Latex error when using BiocStyle
0
0
Entering edit mode
@freek-manders-23560
Last seen 23 months ago

I can't get the latex style of BiocStyle to work on my current macbook. It worked fine on a previous macbook. I'm getting an error about missing \begin{document} , even though it's in the file. Knitting a html document with BiocStyle does seem to work. Compiling a simple .tex file without BiocStyle also seems to work fine. I have no idea what's going wrong. It would be great if somebody could help me figure out what's going wrong. I'm using MacTex2020. I have added a minimal example below:

\documentclass{article}

<<style, eval=TRUE, echo=FALSE, results=tex>>=
    BiocStyle::latex()
@


\begin{document}
\SweaveOpts{concordance=TRUE}
This is a test
\end{document}

Here is my session info. The first part of the log file is below that.

R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BiocStyle_2.14.4                            MutationalPatterns_1.6.2                   
 [3] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2     GenomicFeatures_1.38.2                     
 [5] AnnotationDbi_1.48.0                        BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1
 [7] BSgenome.Hsapiens.UCSC.hg19_1.4.0           BSgenome_1.54.0                            
 [9] rtracklayer_1.46.0                          Biostrings_2.54.0                          
[11] XVector_0.26.0                              testthat_2.3.2                             
[13] NMF_0.22.0                                  cluster_2.1.0                              
[15] rngtools_1.5                                pkgmaker_0.31.1                            
[17] registry_0.5-1                              GenomicRanges_1.38.0                       
[19] GenomeInfoDb_1.22.1                         IRanges_2.20.2                             
[21] S4Vectors_0.24.4                            Biobase_2.46.0                             
[23] BiocGenerics_0.32.0                         devtools_2.3.0                             
[25] usethis_1.6.1                              

loaded via a namespace (and not attached):
  [1] backports_1.1.7             BiocFileCache_1.10.2        plyr_1.8.6                  lazyeval_0.2.2             
  [5] BiocParallel_1.20.1         ggplot2_3.3.1               gridBase_0.4-7              digest_0.6.25              
  [9] htmltools_0.4.0             foreach_1.5.0               fansi_0.4.1                 magrittr_1.5               
 [13] memoise_1.1.0               covr_3.5.0                  doParallel_1.0.15           remotes_2.1.1              
 [17] matrixStats_0.56.0          askpass_1.1                 prettyunits_1.1.1           colorspace_1.4-1           
 [21] blob_1.2.1                  rappdirs_0.3.1              xfun_0.14                   dplyr_1.0.0                
 [25] callr_3.4.3                 crayon_1.3.4                RCurl_1.98-1.2              roxygen2_7.1.0             
 [29] VariantAnnotation_1.32.0    iterators_1.0.12            glue_1.4.1                  gtable_0.3.0               
 [33] zlibbioc_1.32.0             DelayedArray_0.12.3         pkgbuild_1.0.8              SingleCellExperiment_1.8.0 
 [37] scales_1.1.1                ccfindR_1.6.0               DBI_1.1.0                   bibtex_0.4.2.2             
 [41] Rcpp_1.0.4.6                xtable_1.8-4                progress_1.2.2              bit_1.1-15.2               
 [45] praise_1.0.0                xopen_1.0.0                 rex_1.2.0                   httr_1.4.1                 
 [49] RColorBrewer_1.1-2          ellipsis_0.3.1              pkgconfig_2.0.3             XML_3.99-0.3               
 [53] farver_2.0.3                dbplyr_1.4.4                tidyselect_1.1.0            labeling_0.3               
 [57] rlang_0.4.6                 reshape2_1.4.4              munsell_0.5.0               tools_3.6.3                
 [61] cli_2.0.2                   generics_0.0.2              RSQLite_2.2.0               evaluate_0.14              
 [65] stringr_1.4.0               ggdendro_0.1-20             yaml_2.2.1                  processx_3.4.2             
 [69] knitr_1.28                  bit64_0.9-7                 fs_1.4.1                    purrr_0.3.4                
 [73] pracma_2.2.9                xml2_1.3.2                  biomaRt_2.42.1              compiler_3.6.3             
 [77] rstudioapi_0.11             curl_4.3                    tibble_3.0.1                stringi_1.4.6              
 [81] ps_1.3.3                    desc_1.2.0                  lattice_0.20-41             Matrix_1.2-18              
 [85] vctrs_0.3.1                 pillar_1.4.4                lifecycle_0.2.0             BiocManager_1.30.10        
 [89] Rdpack_0.11-1               cowplot_1.0.0               bitops_1.0-6                rcmdcheck_1.3.3            
 [93] gbRd_0.4-11                 R6_2.4.1                    sessioninfo_1.1.1           codetools_0.2-16           
 [97] MASS_7.3-51.6               assertthat_0.2.1            pkgload_1.1.0               SummarizedExperiment_1.16.1
[101] openssl_1.4.1               rprojroot_1.3-2             withr_2.2.0                 GenomicAlignments_1.22.1   
[105] Rsamtools_2.2.3             GenomeInfoDbData_1.2.2      hms_0.5.3                   grid_3.6.3                 
[109] tidyr_1.1.0                 rmarkdown_2.2

