Test suite issue for BiocStyle
Hi,
I'm trying to package for Debian. When running the test suite I get:
$ LC_ALL=C R --no-save <tests/run_tests.R
R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
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Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.
> BiocGenerics:::testPackage("BiocStyle")
Writing to file maketitle_test_1.tex
Processing code chunks with options ...
1 : keep.source term tex (label = style, maketitle_test_1.Rnw:5)
You can now run (pdf)latex on 'maketitle_test_1.tex'
Timing stopped at: 1.27 0.472 1.729
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'maketitle_test_1.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Argument of \Hy@scantitle has an extra }.
<inserted text>
\par
l.166 \renewcommand{\title}
[1]{\def\@bioctitle{#1}\@oldtitle{#1}}
! Paragraph ended before \Hy@scantitle was complete.
<to be read again>
\par
l.166 \renewcommand{\title}
[1]{\def\@bioctitle{#1}\@oldtitle{#1}}
! LaTeX Error: Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Illegal parameter number in definition of \@.
<to be read again>
1
l.166 \renewcommand{\title}[1]{\def\@bioctitle{#1
}\@oldtitle{#1}}
! Use of \@ doesn't match its definition.
l.166 ...command{\title}[1]{\def\@bioctitle{#1}\@o
ldtitle{#1}}
If you say, e.g., `\def\a1{...}', then you must always
put `1' after `\a', since control sequence names are
! You can't use `macro parameter character #' in horizontal mode.
l.166 ...title}[1]{\def\@bioctitle{#1}\@oldtitle{#
1}}
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! LaTeX Error: Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
So I tried to check other things:
$ R CMD Sweave LatexStyle2.Rnw
$ pdflatex LatexStyle2.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./LatexStyle2.tex
LaTeX2e <2019-10-01> patch level 3
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2019/10/25 v1.4k Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/lib/R/site-library/BiocStyle/resources/tex/Bioconductor.sty
LaTeX Warning: You have requested package `/usr/lib/R/site-library/BiocStyle/resources/tex/Bioconductor',
but the package provides `Bioconductor'.
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/dvipsnam.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifluatex.sty)))
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hycolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/xcolor-patch.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hopatch.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/uniquecounter.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifxetex.sty))
Package geometry Warning: Over-specification in `h'-direction.
`width' (384.1122pt) is ignored.
(/usr/share/texlive/texmf-dist/tex/latex/bera/beramono.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty)
(/usr/share/texlive/texmf-dist/tex/latex/titlesec/titlesec.sty)
(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty)
! LaTeX Error: Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.164 \let\@bi
octitle\@empty
?
So this boils down to an issue in file
inst/resources/tex/Bioconductor.sty
...
163 %% Title
164 \let\@bioctitle\@empty
165 \let\@oldtitle\title
166 \renewcommand{\title}[1]{\def\@bioctitle{#1}\@oldtitle{#1}}
...
I admit line 164 looks not really suspicious to me - so may be
something is wrong before that line.
Could you please have a look?
Kind regards
Andreas.
--
http://fam-tille.de
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