Merge pull request #342 from stitam/new_release

Final edits before v1.1.2

.Rbuildignore

@@ -26,3 +26,5 @@ README_cache
 
 codemeta.json
 ^codemeta\.json$
+
+cran-comments.md

DESCRIPTION

@@ -7,8 +7,8 @@ Description: Chemical information from around the web. This package interacts
     Flavornet, NIST Chemistry WebBook, OPSIN, PAN Pesticide Database, PubChem,
     SRS, Wikidata.
 Type: Package
-Version: 1.1.1.9004
-Date: 2021-02-07
+Version: 1.1.2
+Date: 2021-12-06
 License: MIT + file LICENSE
 URL: https://docs.ropensci.org/webchem/, https://github.com/ropensci/webchem
 BugReports: https://github.com/ropensci/webchem/issues

NEWS.md

@@ -1,4 +1,4 @@
-# webchem (development version)
+# webchem 1.1.2
 
 ## NEW FEATURES
 
@@ -7,7 +7,7 @@
 ## BUG FIXES
 
 * ci_query() can no longer query chemicals by name.
-* non-exported function ping_pubchem_pw() was incorrectly reporting that PUG VIEW was down.  This has been fixed.
+* Non-exported function ping_pubchem_pw() was incorrectly reporting that PUG VIEW was down.  This has been fixed.
 * is.cas() now catches whitespaces correctly.
 * aw_query() was renamed and adapted to bcpc_query, as the alanwood site has moved
 
@@ -59,8 +59,8 @@
 
 ## MINOR IMPROVEMENTS
 
-* all `get_*()` functions now output tibbles with a column for the query and a column for the retrieved ID.
-* changes to arguments in `get_*()` functions to make them more consistent.
+* All `get_*()` functions now output tibbles with a column for the query and a column for the retrieved ID.
+* Changes to arguments in `get_*()` functions to make them more consistent.
 * aw_idx.rda is no longer included in the package as a data set. Instead, it is built by build_aw_idx() to tempdir().
 
 
@@ -91,7 +91,7 @@
 ## MINOR IMPROVEMENTS
 
 * as.cas() added.
-* removed documentation files for non-exported functions that were only used internally.
+* Removed documentation files for non-exported functions that were only used internally.
 
 ## BUG FIXES
 
@@ -129,7 +129,7 @@
 * cs_prop() did not parse scientific number correctly.
 * is.smiles() failed because of changes in rcdk.
 * cir_query() failed with identifiers containing spaces (e.g. 'acetic acid').
-* several other functions failed with identifiers containing spaces & returned wrong distance.
+* Aeveral other functions failed with identifiers containing spaces & returned wrong distance.
 
 ## DEPRECATED FUNCTIONS
 
@@ -179,11 +179,11 @@
 
 
 ## NEW FEATURES
-* added ping_pubchem() to check whether pubchem is up & running.
-* added cs_web_ping () to check whether the chemspider webpage is functional.
+* Added ping_pubchem() to check whether pubchem is up & running.
+* Added cs_web_ping () to check whether the chemspider webpage is functional.
 
 ## MINOR IMPROVEMENTS
-* updated allan wood index.
+* Updated allan wood index.
 
 ## BUG FIXES
 * pc_prop() returned to many rows if last cid supplied was NA.
@@ -202,16 +202,16 @@
 
 
 ## NEW FEATURES
-* added cts_to() and cts_from() to retrieve possible ids that can be queried.
+* Added cts_to() and cts_from() to retrieve possible ids that can be queried.
 * cts_*(), pp_query(), cir_query(), get_cid(), get_etoxid(), etox_*(), pan_query() get_wdid(), aw_query(), get_csid(), cs_prop(), cs_compinfo() and ci_query() can handle multiple inputs.
 * pc_prop() queries properties and pc_synonmy() synonyms from PUG-REST.
-* added extractors for webchem objects: cas(), inchikey() and smiles().
+* Added extractors for webchem objects: cas(), inchikey() and smiles().
 
 
 ## MINOR IMPROVEMENTS
-* rewrite of pubchem functions using PUG-REST.
-* chemspider: better use of NA in input (=return NA).
-* more robust matching in get_etoxid.
+* Rewrite of pubchem functions using PUG-REST.
+* ChemSpider: better use of NA in input (=return NA).
+* More robust matching in get_etoxid.
 
