Merge pull request #405 from stitam/new_release

More edits before releasing v1.3.0

R/utils.R

@@ -489,7 +489,7 @@ matcher <-
         if (length(x) != length(result))
           stop("Can't use match = 'best' without query matches for each output")
         if (verbose) message("Returning best.")
-        dd <- adist(query, result) / nchar(result)
+        dd <- utils::adist(query, result) / nchar(result)
         return(x[which.min(dd)])
       } else if (match == "first") {
         if (verbose) message("Returning first.")

R/webchem-defunct.R

@@ -78,45 +78,6 @@ ci_query <- function() {
   )
 }
 
-cas.ci_query <- function() {
-  .Defunct(
-    "cas.ci_query",
-    package = "webchem",
-    msg = paste0(
-      "cas.ci_query() has been removed from the package because NLM had ",
-      "retired ChemIDplus. According to NLM all data found in ChemIDplus is ",
-      "available in PubChem. 'webchem' provides a number of functions for ",
-      "programmatically accessing PubChem."
-    )
-  )
-}
-
-inchikey.ci_query <- function() {
-  .Defunct(
-    "inchikey.ci_query",
-    package = "webchem",
-    msg = paste0(
-      "inchikey.ci_query() has been removed from the package because NLM had ",
-      "retired ChemIDplus. According to NLM all data found in ChemIDplus is ",
-      "available in PubChem. 'webchem' provides a number of functions for ",
-      "programmatically accessing PubChem."
-    )
-  )
-}
-
-smiles.ci_query <- function() {
-  .Defunct(
-    "smiles.ci_query",
-    package = "webchem",
-    msg = paste0(
-      "smiles.ci_query() has been removed from the package because NLM had ",
-      "retired ChemIDplus. According to NLM all data found in ChemIDplus is ",
-      "available in PubChem. 'webchem' provides a number of functions for ",
-      "programmatically accessing PubChem."
-    )
-  )
-}
-
 #' @rdname webchem-defunct
 #' @export
 pan_query <- function() {
@@ -129,38 +90,3 @@ pan_query <- function() {
     )
   )
 }
-
-cas.pan_query <- function() {
-  .Defunct(
-    "cas.pan_query",
-    package = "webchem",
-    msg = paste0(
-      "cas.pan_query() has been removed from the package because programmatic ",
-      "access to the Pesticide Action Network database is no longer supported."
-    )
-  )
-}
-
-inchikey.pan_query <- function() {
-  .Defunct(
-    "inchikey.pan_query",
-    package = "webchem",
-    msg = paste0(
-      "inchikey.pan_query() has been removed from the package because ",
-      "programmatic access to the Pesticide Action Network database is no ",
-      "longer supported."
-    )
-  )
-}
-
-smiles.pan_query <- function() {
-  .Defunct(
-    "smiles.pan_query",
-    package = "webchem",
-    msg = paste0(
-      "smiles.pan_query() has been removed from the package because ",
-      "programmatic access to the Pesticide Action Network database is no ",
-      "longer supported."
-    )
-  )
-}

codemeta.json

@@ -2,7 +2,7 @@
   "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
   "@type": "SoftwareSourceCode",
   "identifier": "webchem",
-  "description": "Chemical information from around the web. This package interacts with a suite of web services for chemical information. Sources include: Alan Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver, ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet, NIST Chemistry WebBook, OPSIN, PAN Pesticide Database, PubChem, SRS, Wikidata.",
+  "description": "Chemical information from around the web. This package interacts with a suite of web services for chemical information. Sources include: Alan Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver, ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet, NIST Chemistry WebBook, OPSIN, PubChem, SRS, Wikidata.",
   "name": "webchem: Chemical Information from the Web",
   "relatedLink": ["https://docs.ropensci.org/webchem/", "https://CRAN.R-project.org/package=webchem"],
   "codeRepository": "https://github.com/ropensci/webchem",
@@ -350,7 +350,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "667.224KB",
+  "fileSize": "626.9KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

cran-comments.md

@@ -1,3 +1,8 @@
+# webchem 1.3.0
+
+* This minor relese defuncts two functions, `ci_query()` and `pan_query()` because the webservices they were interacting with are no longer available.
+* Submission was rejected on 2023-05-04 due to the following check log entry: "Apparent methods for exported generics not registered: cas.ci_query inchikey.ci_query smiles.ci_query". This has been fixed.
+
 # webchem 1.1.3
 
 * Found the following (possibly) invalid URLs: https://www.gsbl.de (moved to