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" <lcoll...@jhu.edu> > To: "bioc-devel" <bioc-devel@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. > > _______________________________________________ > 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
