Merge PR #44

Author: mwmclean

.Rbuildignore

@@ -15,4 +15,4 @@ RefManageR-Ex.R
 ^paper.bib$
 ^paper.md$
 ^codemeta.json$
-^CONTRIBUTING.md$
+^CONTRIBUTING.md$

.appveyor.yml

@@ -1,7 +1,7 @@
 init:
   ps: |
         $ErrorActionPreference = "Stop"
-        Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
+        Invoke-WebRequest https://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
         Import-Module '..\appveyor-tool.ps1'
 install:
   ps: Bootstrap
@@ -14,10 +14,10 @@ environment:
   matrix:
     - R_VERSION: devel
       POPPLERQT5FILE: 'dev\windows\appveyor\poppler-qt5-debug.zip'
-      CRAN: http://cran.rstudio.com
+      CRAN: https://cran.rstudio.com
     - R_VERSION: release
       RTOOLS_VERSION: 32
-      CRAN: http://cran.rstudio.com
+      CRAN: https://cran.rstudio.com
       POPPLERQT5FILE: 'dev\windows\appveyor\poppler-qt5-debug.zip'
   global:
     NOT_CRAN: true
@@ -27,7 +27,7 @@ build_script:
 #  - travis-tool.sh install_r devtools
 #  - Rscript -e 'devtools::install_github("romainfrancois/bibtex")'
 #  - travis-tool.sh install_github romainfrancois/bibtex
-#  - Rscript -e "install.packages('covr', repos = 'http://cran.rstudio.com')"
+#  - Rscript -e "install.packages('covr', repos = 'https://cran.rstudio.com')"
 #  - travis-tool.sh install_github jimhester/covr
 #  - travis-tool.sh install_github rstats-db/RSQLite
 

.travis.yml

@@ -1,11 +1,11 @@
-# see http://docs.travis-ci.com/user/languages/r/
+# see https://docs.travis-ci.com/user/languages/r/
 language: r
 
 # Be strict when checking our package
 warnings_are_errors: true
 
 # before_script:
-#  - wget http://poppler.freedesktop.org/poppler-0.32.0.tar.xz
+#  - wget https://poppler.freedesktop.org/poppler-0.32.0.tar.xz
 #  - tar poppler-0.32.0.tar.xz
 #  - export PATH=$PATH:$PWD/poppler-0.32.0
 
@@ -14,7 +14,7 @@ before_install:
   - echo `which pdfinfo`
 
 # install:
-#  - wget http://poppler.freedesktop.org/poppler-0.32.0.tar.xz
+#  - wget https://poppler.freedesktop.org/poppler-0.32.0.tar.xz
 #  - tar -xJf poppler-0.32.0.tar.xz
 #  - cd poppler-0.32.0 && ./configure --prefix=/usr && make && make install
 
@@ -27,7 +27,7 @@ r_packages:
  - covr
 
 r_build_args: '--no-build-vignettes'
- 
+
 # remove default --as-cran so testthat tests are run (also avoids to useless check notes)
 r_check_args: '--ignore-vignettes'
 

R/04InternalFunctions.R

@@ -676,7 +676,7 @@ ProcessArxiv <- function(arxinfo){
     regm <- regmatches(arxinfo, m)
     res$eprint <- regm[[1]][2]
   }
-  res$url <- paste0('http://arxiv.org/abs/', res$eprint)
+  res$url <- paste0('https://arxiv.org/abs/', res$eprint)
   res
 }
 
@@ -723,7 +723,7 @@ ProcessArxiv <- function(arxinfo){
 ##                                                useBytes = TRUE))[[1]][2])){
 ##     res$eprinttype <- "arxiv"
 ##     res$eprint <- eprint
-##     res$url <- paste0("http://arxiv.org/abs/", eprint)
+##     res$url <- paste0("https://arxiv.org/abs/", eprint)
 ##     attr(res, "entry") <- "misc"
 ##   }else{
 ##     if (is.na(numbers) || numbers == "" || as.character(year) == numbers){
@@ -797,7 +797,7 @@ ParseGSCitesNew <- function(title, author, year, src, cited_by, encoding,
                                                useBytes = TRUE))[[1]][2])){
     res$eprinttype <- "arxiv"
     res$eprint <- eprint
-    res$url <- paste0("http://arxiv.org/abs/", eprint)
+    res$url <- paste0("https://arxiv.org/abs/", eprint)
     attr(res, "entry") <- "misc"
   }else{
     if (is.na(numbers) || numbers == "" || as.character(year) == numbers){

R/BibEntryAssignOp.R

@@ -17,7 +17,7 @@
 #'   title = "My Work", year = "2012")
 #' bib$year <- 2014
 #' bib$author <- "McLean, M. W. and Carroll, R. J." 
-#' bib$url <- "http://example.com"
+#' bib$url <- "https://example.com"
 #' bib
 #' 
 #' bib <- c(bib, as.BibEntry(citation()))

