Merge pull request #432 from stitam/newrelease

Final edits before v1.3.1

Author: stitam

DESCRIPTION

@@ -6,7 +6,7 @@ Description: Chemical information from around the web. This package interacts
     ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet,
     NIST Chemistry WebBook, OPSIN, PubChem, SRS, Wikidata.
 Type: Package
-Version: 1.3.0
+Version: 1.3.1
 License: MIT + file LICENSE
 URL: https://docs.ropensci.org/webchem/, https://github.com/ropensci/webchem
 BugReports: https://github.com/ropensci/webchem/issues
@@ -26,7 +26,7 @@ LazyLoad: yes
 LazyData: yes
 Encoding: UTF-8
 Depends:
-    R (>= 3.0)
+    R (>= 4.1.0)
 Imports:
     xml2,
     httr,

NEWS.md

@@ -1,11 +1,11 @@
-# dev
+# webchem 1.3.1
 
 ## BUG FIXES
 
 * `pc_prop()` returned `NA` without much further explanation if any of the queries were not positive integers. The updated function attempts to coerce queries to positive integers, only progresses valid queries, and prints informative messages along the way if verbose messages are enabled.
 * `srs_query()` broke because the URL was no longer working. We have updated the URL.
 * `is.inchikey(type = "chemspider")` broke because the URL was no longer working. We have updated the URL but the function now requires an API key like all other ChemSpider functions.
-* `pc_prop()` failed with `properties = NULL` because the list of accepted property names had changed. The have updated the list.
+* `pc_prop()` failed with `properties = NULL` because the list of accepted property names had changed. We have updated the list.
 
 # webchem 1.3.0
 

R/jagst.R

@@ -16,5 +16,5 @@
 #'   \item{value}{concentration in ug/L}
 #'   \item{qual}{qualifier, indicating values < LOQ}
 #' }
-#' @source \url{https://udo.lubw.baden-wuerttemberg.de/public/pages/home/index.xhtml}
+#' @source \url{https://udo.lubw.baden-wuerttemberg.de/public/}
 "jagst"

R/opsin.R

@@ -1,7 +1,7 @@
 #' OPSIN web interface
 #'
 #' Query the OPSIN  (Open Parser for Systematic IUPAC nomenclature) web service
-#' \url{https://opsin.ch.cam.ac.uk/instructions.html}.
+#' \url{https://www.ebi.ac.uk/opsin}.
 #'
 #' @import jsonlite httr xml2
 #' @import tibble

R/ping.R

@@ -49,7 +49,7 @@ ping_service <-
                "chembl" = "https://www.ebi.ac.uk/chembl/api/data/molecule/CHEMBL1082.json",
                "cir" = "http://cactus.nci.nih.gov/chemical/structure/Triclosan/cas/xml",
                "cts" = "http://cts.fiehnlab.ucdavis.edu/service/compound/XEFQLINVKFYRCS-UHFFFAOYSA-N",
-               "cs_web" = "http://www.chemspider.com/Chemical-Structure.5363.html",
+               "cs_web" = "https://www.chemspider.com/Chemical-Structure.5363.html",
                "fn" = "http://www.flavornet.org/info/121-33-5.html",
                "nist" = "https://webbook.nist.gov/cgi/cbook.cgi?Name=2-hexene&Units=SI",
                "opsin" = "https://opsin.ch.cam.ac.uk/opsin/cyclopropane.json",

README.Rmd

@@ -44,11 +44,11 @@ At least some of the data in the following sources is accesible through `webchem
 - [ChEBI](https://www.ebi.ac.uk/chebi/)
 - [Chemical Identifier Resolver (CIR)](https://cactus.nci.nih.gov/chemical/structure)
 - [Chemical Translation Service (CTS)](http://cts.fiehnlab.ucdavis.edu/)
-- [ChemSpider](http://www.chemspider.com/) (requires an [API token](https://developer.rsc.org/))
+- [ChemSpider](https://www.chemspider.com/) (requires an [API token](https://developer.rsc.org/))
 - [ETOX](http://webetox.uba.de/webETOX/index.do)
 - [Flavornet](http://www.flavornet.org) 
 - [NIST](https://webbook.nist.gov) (currently gas chromatography retention indices only)
-- [OPSIN](http://opsin.ch.cam.ac.uk/instructions.html)
+- [OPSIN](https://www.ebi.ac.uk/opsin/)
 - [PubChem](https://pubchem.ncbi.nlm.nih.gov/)
 - [U.S. EPA Substance Registry Service (SRS)](https://cdxnodengn.epa.gov/cdx-srs-rest/)
 - [Wikidata](https://www.wikidata.org/wiki/Wikidata:WikiProject_Chemistry)

README.md

@@ -42,13 +42,13 @@ documentation
 - [Chemical Identifier Resolver
   (CIR)](https://cactus.nci.nih.gov/chemical/structure)
 - [Chemical Translation Service (CTS)](http://cts.fiehnlab.ucdavis.edu/)
-- [ChemSpider](http://www.chemspider.com/) (requires an [API
+- [ChemSpider](https://www.chemspider.com/) (requires an [API
   token](https://developer.rsc.org/))
 - [ETOX](http://webetox.uba.de/webETOX/index.do)
 - [Flavornet](http://www.flavornet.org)
 - [NIST](https://webbook.nist.gov) (currently gas chromatography
   retention indices only)
-- [OPSIN](http://opsin.ch.cam.ac.uk/instructions.html)
+- [OPSIN](https://www.ebi.ac.uk/opsin/)
 - [PubChem](https://pubchem.ncbi.nlm.nih.gov/)
 - [U.S. EPA Substance Registry Service
   (SRS)](https://cdxnodengn.epa.gov/cdx-srs-rest/)

codemeta.json

@@ -8,13 +8,13 @@
   "codeRepository": "https://github.com/ropensci/webchem",
   "issueTracker": "https://github.com/ropensci/webchem/issues",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "1.3.0",
+  "version": "1.3.1",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.3.0 (2023-04-21)",
+  "runtimePlatform": "R version 4.5.0 (2025-04-11)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -190,6 +190,7 @@
       "@type": "SoftwareApplication",
       "identifier": "vcr",
       "name": "vcr",
+      "version": ">= 0.6.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -204,7 +205,7 @@
       "@type": "SoftwareApplication",
       "identifier": "R",
       "name": "R",
-      "version": ">= 3.0"
+      "version": ">= 4.1.0"
     },
     "2": {
       "@type": "SoftwareApplication",
@@ -350,7 +351,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "626.9KB",
+  "fileSize": "641.472KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",