Yeah, this was because pandoc-citeproc was not installed. So it should go
away....
Dan
----- Original Message -----
> From: "lcollado" <lcoll...@jhu.edu>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "Vincent Carey" <st...@channing.harvard.edu>, "bioc-devel"
> <bioc-devel@r-project.org>
> Sent: Friday, May 6, 2016 11:21:33 AM
> Subject: Re: [Bioc-devel] how to declare vignette processing properly
> Hi,
>
> I had the same error at derfinder's devel build report yesterday
> morning (v1.7.0), and it went away on the build from yesterday
> afternoon (v1.7.1).
>
> 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.
>
>
> So I think that it'll go away on the build report for yriMulti. You
> can see at the end of
> http://bioconductor.org/packages/release/bioc/vignettes/regionReport/inst/doc/bumphunterExampleOutput.html#reproducibility
> that BioC uses pandoc version 1.16.0.2
>
> Best,
> Leo
>
> 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
>>
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
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