fix pkg list

nexomis · Jun 9, 2024 · 6247ee5 · 6247ee5
1 parent c85ca34
commit 6247ee5
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Showing 4 changed files with 15 additions and 35 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -6,7 +6,7 @@ LABEL org.opencontainers.image.description="Nexoverse is a list of packages used
 LABEL org.opencontainers.image.vendor="Nexomis"
 LABEL org.opencontainers.image.licenses="Apache-2.0"
 
-COPY install_cran.r install_bioc.r nexoverse.cran.txt nexoverse.bioc.txt  /root/
+COPY install.r nexoverse.cran.txt nexoverse.bioc.txt  /root/
 
-RUN Rscript /root/install_cran.r /root/nexoverse.cran.txt \
-  && Rscript /root/install_bioc.r /root/nexoverse.bioc.txt
+RUN Rscript /root/install.r cran /root/nexoverse.cran.txt \
+  && Rscript /root/install.r bioc /root/nexoverse.bioc.txt
diff --git a/install_cran.r → install.r b/install_cran.r → install.r
@@ -3,21 +3,26 @@ if (length(args) == 0) {
   stop("No arguments provided. Please specify a file name.")
 }
 
-input_file <- args[1]
+source_type <- args[1]
+input_file <- args[2]
 
 listpackages = read.table(input_file, header = F)$V1
 
 rspm::enable()
 
 for (pkg_name in listpackages){
-    if (pkg_name != "" & length(find.package(pkg_name, quiet = T)) == 0) {
+    if ( (!startsWith(pkg_name, "#")) & pkg_name != "" & length(find.package(pkg_name, quiet = T)) == 0) {
         print("")
         print("######################################################")
         print("#######          START PACKAGE INSTALL         #######")
         print(pkg_name)
         print("######################################################")
         print("")
-        install.packages(pkg_name, clean = TRUE)
+        if (source_type == "cran"){
+          install.packages(pkg_name, clean = TRUE)
+        } else if (source_type == "bioc") {
+          BiocManager::install(pkg_name, clean = TRUE, ask = FALSE, update = FALSE)
+        }
     }
 } 
 

diff --git a/install_bioc.r b/install_bioc.r
diff --git a/nexoverse.cran.txt b/nexoverse.cran.txt
@@ -1,9 +1,10 @@
+# commented for package with a bug during install resulting in large size images
 assertthat
 BiocManager
 circlize
 cli
 collapse
-copula
+#copula 
 cowplot
 data.table
 dendextend
@@ -17,7 +18,7 @@ factoextra
 fastmatch
 furrr
 future
-GenOrd
+#GenOrd
 ggdendro
 GGally
 ggfortify
@@ -33,7 +34,7 @@ jinjar
 jpeg
 jquerylib
 knitr
-LaplacesDemon
+#LaplacesDemon
 logging
 magrittr
 matrixStats