add repos param to all modules

d3b-center · Oct 7, 2024 · c733899 · c733899
1 parent d1b5339
commit c733899
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Showing 3 changed files with 29 additions and 29 deletions.
diff --git a/analyses/dge_pathway_analysis/00-setup.R b/analyses/dge_pathway_analysis/00-setup.R
@@ -2,26 +2,26 @@
 
 # CRAN packages
 if (!require("optparse", quietly = TRUE))
-  install.packages("optparse")
+  install.packages("optparse", repos = "http://cran.us.r-project.org")
 
 if (!require("tidyverse", quietly = TRUE))
-  install.packages("tidyverse")
+  install.packages("tidyverse", repos = "http://cran.us.r-project.org")
 
 if (!require("reshape2", quietly = TRUE))
-  install.packages("reshape2")
+  install.packages("reshape2", repos = "http://cran.us.r-project.org")
 
 if (!require("msigdbr", quietly = TRUE))
-  install.packages("msigdbr")
+  install.packages("msigdbr", repos = "http://cran.us.r-project.org")
 
 if (!require("ggplot2", quietly = TRUE))
-  install.packages("ggplot2")
+  install.packages("ggplot2", repos = "http://cran.us.r-project.org")
 
 if (!require("ggpubr", quietly = TRUE))
-  install.packages("ggpubr")
+  install.packages("ggpubr", repos = "http://cran.us.r-project.org")
 
 # Bioc packages
 if (!require("BiocManager", quietly = TRUE))
-  install.packages("BiocManager")
+  install.packages("BiocManager", repos = "http://cran.us.r-project.org")
 
 if (!require("DESeq2", quietly = TRUE))
   BiocManager::install("DESeq2")

diff --git a/analyses/methylation_analysis/00-setup.R b/analyses/methylation_analysis/00-setup.R
@@ -2,23 +2,23 @@
 
 # CRAN packages
 if (!require("optparse", quietly = TRUE))
-  install.packages("optparse")
+  install.packages("optparse", repos = "http://cran.us.r-project.org")
 
 if (!require("tidyverse", quietly = TRUE))
-  install.packages("tidyverse")
+  install.packages("tidyverse", repos = "http://cran.us.r-project.org")
 
 if (!require("data.table", quietly = TRUE))
-  install.packages("data.table")
+  install.packages("data.table", repos = "http://cran.us.r-project.org")
 
 if (!require("dplyr", quietly = TRUE))
-  install.packages("dplyr")
+  install.packages("dplyr", repos = "http://cran.us.r-project.org")
 
 if (!require("msigdbr", quietly = TRUE))
-  install.packages("msigdbr")
+  install.packages("msigdbr", repos = "http://cran.us.r-project.org")
 
 # Bioc packages
 if (!require("BiocManager", quietly = TRUE))
-  install.packages("BiocManager")
+  install.packages("BiocManager", repos = "http://cran.us.r-project.org")
 
 if (!require("missMethyl", quietly = TRUE))
   BiocManager::install("missMethyl")

diff --git a/analyses/post_clustering_associations/00-setup.R b/analyses/post_clustering_associations/00-setup.R
@@ -2,49 +2,49 @@
 
 # CRAN packages
 if (!require("optparse", quietly = TRUE))
-  install.packages("optparse")
+  install.packages("optparse", repos = "http://cran.us.r-project.org")
 
 if (!require("tidyverse", quietly = TRUE))
-  install.packages("tidyverse")
+  install.packages("tidyverse", repos = "http://cran.us.r-project.org")
 
 if (!require("corrplot", quietly = TRUE))
-  install.packages("corrplot")
+  install.packages("corrplot", repos = "http://cran.us.r-project.org")
 
 if (!require("data.table", quietly = TRUE))
-  install.packages("data.table")
+  install.packages("data.table", repos = "http://cran.us.r-project.org")
 
 if (!require("ggplotify", quietly = TRUE))
-  install.packages("ggplotify")
+  install.packages("ggplotify", repos = "http://cran.us.r-project.org")
 
 if (!require("ggpubr", quietly = TRUE))
-  install.packages("ggpubr")
+  install.packages("ggpubr", repos = "http://cran.us.r-project.org")
 
 if (!require("gplots", quietly = TRUE))
-  install.packages("gplots")
+  install.packages("gplots", repos = "http://cran.us.r-project.org")
 
 if (!require("gridExtra", quietly = TRUE))
-  install.packages("gridExtra")
+  install.packages("gridExtra", repos = "http://cran.us.r-project.org")
 
 if (!require("gtsummary", quietly = TRUE))
-  install.packages("gtsummary")
+  install.packages("gtsummary", repos = "http://cran.us.r-project.org")
 
 if (!require("mclust", quietly = TRUE))
-  install.packages("mclust")
+  install.packages("mclust", repos = "http://cran.us.r-project.org")
 
 if (!require("networkD3", quietly = TRUE))
-  install.packages("networkD3")
+  install.packages("networkD3", repos = "http://cran.us.r-project.org")
 
 if (!require("pheatmap", quietly = TRUE))
-  install.packages("pheatmap")
+  install.packages("pheatmap", repos = "http://cran.us.r-project.org")
 
 if (!require("randomcoloR", quietly = TRUE))
-  install.packages("randomcoloR")
+  install.packages("randomcoloR", repos = "http://cran.us.r-project.org")
 
 if (!require("survival", quietly = TRUE))
-  install.packages("survival")
+  install.packages("survival", repos = "http://cran.us.r-project.org")
 
 if (!require("survminer", quietly = TRUE))
-  install.packages("survminer")
+  install.packages("survminer", repos = "http://cran.us.r-project.org")
 
 if (!require("webshot", quietly = TRUE))
-  install.packages("webshot")
+  install.packages("webshot", repos = "http://cran.us.r-project.org")