[Bioc-devel] how to declare vignette processing properly
Vincent Carey
stvjc at channing.harvard.edu
Fri May 6 20:00:53 CEST 2016
on a system with pandoc-citeproc, this error is avoided. good call dan!
On Fri, May 6, 2016 at 1:15 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:
> Is pandoc-citeproc installed?
>
>
> ----- Original Message -----
> > From: "Vincent Carey" <stvjc at channing.harvard.edu>
> > To: "Andrzej Oleś" <andrzej.oles at gmail.com>
> > Cc: "bioc-devel" <bioc-devel at r-project.org>
> > Sent: Friday, May 6, 2016 9:44:06 AM
> > Subject: Re: [Bioc-devel] how to declare vignette processing properly
>
> > Thanks Andrzej, can you give a bit more diagnosis? Is 1.13.1 too old?
> >
> > %derby01> pandoc -v
> >
> > pandoc 1.13.1
> >
> > Compiled with texmath 0.8, highlighting-kate 0.5.11.
> >
> > Syntax highlighting is supported for the following languages:
> >
> > abc, actionscript, ada, agda, apache, asn1, asp, awk, bash, bibtex,
> > boo, c,
> >
> > changelog, clojure, cmake, coffee, coldfusion, commonlisp, cpp, cs,
> css,
> >
> > curry, d, diff, djangotemplate, dockerfile, dot, doxygen, doxygenlua,
> > dtd,
> >
> > eiffel, email, erlang, fasm, fortran, fsharp, gcc, glsl, gnuassembler,
> > go,
> >
> > haskell, haxe, html, ini, isocpp, java, javadoc, javascript, json,
> jsp,
> >
> > julia, latex, lex, lilypond, literatecurry, literatehaskell, lua, m4,
> >
> > makefile, mandoc, markdown, mathematica, matlab, maxima, mediawiki,
> >
> > metafont, mips, modelines, modula2, modula3, monobasic, nasm, noweb,
> >
> > objectivec, objectivecpp, ocaml, octave, opencl, pascal, perl, php,
> > pike,
> >
> > postscript, prolog, pure, python, r, relaxng, relaxngcompact, rest,
> > rhtml,
> >
> > roff, ruby, rust, scala, scheme, sci, sed, sgml, sql, sqlmysql,
> >
> > sqlpostgresql, tcl, tcsh, texinfo, verilog, vhdl, xml, xorg, xslt,
> xul,
> >
> > yacc, yaml, zsh
> >
> > Default user data directory: /udd/stvjc/.pandoc
> >
> > Copyright (C) 2006-2014 John MacFarlane
> >
> > Web: http://johnmacfarlane.net/pandoc
> >
> > This is free software; see the source for copying conditions.
> >
> > There is no warranty, not even for merchantability or fitness
> >
> > for a particular purpose.
> >
> > On Fri, May 6, 2016 at 12:30 PM, Andrzej Oleś <andrzej.oles at gmail.com>
> > wrote:
> >
> >> Hi Vince,
> >>
> >> this is most probably due to missing/incorrect pandoc installation.
> >>
> >> Cheers,
> >> Andrzej
> >>
> >> On Fri, May 6, 2016 at 6:18 PM, Vincent Carey <
> stvjc at channing.harvard.edu>
> >> wrote:
> >>
> >>> this is for the current svn version of yriMulti, from 00check.log
> >>>
> >>> * checking re-building of vignette outputs ... WARNING
> >>>
> >>> Error in re-building vignettes:
> >>>
> >>> ...
> >>>
> >>> Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if
> >>> (grepl("\\.[Rr]rst$", :
> >>>
> >>> It seems you should call rmarkdown::render() instead of
> >>> knitr::knit2html() because yriMulti.Rmd appears to be an R Markdown v2
> >>> document.
