[Debian-med-packaging] Bug#831259: pycorrfit: FTBFS: latex errors
Lucas Nussbaum
lucas at debian.org
Thu Jul 14 09:54:06 UTC 2016
Source: pycorrfit
Version: 0.9.5+dfsg-1
Severity: serious
Tags: stretch sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20160714 qa-ftbfs
Justification: FTBFS on amd64
Hi,
During a rebuild of all packages in sid, your package failed to build on
amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/«BUILDDIR»/pycorrfit-0.9.5+dfsg'
> cd doc && pdflatex -synctex=1 -interaction=nonstopmode PyCorrFit_doc.tex
> This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
> restricted \write18 enabled.
> entering extended mode
> (./PyCorrFit_doc.tex
> LaTeX2e <2016/03/31> patch level 1
> Babel <3.9r> and hyphenation patterns for 3 language(s) loaded.
> (/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrartcl.cls
> Document Class: scrartcl 2016/06/14 v3.21 KOMA-Script document class (article)
> (/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrkbase.sty
> (/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrbase.sty
> (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrlfile.sty
> Package scrlfile, 2016/06/14 v3.21 KOMA-Script package (loading files)
> Copyright (C) Markus Kohm
>
> ))) (/usr/share/texlive/texmf-dist/tex/latex/koma-script/tocbasic.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrsize12pt.clo)
> (/usr/share/texlive/texmf-dist/tex/latex/koma-script/typearea.sty
> Package typearea, 2016/06/14 v3.21 KOMA-Script package (type area)
> Copyright (C) Frank Neukam, 1992-1994
> Copyright (C) Markus Kohm, 1994-
>
> )) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
> (/usr/share/texlive/texmf-dist/tex/latex/ucs/utf8x.def))
> (/usr/share/texlive/texmf-dist/tex/latex/ucs/ucs.sty
> (/usr/share/texlive/texmf-dist/tex/latex/ucs/data/uni-global.def))
> (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty
> (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf
> (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def)))
> (/usr/share/texlive/texmf-dist/tex/latex/SIstyle/sistyle.sty
> (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
> (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)))
> (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
> (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
> (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
> (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
> For additional information on amsmath, use the `?' option.
> (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))
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> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/cite/cite.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/subfig/subfig.sty
> (/usr/share/texlive/texmf-dist/tex/latex/caption/caption.sty
> (/usr/share/texlive/texmf-dist/tex/latex/caption/caption3.sty)))
> (/usr/share/texlive/texmf-dist/tex/latex/tools/tabularx.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
> (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
> (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
> Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
> <2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
> (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
> (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
> (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
> (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/xcolor/svgnam.def))
> (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
> (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
> (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)))
> (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
> (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
> (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
> (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
>
> Package hyperref Warning: Unexpected value for option `pdftex'
> (hyperref) is ignored on input line 4362.
>
> )
>
> Package hyperref Message: Driver: hpdftex.
>
> (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
> (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
> (/usr/share/texlive/texmf-dist/tex/latex/was/upgreek.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/doi/doi.sty)
> No file PyCorrFit_doc.aux.
> (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
> (/usr/share/texlive/texmf-dist/tex/latex/ucs/ucsencs.def)
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> *geometry* driver: auto-detecting
> *geometry* detected driver: pdftex
> (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
> [Loading MPS to PDF converter (version 2006.09.02).]
> ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
> (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
> (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
> (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
> (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
> <Images/PyCorrFit_logo_dark.pdf, id=4, 632.34161pt x 184.96548pt>
> <use Images/PyCorrFit_logo_dark.pdf>
> (/usr/share/texlive/texmf-dist/tex/latex/ucs/data/uni-0.def)
> <use Images/PyCorrFit_logo_dark.pdf> <use Images/PyCorrFit_logo_dark.pdf>
> [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map} <./Images/PyCorrFit_logo_
> dark.pdf>] (./PyCorrFit_doc_content.tex
> Underfull \hbox (badness 10000) in paragraph at lines 5--6
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> []\OT1/cmr/m/n/12 APD: Pho-ton Count-ing De-vice from PerkinElmer Op-to-elec-tr
> on-ics, Model: \OT1/cmtt/m/n/12 SPCM-CD3017
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> Overfull \hbox (20.19075pt too wide) in paragraph at lines 38--41
> \OT1/cmr/m/n/12 Correlator: Flex02-01D/C from cor-re-la-tor.com with the shippe
> d soft-ware \OT1/cmtt/m/n/12 flex02-1dc.exe\OT1/cmr/m/n/12 .
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> Overfull \hbox (2.02393pt too wide) in paragraph at lines 57--59
> \OT1/cmtt/m/n/12 pypi . python . org / pypi / pip$[][]\OT1/cmr/m/n/12 ) and can
> be in-stalled via[][][][][] \OT1/cmtt/m/n/12 pip install pycorrfit$ $[GUI]\OT1
> /cmr/m/n/12 .
