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--- r-software [2021/01/25 12:39] – aorth
+++ r-software [2021/05/06 10:14] – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 4.0 (4.0.3)
+  * Version: 4.0 (4.0.5)
   * Added: February, 2015
-  * Updated: December, 2020
+  * Updated: May, 2021
   * Link: https://www.r-project.org/
@@ Line 26: / Line 26: @@
 <code>$ cd /tmp
-$ wget https://cran.r-project.org/src/base/R-4/R-4.0.3.tar.gz
+$ wget https://cran.r-project.org/src/base/R-4/R-4.0.5.tar.gz
-$ cd R-4.0.3
+$ tar xf R-4.0.5.tar.gz
+$ cd R-4.0.5
 # install packages to enable capabilities in R
 $ sudo yum install libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel glibc-headers pcre2-devel.x86_64
@@ Line 37: / Line 38: @@
 $ ./configure --enable-R-shlib --prefix=/export/apps/R/4.0
 $ make -j4
+$ sudo mv /export/apps/R/4.0.3
 $ sudo mkdir -p /export/apps/R/4.0
 $ sudo chown aorth:aorth /export/apps/R/4.0
-$ make install</code>
+$ make install
+$ sudo rm -rf /export/apps/R/4.0.3</code>
 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:
@@ Line 50: / Line 53: @@
 > install.packages("poppr", repos="https://cran.r-project.org")
 > install.packages("vcfR", repos="https://cran.r-project.org")
+> install.packages("devtools", repos="https://cran.r-project.org")
+> library(devtools)
+> install_github("HenrikBengtsson/TopDom")
+> install_github("lucidif/HiCeekR", repos=BiocManager::repositories())
 > q()
 $ sudo chown -R root:root /export/apps/R/4.0</code>