First part of log file:

This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020) (preloaded format=pdflatex 2020.5.1)  15 JUN 2020 15:44
entering extended mode
 restricted \write18 enabled.
 %&-line parsing enabled.
**test.tex
(./test.tex
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-03-06>
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/article.cls
Document Class: article 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/size10.clo
File: size10.clo 2019/12/20 v1.4l Standard LaTeX file (size option)
)
\c@part=\count167
\c@section=\count168
\c@subsection=\count169
\c@subsubsection=\count170
\c@paragraph=\count171
\c@subparagraph=\count172
\c@figure=\count173
\c@table=\count174
\abovecaptionskip=\skip47
\belowcaptionskip=\skip48
\bibindent=\dimen134
)
(/Users/freekmanders/Library/R/3.6/library/BiocStyle/resources/tex/Bioconductor
.sty

LaTeX Warning: You have requested package `/Users/freekmanders/Library/R/3.6/li
brary/BiocStyle/resources/tex/Bioconductor',
               but the package provides `Bioconductor'.

Package: Bioconductor 2016/06/22 Bioconductor LaTeX Style
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/ifthen.sty
Package: ifthen 2014/09/29 v1.1c Standard LaTeX ifthen package (DPC)
)
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics/color.sty
Package: color 2019/11/23 v1.2a Standard LaTeX Color (DPC)

(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics-cfg/color.cfg
File: color.cfg 2016/01/02 v1.6 sample color configuration
)
Package color Info: Driver file: pdftex.def on input line 147.

(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics-def/pdftex.def
File: pdftex.def 2018/01/08 v1.0l Graphics/color driver for pdftex
)
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics/dvipsnam.def
File: dvipsnam.def 2016/06/17 v3.0m Driver-dependent file (DPC,SPQR)
))
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/hyperref.sty
Package: hyperref 2020/01/14 v7.00d Hypertext links for LaTeX

(/usr/local/texlive/2020/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty
Package: ltxcmds 2019/12/15 v1.24 LaTeX kernel commands for general use (HO)
)
(/usr/local/texlive/2020/texmf-dist/tex/generic/iftex/iftex.sty
Package: iftex 2020/03/06 v1.0d TeX engine tests
)
(/usr/local/texlive/2020/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
Package: pdftexcmds 2019/11/24 v0.31 Utility functions of pdfTeX for LuaTeX (HO
)

(/usr/local/texlive/2020/texmf-dist/tex/generic/infwarerr/infwarerr.sty
Package: infwarerr 2019/12/03 v1.5 Providing info/warning/error messages (HO)
)
Package pdftexcmds Info: \pdf@primitive is available.
Package pdftexcmds Info: \pdf@ifprimitive is available.
Package pdftexcmds Info: \pdfdraftmode found.
)
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics/keyval.sty
Package: keyval 2014/10/28 v1.15 key=value parser (DPC)
\KV@toks@=\toks15
)
(/usr/local/texlive/2020/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty
Package: kvsetkeys 2019/12/15 v1.18 Key value parser (HO)
)
(/usr/local/texlive/2020/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty
Package: kvdefinekeys 2019-12-19 v1.6 Define keys (HO)
)
(/usr/local/texlive/2020/texmf-dist/tex/generic/pdfescape/pdfescape.sty
Package: pdfescape 2019/12/09 v1.15 Implements pdfTeX's escape features (HO)
)
(/usr/local/texlive/2020/texmf-dist/tex/latex/hycolor/hycolor.sty
Package: hycolor 2020-01-27 v1.10 Color options for hyperref/bookmark (HO)
)
(/usr/local/texlive/2020/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty
Package: letltxmacro 2019/12/03 v1.6 Let assignment for LaTeX macros (HO)
)
(/usr/local/texlive/2020/texmf-dist/tex/latex/auxhook/auxhook.sty
Package: auxhook 2019-12-17 v1.6 Hooks for auxiliary files (HO)
)
(/usr/local/texlive/2020/texmf-dist/tex/latex/kvoptions/kvoptions.sty
Package: kvoptions 2019/11/29 v3.13 Key value format for package options (HO)
)
\@linkdim=\dimen135
\Hy@linkcounter=\count175
\Hy@pagecounter=\count176