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> [][][]\OT1/cmr/m/n/10 See also the wiki ar-ti-cle at [][]$\OT1/cmtt/m/n/10 http
> s : / / github . com / FCS-[]analysis / PyCorrFit / wiki /
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> <Images/PyCorrFit_Screenshot_Main.png, id=68, 1068.99374pt x 680.5425pt>
> <use Images/PyCorrFit_Screenshot_Main.png>
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> ! Class scrartcl Error: undefined old font command `\rm'.
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> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
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> l.92 ... = \SI{28}{\mu s})$. \label{fig:mainwin} }
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> ! Class scrartcl Error: undefined old font command `\rm'.
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> See the scrartcl class documentation for explanation.
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> \OT1/cmr/m/it/12 Py-Corr-Fit\OT1/cmr/m/n/12 . First, edit the code for [][]\OT1
> /cmtt/m/n/12 init[][].py \OT1/cmr/m/n/12 and then add the script \OT1/cmtt/m/n/
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> l.501 ...in the effective detection volume $V_{\rm
> eff} = \int W(\vec{r}) \...
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> ...
>
> l.548 ...of oberved particles $C = N/V = n/V_{\rm
> eff} = n/ (\pi^{3/2}w_0^2...
>
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> ! Class scrartcl Error: undefined old font command `\rm'.
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> See the scrartcl class documentation for explanation.
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> ...
>
> l.548 ...n to define the diffusion time $\tau_{\rm
> diff} = {w_0}^2/4D_t$ and...
>
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> ! Class scrartcl Error: undefined old font command `\rm'.
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> See the scrartcl class documentation for explanation.
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> ...
>
> l.551 G(\tau) \stackrel{\rm def}{=}
> G^{\rm D}(\tau) = \frac{1}{n} \overbrac...
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.551 G(\tau) \stackrel{\rm def}{=} G^{\rm
> D}(\tau) = \frac{1}{n} \overbrac...
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.551 ...c{\tau}{\tau_{\rm {diff}}} \right) ^{-1}}
> ^{\rm 2D} \overbrace{ \lef...
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.551 ...u}{\tau_{\rm {diff}}} \right) ^{-1}}^{\rm
> 2D} \overbrace{ \left(1+\...
>
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> ! Class scrartcl Error: undefined old font command `\rm'.
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> l.551 ...}^2 \, \tau_{\rm {diff}}} \right)^{-1/2}}
> ^{\rm 3D}
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> l.551 ..., \tau_{\rm {diff}}} \right)^{-1/2}}^{\rm
> 3D}
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> ...
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> l.560 G(\tau) \stackrel{\rm def}{=}
> G^{\rm T}(\tau) G^{\rm D}(\tau) = \left...
>
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> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.560 G(\tau) \stackrel{\rm def}{=} G^{\rm
> T}(\tau) G^{\rm D}(\tau) = \left...
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.560 ...ackrel{\rm def}{=} G^{\rm T}(\tau) G^{\rm
> D}(\tau) = \left( 1+ \fra...
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.560 ...T} \exp\left[-\frac{\tau}{\tau_{\rm trp}}
> \right] \right)G^{\rm D}(...
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.560 ...au}{\tau_{\rm trp}} \right] \right)G^{\rm
> D}(\tau)
>
> LaTeX Warning: Hyper reference `eq11' on page 19 undefined on input line 563.
>
>
> LaTeX Warning: Reference `eq11' on page 19 undefined on input line 563.
>
>
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>
>
> LaTeX Warning: Reference `eq12' on page 19 undefined on input line 574.
>
> [19]
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.577 G^{\rm
> D}(\tau) = \sum_{k=1}^m F_k G^{\rm D}(\tau) = \frac{1}{n} \sum...
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.577 G^{\rm D}(\tau) = \sum_{k=1}^m F_k G^{\rm
> D}(\tau) = \frac{1}{n} \sum...
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.577 ... \left(1+\frac{\tau}{\tau_{{\rm diff},k}}
> \right) ^{-1} \left(1+\fr...
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.577 ...au}{\textit{SP}^2 \, \tau_{{\rm diff},k}}
> \right)
>
> LaTeX Warning: Citation `Meseth1999' on page 20 undefined on input line 579.
>
>
> LaTeX Warning: Citation `Thompson1991' on page 20 undefined on input line 579.
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.582 G^{\rm
> D}(\tau) = \frac{1}{n \left( \sum_k F_k \alpha_k \right)^2} \s...
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.584 ...ell as the real molar fractions $F_k^{\rm
> cor}$ \cite{Thompson1991}
>
> LaTeX Warning: Citation `Thompson1991' on page 20 undefined on input line 584.
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
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> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.587 n = \frac{1}{G^{\rm D}(0)}
> \frac{\sum_k F_k^{\rm {cor}} \alpha_k^2}{\...
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.587 ...sum_k F_k^{\rm {cor}} \alpha_k \right)^2}
> \quad\mbox {with} \quad F...
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.587 ...sum_k F_k^{\rm {cor}} \alpha_k \right)^2}
> \quad\mbox {with} \quad F...
