Merge pull request #301 from stitam/new_release

Final final edits before v1.1

DESCRIPTION

@@ -10,7 +10,7 @@ Type: Package
 Version: 1.1.0
 Date: 2020-10-01
 License: MIT + file LICENSE
-URL: https://docs.ropensci.org/webchem, https://github.com/ropensci/webchem
+URL: https://docs.ropensci.org/webchem/, https://github.com/ropensci/webchem
 BugReports: https://github.com/ropensci/webchem/issues
 Authors@R: c(person("Eduard", "Szöcs", role = "aut"),
     person("Robert", "Allaway", role = "ctb"),    
@@ -49,6 +49,7 @@ Suggests:
     robotstxt,
     knitr,
     rmarkdown,
-    plot.matrix
+    plot.matrix,
+    usethis
 RoxygenNote: 7.1.1
 VignetteBuilder: knitr

R/alanwood.R

@@ -1,7 +1,7 @@
-#' Query http://www.alanwood.net/pesticides
+#' Query http://www.alanwood.net/pesticides/
 #'
 #' Query Alan Woods Compendium of Pesticide Common Names
-#' \url{http://www.alanwood.net/pesticides}
+#' \url{http://www.alanwood.net/pesticides/}
 #' @import xml2
 #' @importFrom stats rgamma
 #'
@@ -167,15 +167,15 @@ aw_query <- function(query, from = c("name", "cas"), verbose = TRUE,
 #' Function to build index
 #'
 #' This function builds an index of Alan Woods Compendium of Pesticides
-#' \url{http://www.alanwood.net/pesticides} and saves it to
+#' \url{http://www.alanwood.net/pesticides/} and saves it to
 #' \code{\link{tempdir}}.
 #' @import xml2
 #'
 #' @param verbose logical; print message during processing to console?
 #' @param force_build logical; force building a new index?
 #' @return a data.frame
 #' @seealso \code{\link{aw_query}}, \code{\link{tempdir}}
-#' @source \url{http://www.alanwood.net/pesticides}
+#' @source \url{http://www.alanwood.net/pesticides/}
 #' @noRd
 build_aw_idx <- function(verbose = TRUE, force_build = FALSE) {
   if (!ping_service("aw")) stop(webchem_message("service_down"))

R/cir.R

@@ -1,7 +1,7 @@
 #' Query Chemical Identifier Resolver
 #'
 #' A interface to the Chemical Identifier Resolver (CIR).
-#'  (\url{http://cactus.nci.nih.gov/chemical/structure_documentation}).
+#'  (\url{https://cactus.nci.nih.gov/chemical/structure_documentation}).
 #'
 #' @import xml2
 #' @importFrom utils URLencode
@@ -75,12 +75,12 @@
 #'    \item \code{'name_by_cir'} (Lookup in name index of CIR),
 #'    \item \code{'name_by_opsin'} (Lookup in OPSIN),
 #'    \item \code{'name_by_chemspider'} (Lookup in ChemSpider,
-#'    \url{http://cactus.nci.nih.gov/blog/?p=1386}),
+#'    \url{https://cactus.nci.nih.gov/blog/?p=1386}),
 #'    \item \code{'smiles'} (Lookup SMILES),
 #'    \item \code{'stdinchikey'}, \code{'stdinchi'} (InChI),
 #'    \item \code{'cas_number'} (CAS Number),
 #'    \item \code{'name_pattern'} (Google-like pattern search
-#'    (\url{http://cactus.nci.nih.gov/blog/?p=1456})
+#'    (\url{https://cactus.nci.nih.gov/blog/?p=1456})
 #'    Note, that the pattern search can be combined with other resolvers,
 #'    e.g. \code{resolver = 'name_by_chemspider,name_pattern'}.
 #'
@@ -91,10 +91,10 @@
 #' @references
 #' \code{cir} relies on the great CIR web service created by the CADD
 #' Group at NCI/NIH! \cr
-#' \url{http://cactus.nci.nih.gov/chemical/structure_documentation}, \cr
-#' \url{http://cactus.nci.nih.gov/blog/?cat=10}, \cr
-#' \url{http://cactus.nci.nih.gov/blog/?p=1386}, \cr
-#' \url{http://cactus.nci.nih.gov/blog/?p=1456}, \cr
+#' \url{https://cactus.nci.nih.gov/chemical/structure_documentation}, \cr
+#' \url{https://cactus.nci.nih.gov/blog/?cat=10}, \cr
+#' \url{https://cactus.nci.nih.gov/blog/?p=1386}, \cr
+#' \url{https://cactus.nci.nih.gov/blog/?p=1456}, \cr
 #'
 #'
 #' @examples
@@ -179,7 +179,7 @@ cir_query <- function(identifier, representation = "smiles",
 #' Query Chemical Identifier Resolver Images
 #'
 #' A interface to the Chemical Identifier Resolver (CIR).
-#'  (\url{http://cactus.nci.nih.gov/chemical/structure_documentation}).
+#'  (\url{https://cactus.nci.nih.gov/chemical/structure_documentation}).
 #'
 #' @param query character; Search term. Can be any common chemical identifier
 #' (e.g. CAS, INCHI(KEY), SMILES etc.)
@@ -228,10 +228,10 @@ cir_query <- function(identifier, representation = "smiles",
 #' @references
 #' \code{cir} relies on the great CIR web service created by the CADD
 #' Group at NCI/NIH! \cr
-#' \url{http://cactus.nci.nih.gov/chemical/structure_documentation}, \cr
-#' \url{http://cactus.nci.nih.gov/blog/?cat=10}, \cr
-#' \url{http://cactus.nci.nih.gov/blog/?p=1386}, \cr
-#' \url{http://cactus.nci.nih.gov/blog/?p=1456}, \cr
+#' \url{https://cactus.nci.nih.gov/chemical/structure_documentation}, \cr
+#' \url{https://cactus.nci.nih.gov/blog/?cat=10}, \cr
+#' \url{https://cactus.nci.nih.gov/blog/?p=1386}, \cr
+#' \url{https://cactus.nci.nih.gov/blog/?p=1456}, \cr
 #'
 #'
 #' @examples