(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/pd1enc.def
File: pd1enc.def 2020/01/14 v7.00d Hyperref: PDFDocEncoding definition (HO)
Now handling font encoding PD1 ...
... no UTF-8 mapping file for font encoding PD1
)
(/usr/local/texlive/2020/texmf-dist/tex/generic/intcalc/intcalc.sty
Package: intcalc 2019/12/15 v1.3 Expandable calculations with integers (HO)
)
(/usr/local/texlive/2020/texmf-dist/tex/generic/etexcmds/etexcmds.sty
Package: etexcmds 2019/12/15 v1.7 Avoid name clashes with e-TeX commands (HO)
)
\Hy@SavedSpaceFactor=\count177
Package hyperref Info: Option `pdfpagelabels' set `true' on input line 4421.
Package hyperref Info: Option `plainpages' set `false' on input line 4421.
Package hyperref Info: Option `bookmarks' set `true' on input line 4421.
Package hyperref Info: Option `bookmarksopen' set `true' on input line 4421.
Package hyperref Info: Option `bookmarksnumbered' set `true' on input line 4421
.
Package hyperref Info: Option `hyperfootnotes' set `false' on input line 4421.
Package hyperref Info: Option `colorlinks' set `true' on input line 4421.
Package hyperref Info: Option `breaklinks' set `true' on input line 4421.
Package hyperref Info: Option `raiselinks' set `true' on input line 4421.
Package hyperref Info: Option `pdfusetitle' set `true' on input line 4421.
Package hyperref Info: Hyper figures OFF on input line 4547.
Package hyperref Info: Link nesting OFF on input line 4552.
Package hyperref Info: Hyper index ON on input line 4555.
Package hyperref Info: Plain pages OFF on input line 4562.
Package hyperref Info: Backreferencing OFF on input line 4567.
Package hyperref Info: Implicit mode ON; LaTeX internals redefined.
Package hyperref Info: Bookmarks ON on input line 4800.
\c@Hy@tempcnt=\count178

(/usr/local/texlive/2020/texmf-dist/tex/latex/url/url.sty
\Urlmuskip=\muskip16
Package: url 2013/09/16  ver 3.4  Verb mode for urls, etc.
)
LaTeX Info: Redefining \url on input line 5159.
\XeTeXLinkMargin=\dimen136

(/usr/local/texlive/2020/texmf-dist/tex/generic/bitset/bitset.sty
Package: bitset 2019/12/09 v1.3 Handle bit-vector datatype (HO)

(/usr/local/texlive/2020/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty
Package: bigintcalc 2019/12/15 v1.5 Expandable calculations on big integers (HO
)
))
\Fld@menulength=\count179
\Field@Width=\dimen137
\Fld@charsize=\dimen138
Package hyperref Info: Hyper figures OFF on input line 6430.
Package hyperref Info: Link nesting OFF on input line 6435.
Package hyperref Info: Hyper index ON on input line 6438.
Package hyperref Info: backreferencing OFF on input line 6445.
Package hyperref Info: Link coloring ON on input line 6448.
Package hyperref Info: Link coloring with OCG OFF on input line 6455.
Package hyperref Info: PDF/A mode OFF on input line 6460.
LaTeX Info: Redefining \ref on input line 6500.
LaTeX Info: Redefining \pageref on input line 6504.

(/usr/local/texlive/2020/texmf-dist/tex/generic/atbegshi/atbegshi.sty
Package: atbegshi 2019/12/05 v1.19 At begin shipout hook (HO)
)
\Hy@abspage=\count180
\c@Item=\count181
)
Package hyperref Info: Driver: hpdftex.

