Differences

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--- r-software [2019/10/27 13:45] – aorth
+++ r-software [2019/10/27 15:44] – aorth
@@ Line 18: / Line 18: @@
 $ R</code>
-Here is a good resource on [[https://www.osc.edu/resources/getting_started/howto/howto_install_local_r_packages|installing R packages into user libraries]].
+Use ''installed.packages()'' to check the list of packages installed in the ILRI environment by default. Here is a good resource on [[https://www.osc.edu/resources/getting_started/howto/howto_install_local_r_packages|installing R packages into user libraries]] if you need other packages.
 ===== Installation ======
@@ Line 42: / Line 42: @@
 $ make install</code>
-Then install some common libraries used by our users (to save space, overhead from tens of thousands of header and library files, and users's time):
+Then install some common libraries used by our users because some of them are quite complicated, and installing them globally saves tens of thousands of header files and libraries being installed into user libraries anyways:
+<code>$ export LD_LIBRARY_PATH=/export/apps/gdal/2.4.2/lib
+> install.packages("BiocManager", repos="https://cran.r-project.org")
+> install.packages("sf", repo="https://cloud.r-project.org", configure.args=c(sf = "--with-gdal-config=/export/apps/gdal/2.4.2/bin/gdal-config"))
+> install.packages("poppr", repos="https://cran.r-project.org")
+> install.packages("vcfR", repos="https://cran.r-project.org")</code>