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[Bioc-devel] how to declare vignette processing properly

7 messages · Andrzej Oleś, Vincent Carey, Leonardo Collado Torres +1 more

Original
Vincent Carey
# 
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.
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
Andrzej Oleś
# 
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:

  
  


  


      

    

    

      
      

        


  

        

      Vincent Carey
    

    

      
      #
    

  


  

      
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 Ole? <andrzej.oles at gmail.com>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Dan Tenenbaum
    

    

      
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Is pandoc-citeproc installed?


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      Vincent Carey
    

    

      
      #
    

  


  

      
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:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Leonardo Collado Torres
    

    

      
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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:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Dan Tenenbaum
    

    

      
      #
    

  


  

      
Yeah, this was because pandoc-citeproc was not installed. So it should go away....

Dan

----- Original Message -----