bioconductor: modern bioc DESCRIPTION files have Repository (#729)

Look at biocViews before Repository when deciding if a package is from Bioconductor.

See rstudio/rsconnect#1134

Author: aronatkins

NEWS.md

@@ -5,6 +5,10 @@
 - Improve package installation in a multi-process environment. Do less work
   when a target package is in the cache and write package `DESCRIPTION`
   updates to temporary files before persisting. (#720)
+- When determining the package source, consider `biocViews` before
+  `Repository`. Recent Bioconductor package `DESCRIPTION` files include the
+  `Repository` field, which caused Packrat to believe that those packages
+  originated from a CRAN-like repository, not Bioconductor. (#729)
 
 # Packrat 0.9.2
 

R/pkg.R

@@ -376,6 +376,13 @@ inferPackageRecord <- function(df, available = availablePackages()) {
   } else if (identical(as.character(df$Priority), 'base')) {
     # It's a base package!
     return(NULL)
+  } else if (length(df$biocViews)) {
+    # It's Bioconductor!
+    return(structure(list(
+      name = name,
+      source = 'Bioconductor',
+      version = ver
+    ), class = c('packageRecord', 'Bioconductor')))
   } else if (length(df$Repository) && identical(as.character(df$Repository), 'CRAN')) {
     # It's CRAN!
     return(structure(list(
@@ -390,13 +397,6 @@ inferPackageRecord <- function(df, available = availablePackages()) {
       source = as.character(df$Repository),
       version = ver
     ), class = c('packageRecord', 'CustomCRANLikeRepository')))
-  } else if (length(df$biocViews)) {
-    # It's Bioconductor!
-    return(structure(list(
-      name = name,
-      source = 'Bioconductor',
-      version = ver
-    ), class = c('packageRecord', 'Bioconductor')))
   } else if (name %in% available[, "Package"]) {
     # It's available on CRAN, so get it from CRAN!
     return(structure(list(

packrat.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 88c01d36-523a-49d0-b291-43c5007d3bf2
 
 RestoreWorkspace: No
 SaveWorkspace: No