 ## BUG FIXES
 
@@ -253,14 +253,14 @@ The new ppdb_parse() parses only a html, but does not interact with the database
   - names of returned list changed.
   - result is numeric where appropriate.
 * cir(): result is numeric where appropriate.
-* unified naming scheme of functions.
+* Unified naming scheme of functions.
 * is.inchikey_cs() has been integrated into is.inchikey().
 * aw_query() returns multiple inchikey if found.
 * pan() now returns chemical name and matched synonym.
 
 ## BUG FIXES
 
-* utility functions are not vectorized and throw an error.
+* Utility functions are not vectorized and throw an error.
 * chemid() did mot work with inchikey as input.
 * ppdb_idx returned duplicated CAS values, which caused ppdb() to fail.
 * ppdb() failed in some cases because of false encoding.
@@ -321,7 +321,7 @@ The new ppdb_parse() parses only a html, but does not interact with the database
 
 * alanwood() returns only results for first match in case of multiple links found.
 * physprop() stopped working after change of SRC to https, fixed now.
-* changed etox_* functions to https.
+* Changed etox_* functions to https.
 
 
 ## DEPRECATED FUNCTIONS
@@ -351,8 +351,8 @@ The new ppdb_parse() parses only a html, but does not interact with the database
 
 ## MINOR IMPROVEMENTS
 
-* added exceptions/checks to tests.
-* improved robustness of cir_query().
+* Added exceptions/checks to tests.
+* Improved robustness of cir_query().
 
 ## BUG FIXES
 

R/bcpc.R

@@ -1,7 +1,7 @@
-#' Query http://pesticidecompendium.bcpc.org
+#' Query https://pesticidecompendium.bcpc.org
 #'
 #' Query the BCPC Compendium of Pesticide Common Names
-#' \url{http://pesticidecompendium.bcpc.org}
+#' \url{https://pesticidecompendium.bcpc.org}
 #' formerly known as Alan Woods Compendium of Pesticide Common Names
 #' @import xml2
 #'
@@ -15,7 +15,7 @@
 #' url.
 #' @note for from = 'cas' only the first matched link is returned.
 #' Please respect Copyright, Terms and Conditions
-#' \url{http://pesticidecompendium.bcpc.org/legal.html}!
+#' \url{https://pesticidecompendium.bcpc.org/legal.html}!
 #' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
 #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
 #' Information from the Web. Journal of Statistical Software, 93(13).
@@ -147,7 +147,7 @@ bcpc_query <- function(query, from = c("name", "cas"),
                      r_isomer = gsub(".*\\(R\\)-isomer:(.*)", "\\1", inchi))
         }
       }
-      
+
       out <- list(cname = cname, status = status,
                   pref_iupac_name = pref_iupac_name, iupac_name = iupac_name,
                   cas = cas, formula = formula, activity = activity,

R/chemid.R

@@ -125,7 +125,7 @@ ci_query <- function(query, from = c("rn", "inchikey"),
         physprop <- NA
       } else {
         physprop <- html_table(xml_find_all(ttt, "//h2[contains(., 'Physical Prop')]/following-sibling::div//table"))[[1]]
-        physprop[ , 'Value'] <- as.numeric(physprop[ , 'Value'])
+        physprop[ , 'Value'] <- as.numeric(unlist(physprop[ , 'Value']))
         #= same as physprop
       }
 

