THis file contains instructions ofr managing code (git, documentation, ...)


---------------------------------------------------------------------------------------------
Code Documentation
---------------------------------------------------------------------------------------------
run the following repeatedly until no errors exist ot get the code docuemntation clean

devtools::document()

To create package documentation

On Linux (sc)
1. cd to the project directory
2. run roxygen2::roxygenize(). This will create the Rd files in the man directory of the main package directory
3. on Linux, cd to the diretory above the package directory
4. run R CMD Rd2pdf <packagename>

On Windows ....
Pointing to pdflatex ...

Sys.setenv(PATH=paste(Sys.getenv("PATH"),"C:/Program Files/MiKTeX 2.9/miktex/bin/x64/",sep=";"))

Running documentation - this builds the file ToxValDB_manual.pdf
roxygen2::roxygenise()

Sys.setenv(PATH = paste(Sys.getenv("PATH"), "C:/Program Files/MiKTeX 2.9/miktex/bin/x64", sep=.Platform$path.sep))
Sys.setenv(R_PAPERSIZE="letter")
system("R CMD Rd2pdf . --title=httrpathway httrpathway --output=./httrpathway_manual.pdf --force --no-clean --internals")

---------------------------------------------------------------------------------------------
Managing git and bitbucket
---------------------------------------------------------------------------------------------

adding to the remote bitbucket ...

git config --global user.name "Richard Judson"
git config --global user.email "judson.richard@epa.gov"

cd existing-project
git init
git add --all
git commit -m "Initial Commit"
git remote add origin ssh://git@ccte-bitbucket.epa.gov:7999/httrpat/httrpathway.git

git remote set-url origin ssh://git@ccte-bitbucket.epa.gov:7999/httrpat/httrpathway.git
git push -u origin master

https://ccte-bitbucket.epa.gov/projects/HTTRPAT/repos/httrpathway/browse

---------------------------------------------------------------------------------------------
Installing other required packages
---------------------------------------------------------------------------------------------
To install tcplfit2 from git ...
devtools::install_git("http://ccte-bitbucket.epa.gov/scm/tcplFit2/tcplFit2")

---------------------------------------------------------------------------------------------
Compiling the Vignettes
---------------------------------------------------------------------------------------------