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--- r_antsr_usage [2017/04/10 19:00]
mgstauff [''unsupported URL scheme'' - package installation issue]
+++ r_antsr_usage [2017/04/10 20:28] (current)
mgstauff [Local/User Package Installation]
@@ Line 1: / Line 1: @@
 ===== R =====
+==== Local/User Package Installation ====
+As of R 3.2, R should create a default location for local libraries (i.e. that you install on your own). Check using the ''.libPaths()'' command. It should be something like ''/home/<username>/R/x86_64-pc-linux-gnu-library/3.2''. If you want to install packages somewhere other than the default, you can change this using R_LIBS_USER.
+R_LIBS_USER will by default be the first line shown by ''.libPaths()''. This will change the default installation directory. Also, libraries will be loaded from $R_LIBS_USER first. If not found, it will proceed down the list from .libPaths()
+**HOWEVER** if you define R_LIBS, it will be used before R_LIBS_USER in search and installation paths. This can be confusing. For installation, it's safest to always specify the installation path directly in the install command.
+Some documentation here:
+https://stat.ethz.ch/R-manual/R-devel/library/base/html/libPaths.html
 ==== Managing Packages ====
@@ Line 48: / Line 60: @@
   > install_github("stnava/ANTsR")
-NOTE about R_LIBS environment variable:
-As of R 3.2, R should create a default location for local libraries (i.e. that you install on your own). Check using the ''.libPaths()'' command. It should be something like ''/home/<username>/R/x86_64-pc-linux-gnu-library/3.2''. If you want to install packages somewhere other than the default, you can set R_LIBS.

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