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

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.