test renv

.Rprofile

+source("renv/activate.R")

renv/.gitignore

+library/
+local/
+cellar/
+lock/
+python/
+sandbox/
+staging/

renv/settings.json

+{
+  "bioconductor.version": null,
+  "external.libraries": [],
+  "ignored.packages": [],
+  "package.dependency.fields": [
+    "Imports",
+    "Depends",
+    "LinkingTo"
+  ],
+  "ppm.enabled": null,
+  "ppm.ignored.urls": [],
+  "r.version": null,
+  "snapshot.type": "implicit",
+  "use.cache": true,
+  "vcs.ignore.cellar": true,
+  "vcs.ignore.library": true,
+  "vcs.ignore.local": true,
+  "vcs.manage.ignores": true
+}

workflows/kallisto_collect/kallisto_collect.R

@@ -4,14 +4,11 @@
 #### Load required library
 ################################################
 
-if(!"BiocManager" %in% row.names(installed.packages())){install.packages('BiocManager')}
 
-if(!"sleuth" %in% row.names(installed.packages())){
-  BiocManager::install('pachterlab/sleuth')
-}
-if(!"tidyverse" %in% row.names(installed.packages())){install.packages("tidyverse")}
-if(!"openxlsx" %in% row.names(installed.packages())){install.packages("openxlsx")}
-if(!"jsonlite" %in% row.names(installed.packages())){install.packages("jsonlite")}
+library(sleuth)
+library(tidyverse)
+library(openxlsx)
+library(jsonlite)
 
 ################################################
 #### Read arguments from CLI