(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/hpdftex.def
File: hpdftex.def 2020/01/14 v7.00d Hyperref driver for pdfTeX

(/usr/local/texlive/2020/texmf-dist/tex/latex/atveryend/atveryend.sty
Package: atveryend 2019-12-11 v1.11 Hooks at the very end of document (HO)
Package atveryend Info: \enddocument detected (standard20110627).
)
\Fld@listcount=\count182
\c@bookmark@seq@number=\count183

(/usr/local/texlive/2020/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
Package: rerunfilecheck 2019/12/05 v1.9 Rerun checks for auxiliary files (HO)

(/usr/local/texlive/2020/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty
Package: uniquecounter 2019/12/15 v1.4 Provide unlimited unique counter (HO)
)
Package uniquecounter Info: New unique counter `rerunfilecheck' on input line 2
86.
)
\Hy@SectionHShift=\skip49
) (/usr/local/texlive/2020/texmf-dist/tex/latex/geometry/geometry.sty
Package: geometry 2020/01/02 v5.9 Page Geometry

(/usr/local/texlive/2020/texmf-dist/tex/generic/iftex/ifvtex.sty
Package: ifvtex 2019/10/25 v1.7 ifvtex legacy package. Use iftex instead.
)
\Gm@cnth=\count184
\Gm@cntv=\count185
\c@Gm@tempcnt=\count186
\Gm@bindingoffset=\dimen139
\Gm@wd@mp=\dimen140
\Gm@odd@mp=\dimen141
\Gm@even@mp=\dimen142
\Gm@layoutwidth=\dimen143
\Gm@layoutheight=\dimen144
\Gm@layouthoffset=\dimen145
\Gm@layoutvoffset=\dimen146
\Gm@dimlist=\toks16
)
\hfskip=\skip50
\layoutw=\skip51
\layouth=\skip52
\layouthoff=\skip53
\layoutvoff=\skip54
BiocStyle latex • 341 views
ADD COMMENT
0
Entering edit mode

Next part of the log. It goes on a lot longer after this, but I'm not sure if it's usefull. I can mail it to somebody if needed.

Package geometry Warning: Over-specification in `h'-direction.
    `width' (384.1122pt) is ignored.

\overhang=\skip55
\rightoffset=\skip56
\fltoffset=\skip57
\capoffset=\skip58
(/usr/local/texlive/2020/texmf-dist/tex/latex/bera/beramono.sty
Package: beramono 2004/01/31 (WaS)
)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/fontenc.sty
Package: fontenc 2020/02/11 v2.0o Standard LaTeX package
LaTeX Font Info:    Trying to load font information for T1+lmss on input line 1
12.

(/usr/local/texlive/2020/texmf-dist/tex/latex/lm/t1lmss.fd
File: t1lmss.fd 2009/10/30 v1.6 Font defs for Latin Modern
))
(/usr/local/texlive/2020/texmf-dist/tex/latex/etoolbox/etoolbox.sty
Package: etoolbox 2019/09/21 v2.5h e-TeX tools for LaTeX (JAW)
\etb@tempcnta=\count187
)
(/usr/local/texlive/2020/texmf-dist/tex/latex/titlesec/titlesec.sty
Package: titlesec 2019/10/16 v2.13 Sectioning titles
\ttl@box=\box45
\beforetitleunit=\skip59
\aftertitleunit=\skip60
\ttl@plus=\dimen147
\ttl@minus=\dimen148
\ttl@toksa=\toks17
\titlewidth=\dimen149
\titlewidthlast=\dimen150
\titlewidthfirst=\dimen151
)
(/usr/local/texlive/2020/texmf-dist/tex/latex/framed/framed.sty
Package: framed 2011/10/22 v 0.96: framed or shaded text with page breaks
\OuterFrameSep=\skip61
\fb@frw=\dimen152
\fb@frh=\dimen153
\FrameRule=\dimen154
\FrameSep=\dimen155
)
\voverhang=\skip62


! 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
You're in trouble here.  Try typing  <return>  to proceed.
If that doesn't work, type  X <return>  to quit.

! Argument of \Hy@scantitle has an extra }.
<inserted text>
                \par
l.166 \renewcommand{\title}
                           [1]{\def\@bioctitle{#1}\@oldtitle{#1}}
I've run across a `}' that doesn't seem to match anything.
For example, `\def\a#1{...}' and `\a}' would produce
this error. If you simply proceed now, the `\par' that
I've just inserted will cause me to report a runaway
argument that might be the root of the problem. But if
your `}' was spurious, just type `2' and it will go away.

Runaway argument?
! Paragraph ended before \Hy@scantitle was complete.
<to be read again>
                   \par
l.166 \renewcommand{\title}
                           [1]{\def\@bioctitle{#1}\@oldtitle{#1}}
I suspect you've forgotten a `}', causing me to apply this
control sequence to too much text. How can we recover?
My plan is to forget the whole thing and hope for the best.
ADD REPLY

Login before adding your answer.

Traffic: 545 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6