From 9ac1b42f3c27a50f8067ba4243225488afd4bd8c Mon Sep 17 00:00:00 2001
From: Anna Murphy <anna_murphy1@brown.edu>
Date: Tue, 3 Sep 2024 11:59:13 -0400
Subject: [PATCH] move r dependencies to packages.R

---
 requirements/classes/php1560/packages.R       |  5 +++++
 requirements/classes/php1560/requirements.txt | 15 +--------------
 requirements/classes/php2560/packages.R       |  4 ++++
 requirements/classes/php2560/requirements.txt | 14 --------------
 4 files changed, 10 insertions(+), 28 deletions(-)

diff --git a/requirements/classes/php1560/packages.R b/requirements/classes/php1560/packages.R
index e1dced38..f6a0a7f0 100644
--- a/requirements/classes/php1560/packages.R
+++ b/requirements/classes/php1560/packages.R
@@ -10,3 +10,8 @@
 #                  repos='http://cran.rstudio.com/')
 # BiocManager::install(c("airway", "DESeq2", "vsn", "biomaRt",
 #                        "AnnotationHub", "SummarizedExperiment"))
+
+install.packages(
+    c("HDSinRdata", "GGally", "gt", "gtsummary", "tidyverse", "patchwork", "usmap", "car", "broom", "pROC", "lmtest", "glmnet", "testthat", "microbenchmark"),
+    dependencies=TRUE, 
+    repos='http://cran.rstudio.com/')
diff --git a/requirements/classes/php1560/requirements.txt b/requirements/classes/php1560/requirements.txt
index 47c105a4..353a999a 100644
--- a/requirements/classes/php1560/requirements.txt
+++ b/requirements/classes/php1560/requirements.txt
@@ -1,20 +1,7 @@
 # add class-specific packages here:
 r-ggplot2
 r-dplyr
-r-HDSinRdata
-r-GGally
-r-gt
-r-gtsummary
-r-tidyverse
-r-patchwork
-r-usmap
-r-car
-r-broom
-r-pROC
-r-lmtest
-r-glmnet
-r-testthat
-r-microbenchmark
+
 
 # these are the scipy base packages ( YOU PROBABLY DON'T WANT TO REMOVE THESE )
 dask 
diff --git a/requirements/classes/php2560/packages.R b/requirements/classes/php2560/packages.R
index e1dced38..65c0f489 100644
--- a/requirements/classes/php2560/packages.R
+++ b/requirements/classes/php2560/packages.R
@@ -10,3 +10,7 @@
 #                  repos='http://cran.rstudio.com/')
 # BiocManager::install(c("airway", "DESeq2", "vsn", "biomaRt",
 #                        "AnnotationHub", "SummarizedExperiment"))
+install.packages(
+    c("HDSinRdata", "GGally", "gt", "gtsummary", "tidyverse", "patchwork", "usmap", "car", "broom", "pROC", "lmtest", "glmnet", "testthat", "microbenchmark"),
+    dependencies=TRUE, 
+    repos='http://cran.rstudio.com/')
diff --git a/requirements/classes/php2560/requirements.txt b/requirements/classes/php2560/requirements.txt
index 47c105a4..59164746 100644
--- a/requirements/classes/php2560/requirements.txt
+++ b/requirements/classes/php2560/requirements.txt
@@ -1,20 +1,6 @@
 # add class-specific packages here:
 r-ggplot2
 r-dplyr
-r-HDSinRdata
-r-GGally
-r-gt
-r-gtsummary
-r-tidyverse
-r-patchwork
-r-usmap
-r-car
-r-broom
-r-pROC
-r-lmtest
-r-glmnet
-r-testthat
-r-microbenchmark
 
 # these are the scipy base packages ( YOU PROBABLY DON'T WANT TO REMOVE THESE )
 dask