Fixed little issues so that it ran on all three OS's on the bioconductor submission page. This is the version submitted on april 2, 2014 to bioconductor.

Author: dphansti

.Rbuildignore

@@ -4,9 +4,10 @@
 .Rhistory
 .RData
 .DS_Store
-inst/doc/Sushi-0*.pdf
-inst/doc/Sushi.log
-inst/doc/Sushi.synctex.gz
-inst/doc/Sushi-concordance.tex
-inst/doc/Sushi.tex
-inst/doc/Sushi.toc
+vignettes/Sushi-*.pdf
+vignettes/*.png
+vignettes/Sushi.log
+vignettes/Sushi.synctex.gz
+vignettes/Sushi-concordance.tex
+vignettes/Sushi.tex
+vignettes/Sushi.toc

.gitignore

@@ -2,9 +2,10 @@
 .Rhistory
 .RData
 .DS_Store
-inst/doc/Sushi-*.pdf
-inst/doc/Sushi.log
-inst/doc/Sushi.synctex.gz
-inst/doc/Sushi-concordance.tex
-inst/doc/Sushi.tex
-inst/doc/Sushi.toc
+vignettes/Sushi-*.pdf
+vignettes/*.png
+vignettes/Sushi.log
+vignettes/Sushi.synctex.gz
+vignettes/Sushi-concordance.tex
+vignettes/Sushi.tex
+vignettes/Sushi.toc

DESCRIPTION

@@ -1,10 +1,11 @@
 Package: Sushi
 Type: Package
 Title: Tools for visualizing genomics data
-Version: 1.0
+Description: Flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures
+Version: 0.99.0
 Date: 2014-02-17
 Author: Douglas H Phanstiel <[email protected]>
 Maintainer: Douglas H Phanstiel <[email protected]>
-Description: Tools for visualizing genomics data
+biocViews: DataRepresentation, Visualization, Genetics, Sequencing, Infrastructure,
 License: GPL (>= 2)
-Depends: zoo,biomaRt
+Depends: R (>= 2.10), zoo,biomaRt

NAMESPACE

@@ -1 +1,4 @@
 exportPattern("^[[:alpha:]]+")
+
+import(biomaRt)
+import(zoo)

inst/doc/Rplots.pdf

@@ -13,9 +13,10 @@ plotGenes(geneinfo = NULL, chrom = NULL, chromstart = NULL,
 }
 \arguments{
   \item{geneinfo}{gene info stored in a bed-like format.
-  If NULL it will look up genes in the region using
-  biomart="ensembl" and dataset="hsapiens_gene_ensembl".
-  See also \code{\link{useMart}}}
+  If NULL it will look up genes in the region using biomart
+  (with biomart="ensembl" and
+  dataset="hsapiens_gene_ensembl"). See also
+  \code{\link{useMart}}}
 
   \item{chrom}{chromosome of region to be plotted}
 

man/plotgenes.Rd

@@ -1,5 +1,5 @@
 library('Sushi')
-pdfname = "inst/doc/Figure_dhp_new.pdf"
+pdfname = "inst/doc/Figure_1.pdf"
 Sushi_data = data(package = 'Sushi')
 data(list = Sushi_data$results[,3]) 
 makepdf = TRUE

inst/doc/Figure_dhp_new.pdf vignettes/Figure_1.pdf

@@ -1122,14 +1122,21 @@ dev.off()
 @
 \includegraphics{GWAS3}
 \end{center}
-
+\begin{center}
+<<fig=FALSE, echo=FALSE>>=
+if (file.exists("Rplots.pdf"))
+{
+  file.remove("Rplots.pdf")
+}
+@
+\end{center}
 \section{Appendix}
 
 For illustrative purposes we include a complex figure as published in the accompanying manuscript (Phanstiel, et al.).
 
 \lstinputlisting[language=R, breaklines=TRUE, basicstyle=\small, numbers=left]{PaperFigure.R}
 
-\includegraphics{Figure_dhp_new.pdf}
+\includegraphics{Figure_1.pdf}
 
 \bibliography{Sushi}
 \bibliographystyle{plainnat}