[Bioc-devel] how to declare vignette processing properly
Leonardo Collado Torres
lcollado at jhu.edu
Fri May 6 20:21:33 CEST 2016
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 <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]]
>>
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