R/BibEntryReplaceOp.R

@@ -26,10 +26,10 @@
 #' ## add month to Serban et al., add URL and urldate to Jennings et al., and
 #' ##   add DOI and correct journal to Garcia et al.
 #' bib[seq_len(3L)] <- list(c(date="2013-12"), 
-#'                         c(url="http://bsb.eurasipjournals.com/content/2013/1/13", 
 #'                           urldate = "2014-02-02"), 
 #'                         c(doi="10.1093/bioinformatics/btt608", 
 #'                           journal = "Bioinformatics")) 
+#'                         c(url="https://bsb.eurasipjournals.com/content/2013/1/13", 
 #' print(bib[seq_len(3L)], .opts = list(sorting = "none", bib.style = "alphabetic"))
 #' bib2 <- bib[seq_len(3L)]
 #' bib2[2:3] <- bib[5:6]

R/CommonFormatFuns.R

@@ -222,8 +222,8 @@ GetFormatFunctions <- function(docstyle = "text", DateFormatter){
 
           if (eprinttype %in% c("arxiv", "pubmed", "jstor")){
             base.url <- switch(eprinttype,
-                               jstor = "http://www.jstor.org/stable/",
-                               arxiv = "http://arxiv.org/abs/",
+                               jstor = "https://www.jstor.org/stable/",
+                               arxiv = "https://arxiv.org/abs/",
                                pubmed = paste0("https://eutils.ncbi.nlm.nih.",
                                                "gov/entrez/eutils/",
                                                "elink.fcgi?dbfrom=pubmed&",
@@ -268,9 +268,9 @@ GetFormatFunctions <- function(docstyle = "text", DateFormatter){
 
           if (eprinttype %in% c("arxiv", "pubmed", "jstor")){
             base.url <- switch(eprinttype,
-                               jstor = "http://www.jstor.org/stable/",
-                               arxiv = "http://arxiv.org/abs/",
-                               pubmed = paste0("http://eutils.ncbi.nlm.nih.",
+                               jstor = "https://www.jstor.org/stable/",
+                               arxiv = "https://arxiv.org/abs/",
+                               pubmed = paste0("https://eutils.ncbi.nlm.nih.",
                                                "gov/entrez/eutils/",
                                                "elink.fcgi?dbfrom=pubmed&",
                                                "cmd=prlinks&retmode=ref&id="),

R/GetBibEntryWithDOI.R

@@ -14,7 +14,7 @@
 #' API is temporarily
 #' written to a file and then read back into \code{R} and return as a
 #' \code{BibEntry} object.
-#' @references \url{http://www.doi.org/tools.html}
+#' @references \url{https://www.doi.org/tools.html}
 #' @importFrom httr http_error GET content http_error modify_url
 #' @importFrom utils URLdecode
 #' @seealso \code{\link{ReadCrossRef}}, \code{\link{BibEntry}}

R/GetDOIs.R

@@ -12,9 +12,9 @@
 #' @family pubmed
 #' @note Only entries in \code{bib} that do not already contain a value in the
 #' \sQuote{doi} field will be searched for.
-#' @references \url{http://search.crossref.org/help/api}
+#' @references \url{https://search.crossref.org/help/api}
 #' @examples
-#' if (interactive() && !httr::http_error("http://search.crossref.org")){
+#' if (interactive() && !httr::http_error("https://search.crossref.org")){
 #'   BibOptions(check.entries = FALSE, sorting = "none")
 #'   bib <- ReadBib(system.file("Bib", "RJC.bib", package = "RefManageR"))[1:5]
 #'   bib <- GetDOIs(bib)
@@ -31,7 +31,7 @@ GetDOIs <- function(bib){
     headers <- list('Accept' = 'application/json',
                     'Content-Type' = 'application/json')
 
-    ## json.res <- postForm("http://search.crossref.org/links",
+    ## json.res <- postForm("https://search.crossref.org/links",
     ##              .opts = list(postfields = json.bib, httpheader = headers))
     ## json.res <- try(fromJSON(json.res), TRUE)
     json.res <- httr::POST("https://search.crossref.org/links", body = json.bib,

R/ReadCrossRef.R

@@ -65,9 +65,9 @@
 #' package \code{rcrossref} for larger queries and deep paging
 #' @family pubmed
 #' @references Newer API: \url{https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md},
-#' Older API: \url{http://search.crossref.org/help/api}
+#' Older API: \url{https://search.crossref.org/help/api}
 #' @examples
-#' if (interactive() && !httr::http_error("http://search.crossref.org/")){
+#' if (interactive() && !httr::http_error("https://search.crossref.org/")){
 #'   BibOptions(check.entries = FALSE)
 #'   ## 3 results from the American Statistical Association involving "regression"
 #'   ReadCrossRef("regression", filter = list(prefix="10.1198"), limit = 3)
@@ -107,7 +107,7 @@ ReadCrossRef <- function(query = "", filter = list(), limit = 5, offset = 0,
       if (.is_not_nonempty_text(query))
           stop(gettextf("specify a valid %s", sQuote("query")))
 
-      results <- GET("http://search.crossref.org/dois",
+      results <- GET("https://search.crossref.org/dois",
                          query = list(q=query, year=year,
                          sort=sort, rows=limit))
     }else{
@@ -122,7 +122,7 @@ ReadCrossRef <- function(query = "", filter = list(), limit = 5, offset = 0,
       if (length(filter))
           params$filter <- paste(paste0(names(filter),":",filter),
                                  collapse = ",")
-      results <- GET("http://api.crossref.org/works", query=params)
+      results <- GET("https://api.crossref.org/works", query=params)
     }
     fromj <- content(results, type = "application/json", encoding = "UTF-8")
     if (http_error(results)){