Merge pull request #63 from sterrettJD/fix_R_imports

Fix r imports
sterrettJD · May 6, 2024 · cf60a0f · cf60a0f
2 parents 45f19a8 + cf4dbe6
commit cf60a0f
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Showing 4 changed files with 15 additions and 3 deletions.
diff --git a/src/rule_utils/Gut_metabolic_modules.Rmd b/src/rule_utils/Gut_metabolic_modules.Rmd
@@ -16,6 +16,7 @@ knitr::opts_chunk$set(echo = TRUE)
 
 if (!require("tidyverse")) {
     install.packages("tidyverse", repos="http://cran.us.r-project.org")
+    library("tidyverse")
 }
 
 if (!require("data.table")) {

diff --git a/src/rule_utils/HUMAnN_microshades.Rmd b/src/rule_utils/HUMAnN_microshades.Rmd
@@ -13,6 +13,7 @@ knitr::opts_chunk$set(echo = TRUE)
 
 if (!require("tidyverse")) {
     install.packages("tidyverse", repos="http://cran.us.r-project.org")
+    library("tidyverse")
 }
 
 if (!require("data.table")) {
@@ -21,14 +22,17 @@ if (!require("data.table")) {
 
 if (!require("ggplot2")) {
     install.packages("ggplot2", repos="http://cran.us.r-project.org")
+    library("ggplot2")
 }
 
 if (!require("patchwork")) {
     install.packages("patchwork", repos="http://cran.us.r-project.org")
+    library("patchwork")
 }
 
 if (!require("cowplot")) {
     install.packages("cowplot", repos="http://cran.us.r-project.org")
+    library("cowplot")
 }
 
 if (!require("remotes")) {

diff --git a/src/rule_utils/Metaphlan_microshades.Rmd b/src/rule_utils/Metaphlan_microshades.Rmd
@@ -13,6 +13,7 @@ knitr::opts_chunk$set(echo = TRUE)
 
 if (!require("tidyverse")) {
     install.packages("tidyverse", repos="http://cran.us.r-project.org")
+    library("tidyverse")
 }
 
 if (!require("data.table")) {
@@ -21,14 +22,17 @@ if (!require("data.table")) {
 
 if (!require("ggplot2")) {
     install.packages("ggplot2", repos="http://cran.us.r-project.org")
+    library("ggplot2")
 }
 
 if (!require("patchwork")) {
     install.packages("patchwork", repos="http://cran.us.r-project.org")
+    library("patchwork")
 }
 
 if (!require("cowplot")) {
     install.packages("cowplot", repos="http://cran.us.r-project.org")
+    library("cowplot")
 }
 
 if (!require("remotes")) {

diff --git a/src/rule_utils/nonpareil_curves.Rmd b/src/rule_utils/nonpareil_curves.Rmd
@@ -10,13 +10,16 @@ params:
 knitr::opts_chunk$set(echo = TRUE)
 
 if (!require("Nonpareil")){
-  install.packages('Nonpareil', repos="http://cran.us.r-project.org");  
+  install.packages('Nonpareil', repos="http://cran.us.r-project.org")
+  library("Nonpareil")
 }
 if (!require("data.table")){
-  install.packages('data.table', repos="http://cran.us.r-project.org");
+  install.packages('data.table', repos="http://cran.us.r-project.org")
+  library("data.table")
 }
 if (!require("ggplot2")){
-  install.packages('ggplot2', repos="http://cran.us.r-project.org");
+  install.packages('ggplot2', repos="http://cran.us.r-project.org")
+  library("ggplot2")
 }
 ```