Latex error when using BiocStyle
Entering edit mode
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:


<<style, eval=TRUE, echo=FALSE, results=tex>>=

This is a test

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

[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.
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-03-06>
Document Class: article 2019/12/20 v1.4l Standard LaTeX document class
File: size10.clo 2019/12/20 v1.4l Standard LaTeX file (size option)

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

Package: Bioconductor 2016/06/22 Bioconductor LaTeX Style
Package: ifthen 2014/09/29 v1.1c Standard LaTeX ifthen package (DPC)
Package: color 2019/11/23 v1.2a Standard LaTeX Color (DPC)

File: color.cfg 2016/01/02 v1.6 sample color configuration
Package color Info: Driver file: pdftex.def on input line 147.

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

Package: ltxcmds 2019/12/15 v1.24 LaTeX kernel commands for general use (HO)
Package: iftex 2020/03/06 v1.0d TeX engine tests
Package: pdftexcmds 2019/11/24 v0.31 Utility functions of pdfTeX for LuaTeX (HO

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.
Package: keyval 2014/10/28 v1.15 key=value parser (DPC)
Package: kvsetkeys 2019/12/15 v1.18 Key value parser (HO)
Package: kvdefinekeys 2019-12-19 v1.6 Define keys (HO)
Package: pdfescape 2019/12/09 v1.15 Implements pdfTeX's escape features (HO)
Package: hycolor 2020-01-27 v1.10 Color options for hyperref/bookmark (HO)
Package: letltxmacro 2019/12/03 v1.6 Let assignment for LaTeX macros (HO)
Package: auxhook 2019-12-17 v1.6 Hooks for auxiliary files (HO)
Package: kvoptions 2019/11/29 v3.13 Key value format for package options (HO)

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
Package: intcalc 2019/12/15 v1.3 Expandable calculations with integers (HO)
Package: etexcmds 2019/12/15 v1.7 Avoid name clashes with e-TeX commands (HO)
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.

Package: url 2013/09/16  ver 3.4  Verb mode for urls, etc.
LaTeX Info: Redefining \url on input line 5159.

Package: bitset 2019/12/09 v1.3 Handle bit-vector datatype (HO)

Package: bigintcalc 2019/12/15 v1.5 Expandable calculations on big integers (HO
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.

Package: atbegshi 2019/12/05 v1.19 At begin shipout hook (HO)
Package hyperref Info: Driver: hpdftex.

File: hpdftex.def 2020/01/14 v7.00d Hyperref driver for pdfTeX

Package: atveryend 2019-12-11 v1.11 Hooks at the very end of document (HO)
Package atveryend Info: \enddocument detected (standard20110627).

Package: rerunfilecheck 2019/12/05 v1.9 Rerun checks for auxiliary files (HO)

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

Package: ifvtex 2019/10/25 v1.7 ifvtex legacy package. Use iftex instead.
BiocStyle latex • 341 views
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.

Package: beramono 2004/01/31 (WaS)
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

File: t1lmss.fd 2009/10/30 v1.6 Font defs for Latin Modern
Package: etoolbox 2019/09/21 v2.5h e-TeX tools for LaTeX (JAW)
Package: titlesec 2019/10/16 v2.13 Sectioning titles
Package: framed 2011/10/22 v 0.96: framed or shaded text with page breaks

! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.

l.164 \let\@bi
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>
l.166 \renewcommand{\title}
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>
l.166 \renewcommand{\title}
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.

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