,5000s PDF statistics: 36 PDF objects out of 300000 4 named destinations out of 131072 37 words of extra memory for PDF output out of 65536 Output written on /home/projects/WholeCell/simulation/output/runSimulation/2012 _01_03_20_29_11/summary.pdf (2 pages, 71617 bytes).