[Bioc-devel] Error in building vignette

sergi.picart at upc.edu sergi.picart at upc.edu
Thu Oct 19 10:19:54 CEST 2017

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


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, 


	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list