Merge pull request #116 from rformassspectrometry/jomain

fix: ensure exactmass is numeric

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: CompoundDb
 Type: Package
 Title: Creating and Using (Chemical) Compound Annotation Databases
-Version: 1.9.2
+Version: 1.9.3
 Authors@R: c(person(given = "Jan", family = "Stanstrup",
                     email = "[email protected]",
 		    role = c("aut"),

NEWS.md

@@ -1,5 +1,9 @@
 # CompoundDb version 1.9
 
+## Changes in version 1.9.3
+
+- `compound_tbl_lipidblast`: ensure *exactmass* is of type `numeric`.
+
 ## Changes in version 1.9.2
 
 - `compound_tbl_lipidblast`: add parameter `n` to support reading and

R/createCompDbPackage.R

@@ -370,10 +370,10 @@ compound_tbl_lipidblast <- function(file, collapse = character(), n = -1L,
     nms <- vapply(cmp$names, `[[`, "name", FUN.VALUE = "character")
     mass <- unlist(lapply(cmp$metaData, function(z) {
         if (z$name == "total exact mass")
-            z$value
+            as.numeric(z$value)
     }))
     if (is.null(mass))
-        mass <- NA_character_
+        mass <- NA_real_
     frml <- unlist(lapply(cmp$metaData, function(z) {
         if (z$name == "molecular formula")
             z$value

tests/testthat/test_createCompDbPackage.R

@@ -474,6 +474,14 @@ test_that(".import_lipidblast_json_chunk works", {
 test_that("compound_tbl_lipidblast works with n > 0", {
     f <- system.file("json", "MoNa-LipidBlast_sub.json", package = "CompoundDb")
     ref <- compound_tbl_lipidblast(f)
+    expect_true(is.numeric(ref$exactmass))
+    expect_true(is.character(ref$compound_id))
+    expect_true(is.character(ref$name))
+    expect_true(is.character(ref$inchi))
+    expect_true(is.character(ref$inchikey))
+    expect_true(is.character(ref$formula))
+    expect_true(is.list(ref$synonyms))
     res <- compound_tbl_lipidblast(f, n = 4)
+    expect_true(is.numeric(res$exactmass))
     expect_equal(ref, res)
 })