--- a/tool_dependencies.xml	Sun May 07 15:53:42 2017 -0400
+++ b/tool_dependencies.xml	Sun May 07 16:39:55 2017 -0400
@@ -88,7 +88,6 @@
                     <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/rtracklayer_1.30.4.tar.gz</package>
                     <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/biomaRt_2.26.1.tar.gz</package>
                     <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/GenomicFeatures_1.22.13.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_1.0.0.tar.gz</package>
                     <package>https://cran.r-project.org/src/contrib/lattice_0.20-35.tar.gz</package>
                     <package>https://cran.rstudio.com/src/contrib/igraph_1.0.1.tar.gz</package>
                     <package>https://cran.rstudio.com/src/contrib/rgl_0.98.1.tar.gz</package>
@@ -99,6 +98,10 @@
                     <package>https://cran.rstudio.com/src/contrib/dplyr_0.5.0.tar.gz</package>
                     <package>https://cran.rstudio.com/src/contrib/tidyr_0.6.2.tar.gz</package>
                     <package>https://cran.rstudio.com/src/contrib/reshape2_1.4.2.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/Archive/proto/proto_0.3-10.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/Archive/scales/scales_0.2.4.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/gtable_0.2.0.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_1.0.0.tar.gz</package>
                     <package>https://cran.rstudio.com/src/contrib/mixOmics_6.1.2.tar.gz</package>
                     <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/bumphunter_1.10.0.tar.gz</package>
                     <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/minfi_1.16.1.tar.gz</package>