R/chemspider.R

@@ -42,7 +42,7 @@ cs_check_key <- function() {
 #' @note An API key is needed. Register at \url{https://developer.rsc.org/}
 #' for an API key. Please respect the Terms & Conditions. The Terms & Conditions
 #' can be found at \url{https://developer.rsc.org/terms}.
-#' @references \url{https://developer.rsc.org/compounds-v1/apis}
+#' @references \url{https://developer.rsc.org/docs/compounds-v1-trial/1/overview}
 #' @export
 #' @examples
 #' \dontrun{
@@ -107,7 +107,7 @@ cs_datasources <- function(apikey = NULL, verbose = getOption("verbose")) {
 #' Each API uses a subset of these controls.
 #' The controls that are available for a given function are indicated within the
 #' documentation of the function.
-#' @references \url{https://developer.rsc.org/compounds-v1/apis}
+#' @references \url{https://developer.rsc.org/docs/compounds-v1-trial/1/overview}
 #' @seealso \code{\link{get_csid}}
 #' @export
 #' @examples
@@ -160,7 +160,7 @@ cs_control <- function(datasources = vector(),
 #' @note An API key is needed. Register at \url{https://developer.rsc.org/} for
 #'   an API key. Please respect the Terms & conditions:
 #'   \url{https://developer.rsc.org/terms}.
-#' @references \url{https://developer.rsc.org/compounds-v1/apis}
+#' @references \url{https://developer.rsc.org/docs/compounds-v1-trial/1/overview}
 #' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
 #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
 #' Information from the Web. Journal of Statistical Software, 93(13).
@@ -332,7 +332,7 @@ get_csid <- function(query,
 #' @note An API key is needed. Register at \url{https://developer.rsc.org/}
 #' for an API key. Please respect the Terms & Conditions. The Terms & Conditions
 #' can be found at \url{https://developer.rsc.org/terms}.
-#' @references \url{https://developer.rsc.org/compounds-v1/apis}
+#' @references \url{https://developer.rsc.org/docs/compounds-v1-trial/1/overview}
 #' @references Eduard Szöcs, Tamás Stirling, Eric R. Scott, Andreas Scharmüller,
 #' Ralf B. Schäfer (2020). webchem: An R Package to Retrieve Chemical
 #' Information from the Web. Journal of Statistical Software, 93(13).
@@ -463,7 +463,7 @@ cs_convert <- function(query, from, to, verbose = getOption("verbose"),
 #' @note An API key is needed. Register at \url{https://developer.rsc.org/}
 #' for an API key. Please respect the Terms & Conditions. The Terms & Conditions
 #' can be found at \url{https://developer.rsc.org/terms}.
-#' @references \url{https://developer.rsc.org/compounds-v1/apis}
+#' @references \url{https://developer.rsc.org/docs/compounds-v1-trial/1/overview}
 #' @export
 #' @examples
 #' \dontrun{
@@ -618,7 +618,7 @@ use 'cs_commpinfo()' instead.")
 #' @note An API key is needed. Register at \url{https://developer.rsc.org/}
 #' for an API key. Please respect the Terms & Conditions. The Terms & Conditions
 #' can be found at \url{https://developer.rsc.org/terms}.
-#' @references \url{https://developer.rsc.org/compounds-v1/apis}
+#' @references \url{https://developer.rsc.org/docs/compounds-v1-trial/1/overview}
 #' @seealso \code{\link{get_csid}}, \code{\link{cs_check_key}}
 #' @export
 #' @examples

R/cts.R

@@ -99,6 +99,8 @@ cts_compinfo <- function(query, from = "inchikey",
 #' single named vector.
 #' @details See also \url{http://cts.fiehnlab.ucdavis.edu/}
 #' for possible values of from and to.
+#' @note When this version of webchem was released, CTS was temporarily unable
+#' to convert chemical names to IDs.
 #'
 #' @seealso \code{\link{cts_from}} for possible values in the 'from' argument
 #' and \code{\link{cts_to}} for possible values in the 'to' argument.
@@ -110,11 +112,11 @@ cts_compinfo <- function(query, from = "inchikey",
 #' @examples
 #' \donttest{
 #' # might fail if API is not available
-#' cts_convert("triclosan", "Chemical Name", "inchikey")
+#' cts_convert("XEFQLINVKFYRCS-UHFFFAOYSA-N", "inchikey", "Chemical Name")
 #'
 #' ### multiple inputs
-#' comp <- c("triclosan", "hexane")
-#' cts_convert(comp, "Chemical Name", "cas")
+#' keys <- c("XEFQLINVKFYRCS-UHFFFAOYSA-N", "VLKZOEOYAKHREP-UHFFFAOYSA-N")
+#' cts_convert(keys, "inchikey", "cas")
 #' }
 cts_convert <- function(query,
                         from,

R/webchem-package.R

@@ -38,7 +38,7 @@ if (getRversion() >= "2.15.1")
 #'
 #' This dataset comprises acute ecotoxicity data of 124 insecticides.
 #' The data is publicly available and can be retrieved from the EPA ECOTOX database
-#' (\url{http://cfpub.epa.gov/ecotox/})
+#' (\url{https://cfpub.epa.gov/ecotox/})
 #' It comprises acute toxicity data (D. magna, 48h, Laboratory, 48h) and has been
 #' preprocessed (remove non-insecticides, aggregate multiple value, keep only numeric data etc).
 #'
@@ -47,5 +47,5 @@ if (getRversion() >= "2.15.1")
 #'   \item{cas}{CAS registry number}
 #'   \item{value}{LC50value}
 #' }
-#' @source \url{http://cfpub.epa.gov/ecotox/}
+#' @source \url{https://cfpub.epa.gov/ecotox/}
 "lc50"

