Entering edit mode
Freek Manders
•
0
@freek-manders-23560
Last seen 4.5 years 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>
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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)
)
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\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
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Package: ifthen 2014/09/29 v1.1c Standard LaTeX ifthen package (DPC)
)
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Package: color 2019/11/23 v1.2a Standard LaTeX Color (DPC)
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File: color.cfg 2016/01/02 v1.6 sample color configuration
)
Package color Info: Driver file: pdftex.def on input line 147.
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File: pdftex.def 2018/01/08 v1.0l Graphics/color driver for pdftex
)
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))
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Package: ltxcmds 2019/12/15 v1.24 LaTeX kernel commands for general use (HO)
)
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Package: iftex 2020/03/06 v1.0d TeX engine tests
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Package pdftexcmds Info: \pdf@primitive is available.
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Package pdftexcmds Info: \pdfdraftmode found.
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(/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)
)
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Package: hycolor 2020-01-27 v1.10 Color options for hyperref/bookmark (HO)
)
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)
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Package: auxhook 2019-12-17 v1.6 Hooks for auxiliary files (HO)
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)
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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.