[Bioc-devel] Error in building vignette

[Moritz Gerstung]

Hi all

It looks like a number of packages have failed the latest Windows build due to Vignette/MikTeX issues.

The common denominator appears to be

> Warning: running command  
> '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe"  .. had status 1
> Error in find_vignette_product(name, by = "texi2pdf", engine =  

> engine) :  Failed to locate the 'texi2pdf' output file (by engine  
> 'utils::Sweave') for vignette with name ..


Is there a general MikTeX configuration problem on tokay1?

Cheers

Moritz

> On 19 Oct 2017, at 09:19, sergi.picart at upc.edu wrote:
> 
> Dear developers, 
> 
> I have stumbled upon issues with our package vignette. In the windows build:
> 
> * creating vignettes ...Warning: running command  
> '"C:/Users/biocbuild/bbs-3.6-bioc/R/bin/x64/Rscript" --vanilla  
> --default-packages= -e "tools::buildVignettes(dir = '.', tangle =  
> TRUE)"' had status 1 ERROR Invalid Parameter - /figure-html Warning:  
> running command 'C:\Windows\system32\cmd.exe /c convert  
> "intro_files/figure-html/unnamed-chunk-2-1.png" -trim  
> "intro_files/figure-html/unnamed-chunk-2-1.png"' had status 4 Warning  
> in shell(paste(c(cmd, args), collapse = " ")) : 'convert  
> "intro_files/figure-html/unnamed-chunk-2-1.png" -trim  
> "intro_files/figure-html/unnamed-chunk-2-1.png"' execution failed with  
> error code 4
> 
> Also:
> 
> Warning: 'latex2' is deprecated. Use 'latex' instead.And:
> Warning: running command  
> '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" --quiet --pdf  
> "diffuStats.tex" --max-iterations=20 -I  
> "C:/Users/biocbuild/bbs-3.6-bioc/R/share/texmf/tex/latex" -I  
> "C:/Users/biocbuild/bbs-3.6-bioc/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  
> 'utils::Sweave') for vignette with name 'diffuStats'. The following  
> files exist in directory '.': 'bibliography.bib',  
> 'diffuStats-03_diff2.pdf', 'diffuStats-03_diff3.pdf',  
> 'diffuStats-04_plot.pdf', 'diffuStats-05_plot.pdf',  
> 'diffuStats-concordance.tex', 'diffuStats.Rnw', 'diffuStats.tex',  
> 'diffustats_fig_overview.eps', 'diffustats_fig_profiling.eps',  
> 'intro.R', 'intro.Rmd', 'intro.html'  This keeps me worried as (1) I  
> cannot reproduce it, (2) I don't recall changes that can trigger this,  
> and (3) next release is this month.
> Can this be related to the build system or is it a bug that I should fix?
> 
> Thank you, 
> 
> Sergio
> 
> 	[[alternative HTML version deleted]]
> 
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