README.md

@@ -39,18 +39,18 @@ documentation
     Compendium of Pesticide Common Names)
 -   [ChEBI](https://www.ebi.ac.uk/chebi/)
 -   [Chemical Identifier Resolver
-    (CIR)](http://cactus.nci.nih.gov/chemical/structure)
+    (CIR)](https://cactus.nci.nih.gov/chemical/structure)
 -   [Chemical Translation Service
     (CTS)](http://cts.fiehnlab.ucdavis.edu/)
 -   [ChemIDplus](https://chem.nlm.nih.gov/chemidplus/)
 -   [ChemSpider](http://www.chemspider.com/) (requires an [API
-    token]((https://developer.rsc.org/)))
+    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)
--   [PAN Pesticide Database](http://www.pesticideinfo.org/)
+-   [PAN Pesticide Database](https://www.pesticideinfo.org/)
 -   [PubChem](https://pubchem.ncbi.nlm.nih.gov/)
 -   [U.S. EPA Substance Registry Service
     (SRS)](https://cdxnodengn.epa.gov/cdx-srs-rest/)
@@ -130,4 +130,4 @@ here](https://github.com/ropensci/webchem/blob/master/CONTRIBUTING.md).
     of Conduct](https://ropensci.org/code-of-conduct/). By contributing
     to this project, you agree to abide by its terms.
 
-[![ropensci](http://ropensci.org/public_images/github_footer.png)](http://ropensci.org)
+[![ropensci](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)

codemeta.json

@@ -5,7 +5,7 @@
   ],
   "@type": "SoftwareSourceCode",
   "identifier": "webchem",
-  "description": "Chemical information from around the web. This package interacts \n    with a suite of web services for chemical information. Sources include: Alan\n    Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver,\n    ChEBI, Chemical Translation Service, ChemIDplus, ChemSpider, ETOX,\n    Flavornet, NIST Chemistry WebBook, OPSIN, PAN Pesticide Database, PubChem,\n    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, ChemIDplus, ChemSpider, ETOX, Flavornet, NIST Chemistry WebBook, OPSIN, PAN Pesticide Database, PubChem, SRS, Wikidata.",
   "name": "webchem: Chemical Information from the Web",
   "codeRepository": "https://github.com/ropensci/webchem",
   "relatedLink": [
@@ -15,13 +15,13 @@
   ],
   "issueTracker": "https://github.com/ropensci/webchem/issues",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "1.1.1",
+  "version": "1.1.2",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.0.3 (2020-10-10)",
+  "runtimePlatform": "R version 4.1.2 (2021-11-01)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -189,6 +189,18 @@
         "url": "https://cran.r-project.org"
       },
       "sameAs": "https://CRAN.R-project.org/package=usethis"
+    },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "vcr",
+      "name": "vcr",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=vcr"
     }
   ],
   "softwareRequirements": [
@@ -334,10 +346,15 @@
         "url": "https://cran.r-project.org"
       },
       "sameAs": "https://CRAN.R-project.org/package=rlang"
+    },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "utils",
+      "name": "utils"
     }
   ],
   "readme": "https://github.com/ropensci/webchem/blob/master/README.md",
-  "fileSize": "0KB",
+  "fileSize": "616.471KB",
   "keywords": [
     "rstats",
     "ropensci",
@@ -350,7 +367,7 @@
     "r-package"
   ],
   "releaseNotes": "https://github.com/ropensci/webchem/blob/master/NEWS.md",
-  "contIntegration": "https://codecov.io/gh/ropensci/webchem/branch/master",
+  "contIntegration": ["https://github.com/ropensci/webchem/actions", "https://codecov.io/gh/ropensci/webchem/branch/master"],
   "citation": [
     {
       "@type": "ScholarlyArticle",

cran-comments.md

@@ -0,0 +1,3 @@
+# webchem 1.1.2
+
+* https://developer.rsc.org/, SSL certificate problem: unable to get local issuer certificate: The URLs work and including these URLs in the package is important.