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.587 ...ight)^2} \quad\mbox {with} \quad F_k^{\rm
> {cor}} = \frac{F_k/\alpha...
>
>
> LaTeX Warning: Citation `Koppel1974' on page 20 undefined on input line 592.
>
>
> LaTeX Warning: Citation `Thompson1991' on page 20 undefined on input line 592.
>
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> 592.
>
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> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.595 n = \frac{1}{G^{\rm D}(0)}
> \left( \frac{S-B}{S} \right)^2 = \frac{1}{...
>
>
> LaTeX Warning: Citation `Weidemann2013' on page 20 undefined on input line 597.
>
>
>
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> Type H <return> for immediate help.
> ...
>
> l.600 G_{\times,\rm
> {cor}}(0) = G_{\times, \rm meas}(0) \left( \frac{S_1}{S...
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.600 G_{\times,\rm {cor}}(0) = G_{\times, \rm
> meas}(0) \left( \frac{S_1}{S...
>
>
> LaTeX Warning: Citation `Foo2012' on page 20 undefined on input line 605.
>
>
> LaTeX Warning: Citation `Ries2010' on page 20 undefined on input line 605.
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> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.608 G_\times (\tau) \stackrel{\rm def}{=}
> G_{12} (\tau) = \frac{\langle \...
>
> [20]
>
> LaTeX Warning: Citation `Weidemann2002' on page 21 undefined on input line 610.
>
>
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> Type H <return> for immediate help.
> ...
>
> l.613 ...\mathrm{y}^2}{4 D_t \tau + w_{0,\rm eff}}
> + \frac{d_\mathrm{z}^2}{4...
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.613 ...\mathrm{z}^2}{4 D_t \tau + z_{0,\rm eff}}
> \right)
>
> LaTeX Warning: Citation `Weidemann2002' on page 21 undefined on input line 615.
>
>
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>
> l.618 CC_1 \stackrel{\rm def}{=}
> \frac{G_\times(0)}{G_1(0)} & \propto & \fr...
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
>
> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
>
> l.618 ...} \nonumber \\ CC_2 \stackrel{\rm def}{=}
> \frac{G_\times(0)}{G_2(0)...
>
>
> LaTeX Warning: Citation `Bacia2012' on page 21 undefined on input line 620.
>
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> l.631 \end{align}
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
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> l.631 \end{align}
>
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> ! Class scrartcl Error: undefined old font command `\rm'.
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> l.631 \end{align}
>
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> ! Class scrartcl Error: undefined old font command `\rm'.
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> Type H <return> for immediate help.
> ...
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> l.631 \end{align}
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
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> Type H <return> for immediate help.
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> l.631 \end{align}
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
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> See the scrartcl class documentation for explanation.
> Type H <return> for immediate help.
> ...
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> l.631 \end{align}
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
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> Type H <return> for immediate help.
> ...
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> l.631 \end{align}
>
>
> ! Class scrartcl Error: undefined old font command `\rm'.
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> l.631 \end{align}
>
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>
> <Images/PyCorrFit_Screenshot_CSFCS.png, id=259, 1284.8pt x 783.92876pt>
> <use Images/PyCorrFit_Screenshot_CSFCS.png>
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> \OT1/cmr/m/n/12 The cor-re-la-tion func-tion is a su-per-po-si-tion of the two-
>
>
> LaTeX Warning: Citation `Ries2008' on page 30 undefined on input line 370.
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> ) [30]) [31]
> No file PyCorrFit_doc.bbl.
>
> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1200
> mkdir: cannot create directory '././sbuild-nonexistent': Permission denied
> mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1200
> This is METAFONT, Version 2.7182818 (TeX Live 2016/Debian) (preloaded base=mf)
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> Ok [185] [178] [179] [170] [186])
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> Ok [188] [189] [190]) ) ) )
> (some charht values had to be adjusted by as much as 0.06665pt)
> Font metrics written on tcrm1200.tfm.
> Output written on tcrm1200.600gf (128 characters, 28032 bytes).
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> mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcrm1200.600pk: successfully generated.
> [32] (./PyCorrFit_doc.aux (./PyCorrFit_doc_content.aux))
>
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>
> )
> (see the transcript file for additional information)pdfTeX warning (dest): name
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> b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt8.pfb></usr
> /share/texlive/texmf-dist/fonts/type1/public/amsfonts/euler/eurm10.pfb></usr/sh
> are/texlive/texmf-dist/fonts/type1/public/amsfonts/symbols/msam10.pfb>
> Output written on PyCorrFit_doc.pdf (32 pages, 552684 bytes).
> SyncTeX written on PyCorrFit_doc.synctex.gz.
> Transcript written on PyCorrFit_doc.log.
> make[1]: *** [override_dh_auto_build] Error 1
The full build log is available from:
http://people.debian.org/~lucas/logs/2016/07/14/pycorrfit_0.9.5+dfsg-1_unstable_gcc5.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
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