R/opsin.R

@@ -1,7 +1,7 @@
 #' OPSIN web interface
 #'
 #' Query the OPSIN  (Open Parser for Systematic IUPAC nomenclature) web service
-#' \url{http://opsin.ch.cam.ac.uk/instructions.html}.
+#' \url{https://opsin.ch.cam.ac.uk/instructions.html}.
 #'
 #' @import jsonlite httr xml2
 #' @import tibble
@@ -15,7 +15,7 @@
 #'
 #' @references Lowe, D. M., Corbett, P. T., Murray-Rust, P., & Glen, R. C. (2011).
 #' Chemical Name to Structure: OPSIN, an Open Source Solution. Journal of Chemical Information and Modeling,
-#' 51(3), 739–753. \url{http://doi.org/10.1021/ci100384d}
+#' 51(3), 739–753. \url{https://doi.org/10.1021/ci100384d}
 #' @examples
 #' \donttest{
 #' opsin_query('Cyclopropane')
@@ -37,7 +37,7 @@ opsin_query <- function(query, verbose = TRUE, ...){
       return(empty)
     }
     query_u <- URLencode(query, reserved = TRUE)
-    baseurl <- "http://opsin.ch.cam.ac.uk/opsin/"
+    baseurl <- "https://opsin.ch.cam.ac.uk/opsin/"
     out <- 'json'
     qurl <- paste0(baseurl, query_u, '.', out)
     if (verbose) webchem_message("query", query, appendLF = FALSE)

R/pubchem.R

@@ -275,7 +275,7 @@ get_cid <-
 #' @param properties character vector; properties to retrieve, e.g.
 #' c("MolecularFormula", "MolecularWeight"). If NULL (default) all available
 #' properties are retrieved. See
-#' \url{https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html#_Toc409516770}
+#' \url{https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest}
 #' for a list of all available properties.
 #' @param verbose logical; should a verbose output be printed to the console?
 #' @param ... currently not used.

R/utils.R

@@ -336,7 +336,7 @@ extr_num <- function(x) {
 #' @references Grabner, M., Varmuza, K., & Dehmer, M. (2012). RMol:
 #' a toolset for transforming SD/Molfile structure information into R objects.
 #' Source Code for Biology and Medicine, 7, 12.
-#' \url{http://doi.org/10.1186/1751-0473-7-12}
+#' \url{https://doi.org/10.1186/1751-0473-7-12}
 #' @export
 
 parse_mol <- function(string) {

R/webchem-package.R

@@ -30,7 +30,7 @@ if (getRversion() >= "2.15.1")
 #'   \item{value}{concentration in ug/L}
 #'   \item{qual}{qualifier, indicating values < LOQ}
 #' }
-#' @source \url{http://jdkfg.lubw.baden-wuerttemberg.de/servlet/is/300/}
+#' @source \url{https://udo.lubw.baden-wuerttemberg.de/?highlightglobalid=gewaesserguetedaten}
 "jagst"