Re: [Bioc-devel] Error in building vignette

[Martin Morgan]

On 10/19/2017 06:21 AM, Moritz Gerstung wrote:
Hi all
It looks like a number of packages have failed the latest Windows build due to 
Vignette/MikTeX issues.

'a number' is pretty good -- there were almost 1000 failures in 
Wednesday's build report! Back closer to normal now...

Martin


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.pic...@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

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