From cf5409967a9907c4b6293516ef7098902f48c3e8 Mon Sep 17 00:00:00 2001
From: Mark van der Loo <mark.vanderloo@gmail.com>
Date: Tue, 19 Mar 2024 08:59:10 +0100
Subject: [PATCH] resolved some notes

---
 R/convert_landing.R                      | 4 ++--
 R/crossref.R                             | 8 ++++----
 vignettes/roles_and_responsibilities.Rmd | 3 ++-
 3 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/R/convert_landing.R b/R/convert_landing.R
index 7ce3f774..a81079ae 100644
--- a/R/convert_landing.R
+++ b/R/convert_landing.R
@@ -8,7 +8,7 @@ convert_proofs <- function(issue, action = "report_only", clean = TRUE) {
   share_path <- normalizePath("../../share", mustWork = TRUE)
   web_path <- normalizePath("../../rjournal.github.io", mustWork = TRUE)
 
-  config <- yaml.load_file(file.path(web_path, "_config.yml"))
+  config <- yaml::yaml.load_file(file.path(web_path, "_config.yml"))
   issues <- sapply(config$issues, function(x) x$issue)
   this_issue <- which(issues == issue)
   if (length(this_issue) == 0L) stop("issue not in _config.yml")
@@ -112,7 +112,7 @@ convert_proofs <- function(issue, action = "report_only", clean = TRUE) {
       file.copy(localfrom, file.path(issue, art, "oRJwrapper.pdf"))
       t0 <- try(in_dir(
         file.path(issue, art),
-        texi2pdf("RJwrapper.tex", texinputs = share_path, clean = clean)
+        tools::texi2pdf("RJwrapper.tex", texinputs = share_path, clean = clean)
       ))
       pdf_list <- get_md_from_pdf(localfrom)
       file.copy(file.path(issue, art, "oRJwrapper.pdf"), localfrom)
diff --git a/R/crossref.R b/R/crossref.R
index 28ac354e..16dcdd9f 100644
--- a/R/crossref.R
+++ b/R/crossref.R
@@ -279,7 +279,7 @@ newDeposit <- function(x, out = "") {
 
 ## we need to get into format for crossref
 ## require(yaml)
-## cfg = yaml.load_file("path/to/_config.yml")
+## cfg = yaml::yaml.load_file("path/to/_config.yml")
 ## i = cfg[[ind]]
 ##
 process_config_yml_component <- function(i) {
@@ -313,7 +313,7 @@ load_issues <- function() {
     warning("Not in proper directory: start in RJournal/articles")
     return()
   }
-  cfg <- yaml.load_file("../rjournal.github.io/_config.yml")
+  cfg <- yaml::yaml.load_file("../rjournal.github.io/_config.yml")
   cfg$issues
 }
 
@@ -379,7 +379,7 @@ upload_dois_from_issue <- function(issue,
 ## create a DOI from the an issue component of the config$issues
 ##
 ## require(yaml)
-## cfg = yaml.load_file("../rjournal.github.io/_config.yml")
+## cfg = yaml::yaml.load_file("../rjournal.github.io/_config.yml")
 ## issue = cfg$issue[[length(cfg$issue)]] # last one
 ##
 ## or
@@ -404,7 +404,7 @@ create_doi_from_issue <- function(issue, outdir = "/tmp/DOI_XML/") {
 
 ## create all DOI entries for initial upload
 create_doi_xmls <- function(outdir = "/tmp/DOI_XML/", config = "../rjournal.github.io/_config.yml") {
-  cfg <- yaml.load_file(config)
+  cfg <- yaml::yaml.load_file(config)
   ## identify volume, volnum
   dir.create(outdir)
   sapply(cfg$issues, create_doi_from_issue, outdir = outdir)
diff --git a/vignettes/roles_and_responsibilities.Rmd b/vignettes/roles_and_responsibilities.Rmd
index ccd4446d..7fe07d33 100644
--- a/vignettes/roles_and_responsibilities.Rmd
+++ b/vignettes/roles_and_responsibilities.Rmd
@@ -61,7 +61,8 @@ the EIC ensures that the quarterly issues are produced and published.
 An EE is responsible for
 
 - Proper and timely handling of papers under their responsibility.
-- Take and communicate the editorial decision (Accept/Minor/Major/Reject) for papers under their responsibility.
+- Take the editorial decision (Accept/Minor/Major/Reject) for papers under their responsibility and
+  communicate with the authors.
 - Supporting the EIC in recruiting AEs and EEs.
 
 In particular, the EE communicates with AE and with the authors of submissions.