> >>>
> >>>
> >>> > sessionInfo()
> >>>
> >>> R version 3.3.0 (2016-05-03)
> >>>
> >>> Platform: x86_64-pc-linux-gnu (64-bit)
> >>>
> >>> Running under: CentOS release 6.7 (Final)
> >>>
> >>>
> >>> locale:
> >>>
> >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> >>>
> >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> >>>
> >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> >>>
> >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> >>>
> >>> [9] LC_ADDRESS=C LC_TELEPHONE=C
> >>>
> >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >>>
> >>>
> >>> attached base packages:
> >>>
> >>> [1] stats4 parallel stats graphics grDevices utils
> datasets
> >>>
> >>> [8] methods base
> >>>
> >>>
> >>> other attached packages:
> >>>
> >>> [1] yriMulti_0.0.9
> >>>
> >>> [2] geuvPack_1.3.5
> >>>
> >>> [3] dsQTL_0.9.4
> >>>
> >>> [4] GGBase_3.34.0
> >>>
> >>> [5] snpStats_1.22.0
> >>>
> >>> [6] Matrix_1.2-6
> >>>
> >>> [7] survival_2.39-3
> >>>
> >>> [8] Homo.sapiens_1.3.1
> >>>
> >>> [9] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
> >>>
> >>> [10] org.Hs.eg.db_3.3.0
> >>>
> >>> [11] GO.db_3.3.0
> >>>
> >>> [12] OrganismDbi_1.14.0
> >>>
> >>> [13] GenomicFeatures_1.24.0
> >>>
> >>> [14] AnnotationDbi_1.34.0
> >>>
> >>> [15] SummarizedExperiment_1.2.0
> >>>
> >>> [16] Biobase_2.32.0
> >>>
> >>> [17] GenomicRanges_1.24.0
> >>>
> >>> [18] GenomeInfoDb_1.8.0
> >>>
> >>> [19] IRanges_2.6.0
> >>>
> >>> [20] S4Vectors_0.10.0
> >>>
> >>> [21] BiocGenerics_0.18.0
> >>>
> >>> [22] gQTLBase_1.4.0
> >>>
> >>>
> >>> loaded via a namespace (and not attached):
> >>>
> >>> [1] genefilter_1.54.0 ffbase_0.12.3
> >>> VariantAnnotation_1.18.0
> >>>
> >>> [4] splines_3.3.0 lattice_0.20-33
> rtracklayer_1.32.0
> >>>
> >>>
> >>> [7] base64enc_0.1-3 XML_3.98-1.4 RBGL_1.48.0
> >>>
> >>>
> >>> [10] DBI_0.4 BiocParallel_1.6.0 foreach_1.4.3
> >>>
> >>>
> >>> [13] stringr_1.0.0 zlibbioc_1.18.0
> Biostrings_2.40.0
> >>>
> >>>
> >>> [16] codetools_0.2-14 ff_2.2-13 biomaRt_2.28.0
> >>>
> >>>
> >>> [19] doParallel_1.0.10 BiocInstaller_1.22.1 xtable_1.8-2
> >>>
> >>>
> >>> [22] backports_1.0.2 BSgenome_1.40.0 checkmate_1.7.4
> >>>
> >>>
> >>> [25] graph_1.50.0 annotate_1.50.0 XVector_0.12.0
> >>>
> >>>
> >>> [28] sendmailR_1.2-1 bit_1.1-12 Rsamtools_1.24.0
> >>>
> >>>
> >>> [31] fastmatch_1.0-4 brew_1.0-6 BatchJobs_1.6
> >>>
> >>>
> >>> [34] fail_1.3 digest_0.6.9 stringi_1.0-1
> >>>
> >>>
> >>> [37] BBmisc_1.9 GenomicFiles_1.8.0 grid_3.3.0
> >>>
> >>>
> >>> [40] tools_3.3.0 bitops_1.0-6 magrittr_1.5
> >>>
> >>>
> >>> [43] RCurl_1.95-4.8 RSQLite_1.0.0 iterators_1.0.8
> >>>
> >>>
> >>> [46] GenomicAlignments_1.8.0
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> Bioc-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>
> >>
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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