[Bioc-devel] Tracing a build error on moscato2: could it be that pandoc is not updated?

[Dan Tenenbaum]

Hi Leonardo,

Both moscato2 and zin2 use pandoc 1.13.2.

When I manually run R CMD build derfinder on moscato2 it actually pops up a crash dialog which of course you can't see in the build report.

I'll take a look and see if I can figure out what is going on.
Dan



----- Original Message -----
> From: "lcollado" <lcollado at jhu.edu>
> To: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Wednesday, December 2, 2015 6:56:59 AM
> Subject: [Bioc-devel] Tracing a build error on moscato2: could it be that	pandoc is not updated?

> Hi,
> 
> I'm trying to reproduce a build error on Windows for derfinder
> (v1.5.10) shown at
> http://bioconductor.org/checkResults/devel/bioc-LATEST/derfinder/moscato2-buildsrc.html
> I'm copying the end of the log here:
> 
> Warning: running command '"C:/progra˜2/Pandoc/pandoc" +RTS -K512m -RTS
> derfinder-users-guide.utf8.md --to html --from
> markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures
> --output derfinder-users-guide.html --smart --email-obfuscation none
> --self-contained --standalone --section-divs --table-of-contents
> --toc-depth 3 --template
> "E:\biocbld\bbs-3.3-bioc\R\library\BiocStyle\resources\html\template.html"
> --number-sections --css
> "E:\biocbld\bbs-3.3-bioc\R\library\BiocStyle\resources\html\bioconductor.css"
> --mathjax --variable
> "mathjax-url:https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
> --no-highlight --variable
> "highlightjs=E:\biocbld\bbs-3.3-bioc\R\library\rmarkdown\rmd\h\highlight"'
> had status 6
> Error: processing vignette 'derfinder-users-guide.Rmd' failed with diagnostics:
> pandoc document conversion failed with error 6
> Execution halted
> 
> Which makes it seem like a pandoc error.
> 
> Using derfinder 1.5.9 (this version precisely
> https://github.com/lcolladotor/derfinder/tree/e727675142cba014b916b837d5b445c311981cc9)
> I did not run into errors with a fresh R-devel and pandoc
> installation. Similarly, I did not get errors using the latest
> derfinder version (1.5.10,
> https://github.com/lcolladotor/derfinder/tree/3203a1ecf4dad595ca7604c38fd27b2ec635f942).
> 
>>From the nightly build page results, I know that it had the error
> using 1.5.10. From the logs I can't tell which version of pandoc is
> being used on the build machine moscato2. But maybe that's the
> difference here. Otherwise, anyone got any ideas on how I can
> reproduce this error?
> 
> Thanks,
> Leonardo
> 
> 
> 
> Full logs:
> 
> 
> D:\GitHub>
> D:\GitHub>R CMD build --no-manual --no-resave-data derfinder
> * checking for file 'derfinder/DESCRIPTION' ... OK
> * preparing 'derfinder':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * looking to see if a 'data/datalist' file should be added
> * building 'derfinder_1.5.9.tar.gz'
> 
> 
> D:\GitHub>
> D:\GitHub>R CMD build --no-manual --no-resave-data derfinder
> * checking for file 'derfinder/DESCRIPTION' ... OK
> * preparing 'derfinder':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * looking to see if a 'data/datalist' file should be added
> * building 'derfinder_1.5.10.tar.gz'
> 
> 
> D:\GitHub>R
> 
> R Under development (unstable) (2015-11-29 r69717) -- "Unsuffered Consequences"
> Copyright (C) 2015 The R Foundation for Statistical Computing
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
>  Natural language support but running in an English locale
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> 
>> sessionInfo()
> R Under development (unstable) (2015-11-29 r69717)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 10240)
> 
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>> q()
> 
> Save workspace image? [y/n/c]: n
> 
> D:\GitHub>
> D:\GitHub>pandoc --version
> pandoc 1.15.2
> Compiled with texmath 0.8.4, highlighting-kate 0.6.
> 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, idris, ini, isocpp, java, javadoc, javascript, json,
>    jsp, julia, kotlin, 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: C:\Users\Leonardo\AppData\Roaming\pandoc
> Copyright (C) 2006-2015 John MacFarlane
> Web:  http://pandoc.org
> This is free software; see the source for copying conditions.
> There is no warranty, not even for merchantability or fitness
> for a particular purpose.
> 
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