on a system with pandoc-citeproc, this error is avoided. good call dan! On Fri, May 6, 2016 at 1:15 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote:
> Is pandoc-citeproc installed? > > > ----- Original Message ----- > > From: "Vincent Carey" <st...@channing.harvard.edu> > > To: "Andrzej Oleś" <andrzej.o...@gmail.com> > > Cc: "bioc-devel" <bioc-devel@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.o...@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 < > st...@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@r-project.org mailing list > >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >>> > >> > >> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
