[Bioc-devel] new package build problems

[Dan Tenenbaum]

----- Original Message -----
> From: "Karl Stamm" <karl.stamm at gmail.com>
> To: bioc-devel at r-project.org
> Sent: Monday, September 29, 2014 10:04:40 PM
> Subject: [Bioc-devel] new package build problems
> 
> I'm trying to put together a new package submission, "rgsepd", and
> I've ran
> into an error I can't figure out. Hoping to talk with someone with
> more
> experience on the bioconductor build system.
> 
> The build report is here
> http://bioconductor.org/spb_reports/rgsepd_0.99.2_buildreport_20140929213816.html#moscato1_buildsrc_anchor
> 
> The package has built fine on OSX and Linux, but is now crashing
> trying to
> construct the Vignette on Windows. I don't see any error message
> reported,
> just that the vignette failed. So I don't know how to debug it
> anymore.
> Earlier versions had reported various file-not-found errors, so I
> could
> track them down and fix them, it was file case-sensitivity or
> forward-slash
> vs backslash on various imported files.  On the latest revision
> 0.99.2, the
> moscato1 BUILD failed, but it was working in 0.99.1. I'm kind of at a
> loss,
> does moscato1 not like knitr ?
> The content of the error log only says it didn't make the file, as
> far as I
> can tell:
> 
> * installing the package to build vignettes
> * creating vignettes ...Warning: running command
> '"D:/packagebuilder/R/bin/i386/Rscript" --vanilla --default-packages=
> -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
>  ERROR
> Warning: running command
> '"C:\PROGRA~2\MIKTEX~1.9\miktex\bin\texi2dvi.exe" --quiet --pdf
> "rgsepd.tex" --max-iterations=20 -I
> "D:/packagebuilder/R/share/texmf/tex/latex" -I
> "D:/packagebuilder/R/share/texmf/bibtex/bst"' had status 1
> Error in find_vignette_product(name, by = "texi2pdf", engine =
> engine) :
>   Failed to locate the 'texi2pdf' output file (by engine
> 'knitr::knitr') for vignette with name 'rgsepd'. The following files
> exist in directory '.': 'rgsepd.R', 'rgsepd.Rnw', 'rgsepd.tex'
> Calls: <Anonymous> -> find_vignette_product
> Execution halted
> 

My highly technical explanation for this is that this is a thing that just sometimes happens on windows, and nobody is quite sure why it happens. It happens inconsistently so it's difficult to reproduce and debug. It has been reported to R-devel but hasn't been fixed for this reason.  But almost always the solution is to run the build again and it works fine. I have kicked off another build of your package and verified that R CMD build was successful on windows, you should see the full report shortly.

Dan



> Is there any way to get more information for debugging?
> 
> Thanks for your help.
> 
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> 
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