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Merged
merged 4 commits into from
Jun 9, 2023
Merged

More edits before releasing v1.3.0 #405

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15783b4
Remove extractors for defunct functions
stitam Jun 9, 2023
971f93f
Update namespace reference for adist()
stitam Jun 9, 2023
64abdf2
Update CRAN comments
stitam Jun 9, 2023
73ab1b4
Update codemeta.json
stitam Jun 9, 2023
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2 changes: 1 addition & 1 deletion R/utils.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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.")
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74 changes: 0 additions & 74 deletions R/webchem-defunct.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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() {
Expand All @@ -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."
)
)
}
4 changes: 2 additions & 2 deletions codemeta.json
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Expand Up @@ -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",
Expand Down Expand Up @@ -350,7 +350,7 @@
},
"SystemRequirements": null
},
"fileSize": "667.224KB",
"fileSize": "626.9KB",
"citation": [
{
"@type": "ScholarlyArticle",
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5 changes: 5 additions & 0 deletions cran-comments.md
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@@ -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
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