Line termination change and old code.

.gitignore

@@ -1,44 +1,44 @@
-# Miscellaneous
-.Ds_store
-instructor/
-dev/
-# myScripts/ # We don't want to ignore this so we can save our work to our own fork.
-
-# History files
-.Rhistory
-.Rapp.history
-
-# Session Data files
-# .RData
-
-# Files produced in assingments
-data/APSESphyloSet.mfa
-data/APSEStreeRproml.rds
-
-# Example code in package build process
-*-Ex.R
-
-# Output files from R CMD build
-/*.tar.gz
-
-# Output files from R CMD check
-/*.Rcheck/
-
-# RStudio files
-.Rproj.user/
-
-# produced vignettes
-vignettes/*.html
-vignettes/*.pdf
-
-# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
-.httr-oauth
-
-# knitr and R markdown default cache directories
-/*_cache/
-/cache/
-
-# Temporary files created by R markdown
-*.utf8.md
-*.knit.md
-.Rproj.user
+# Miscellaneous
+.Ds_store
+instructor/
+dev/
+# myScripts/ # We don't want to ignore this so we can save our work to our own fork.
+
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+# .RData
+
+# Files produced in assingments
+data/APSESphyloSet.mfa
+data/APSEStreeRproml.rds
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+/*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+.Rproj.user