Merge pull request #71 from chainsawriot/fix69

Fix #69

DESCRIPTION

@@ -26,7 +26,8 @@ Imports:
     pkgsearch,
     remotes,
     utils,
-    gh
+    gh,
+    vctrs
 Depends: 
     R (>= 3.5.0)
 VignetteBuilder: knitr

R/memo_misc.R

@@ -34,10 +34,21 @@ NULL
     if (bioc_version != "release" && utils::compareVersion(bioc_version, "2.0") == -1) {
         stop("Bioconductor versions < 2.0 are not supported.", call. = FALSE)
     }
-    con <- url(paste0("http://bioconductor.org/packages/", bioc_version, "/bioc/VIEWS"))
-    pkgs <- read.dcf(con)
-    close(con)
-    as.data.frame(pkgs)
+    suffixes <- c("bioc", "data/annotation", "data/experiment", "workflow")
+    output <- data.frame()
+    for (suffix in suffixes) {
+        view_url <- paste0("http://bioconductor.org/packages/", bioc_version, "/", suffix, "/VIEWS")
+        con <- url(view_url)
+        tryCatch({
+            raw_metadata <- suppressWarnings(read.dcf(con))
+            metadata <- as.data.frame(raw_metadata)
+            output <- vctrs::vec_rbind(output, metadata)
+            close(con)
+        }, error = function(e) {
+            close(con)
+        })
+    }
+    output
 }
 
 .memo_search_bioc <- memoise::memoise(.bioc_package_history, cache = cachem::cache_mem(max_age = 60 * 60))

tests/testthat/test_resolve.R

@@ -179,8 +179,18 @@ test_that("issue 68, correct querying of bioc packages from major releases", {
     skip_on_cran()
     expect_equal(.query_biocver("2007-04-27")$version, "2.0")
     expect_false(is.numeric(.query_biocver("2007-04-27")$version))
-    expect_error(.query_snapshot_dependencies_bioc("affy", "2014-10-15"), NA)
+    expect_error(.query_snapshot_dependencies_bioc("affy", "2007-04-15")) ## pre 2.0
+    expect_error(.query_snapshot_dependencies_bioc("affy", "2007-04-27"), NA)
     expect_error(.query_snapshot_dependencies_bioc("affy", "2014-10-15"), NA)
     expect_equal(length(resolve("bioc::affy", snapshot_date = "2007-04-27")$ranglets), 1)
     expect_equal(length(resolve("bioc::affy", snapshot_date = "2014-10-15")$ranglets), 1)
 })
+
+test_that("issue 69, complete bioc information", {
+    skip_if_offline()
+    skip_on_cran()
+    expect_true(nrow(.memo_search_bioc("3.3")) > 1211)
+    expect_true("affydata" %in% .memo_search_bioc("3.3")$Package)
+    expect_equal(.normalize_pkg("affydata", "3.3"), "bioc::affydata")
+    expect_equal(length(resolve("bioc::affydata", snapshot_date = "2016-06-15")$ranglets), 1)
+})