[GenABEL-dev] how to get devel-version of GenABEL packages working on Linux or Mac OS, and how to commit changes

[Yurii Aulchenko]

Here are instructions on how to get dev-version of GenABEL packages
working, assuming you use Linux or Mac OS.

The example is given for MixABEL package.

To get MixABEL running in dev-setting, you need to do a number of
things. Plan to spend about 30 minutes on that. You will need good
Inet connection; you need to be registered as comitter; you also will
need to have Subversion (svn) installed (try 'svn help' to see if it
is; if not, here is the link, which may help:
http://subversion.apache.org/packages.html)

0) In order to commit the code, you need to be registered at the
project dev-site. If you did not so yet, register @R-forge

https://r-forge.r-project.org/account/register.php

and then request to join GenABEl project at

https://r-forge.r-project.org/project/request.php?group_id=505

and wait till this is approved

1) in order to be able to compile dev-dersion, make some changes to .profile

assuming that R s installed at /usr/loca/bin, add to ~/.profile:

R_HOME=/usr/local
export R_HOME

log out and log in again, or start a new terminal/console window

2) install GenABEL et al., 'roxygen', and 'RUnit'; for that from
within R use command

install.packages("GenABEL",dependencies=c("Depends","Suggests"))
install.packages("roxygen")
install.packages("RUnit")

3) Get to the latest code by (you need to be registered
@RForge::GenABEL in order to do next parts)

svn checkout svn+ssh://yourRforgeUserName@svn.r-forge.r-project.org/svnroot/genabel

4) compile and install latest code by

cd genabel/pkg

if you wish to be in sync with latest versions of *ABELs, which are
used by MixABEL (as indicated by MixABEL/DESCRIPTION), do

R CMD INSTALL DatABEL
R CMD INSTALL GenABEL

then install MixABEL with

R CMD INSTALL MixABEL


... now you can start R and run example code I have sent in previous e-mail.

5) you can commit modified MixABEL code by

# get to the point
cd /path_to_where_genabel_is_locally/genabel/pkg/MixABEL
# clean-up
sh ./cleanup
cd ..
# commit
svn commit MixABEL -m "What are the changes about"

That should be it. FINITO!

Hopefully will work ok, and let us know if there is any problem with
this description (or if it worked just fine), also any suggestions on
how to improve this description are most welcome. When this procedure
is approved/modified/extended by you, we will add these instructions
to the dev part of our web-site.

best wishes,
Yurii