Hi,

I created a package which I would submit in Bioconductor. I followed guidelines: regarding "code" I haven't got any errors or "warning" and each function seems to work perfectly. Then for each function, I created .Rd files, using Roxygen2. Again, no errors and no warning, when I "Build" and when I "Check".

However, I got errors when I tried to create vignettes in new Bioconductor LATEX Style 2.0.

I installed BiocStyle package, Miktek and Texlive for 'pdflatex'; I set the environment variable RSTUDIO_PDFLATEX=C:\Program Files\MiKTeX 2.9\miktex\bin\x64\pdflatex.exe;  then I selected 'knitr' as Vignette Builder.

Since it's the first time I create a package, I used a small part of DESeq2.Rnw as example vignette. In particular, I adapted the first 50 lines (more or less). This is the content of 'myPackage.Rnw':

%\VignetteIndexEntry{Vignette of "myPackage" package}
%\VignettePackage{myPackage}
%\VignetteEngine{knitr::knitr}

% To compile this document
% library('knitr'); rm(list=ls()); knit('myPackage.Rnw')

\documentclass{article}

<<style, eval=TRUE, echo=FALSE, results="asis">>=
BiocStyle::latex2()
@

<<knitr, echo=FALSE, results="hide">>=
library("knitr")
opts_chunk$set(
  tidy=FALSE,
  dev="png",
  fig.show="hide",
  fig.width=4, fig.height=4.5,
  fig.pos="tbh",
  cache=TRUE,
  message=FALSE)
@

\author{first auth}
\affil{Center;}

\author{second auth}
\affil{Center;}

\author{third auth}
\affil{Center;}

\title{myPackage: this is my new package}

\begin{document}

\maketitle

\bibliography{library}

\end{document}

So, when I compile clicking on "Compile PDF" button, a .tex file is created but an error occurs when it tries to run pdflatex.exe on 'myPackage.tex':

output file: myPackage.tex

[1] "myPackage.tex"
Running pdflatex.exe on myPackage.tex...failed

Issues: 2 errors:

! LaTeX Error: File `C:/ProgramFiles/R/R-3.3.2/library/BiocStyle/resources/tex/Bioconductor2.sty' not found.

Of course, this is the same Error I obtain when I launch devtools::build():

"C:/PROGRA~1/R/R-33~1.2/bin/x64/Rcmd.exe" build "C:\Users\user\Desktop\myPackage" --no-resave-data --no-manual
* checking for file 'C:\Users\user\Desktop\myPackage/DESCRIPTION' ... OK
* preparing 'myPackage':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Warning: running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "myPackage.tex" --max-iterations=20 -I "C:/PROGRA~1/R/R-33~1.2/share/texmf/tex/latex" -I "C:/PROGRA~1/R/R-33~1.2/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'myPackage.tex' failed

LaTeX errors:
! LaTeX Error: File `C:/ProgramFiles/R/R-3.3.2/library/BiocStyle/resources/tex/Bioconductor2.sty' not found.

Bioconductor2.sty file is in that folder; so, what am I doing wrong?

Thanks in advance,

Mattia.

To address the problem of file paths containing spaces I've added an option in BiocStyle v2.3.28  to copy the supporting files to the vignette directory and refer to them by relative paths. To enable it, use

BiocStyle::latex2(relative.path = TRUE)

Following David Carlisle suggestion, in TeX - LaTeX Stack Exchange Furum, now the problem seems to be solved; 

• I set a new Path in "Root" panel of Miktek Settings:

C:\Program Files\R\R-3.3.2\library\BiocStyle\resources

• Then, I modified two lines in 'myPackage.Rnw' :

\RequirePackage[]{Bioconductor2}

\AtBeginDocument{\bibliographystyle{unsrturl}}

instead of

<<style, eval=TRUE, echo=FALSE, results="asis">>=
BiocStyle::latex2()
@

• I used Sweave instead of knitr, so:

%\VignetteEngine{knitr::knitr}

<<knitr, echo=FALSE, results="hide">>=
library("knitr")
opts_chunk$set(
  tidy=FALSE,
  dev="png",
  fig.show="hide",
  fig.width=4, fig.height=4.5,
  fig.pos="tbh",
  cache=TRUE,
  message=FALSE)
@

•  And finally I compiled the document.

Now, PDF is generated without any errors or warnings.

Mattia.