Bioconductor · LiNk-NY · Jan 9, 2023 · Feb 10, 2023 · Feb 10, 2023 · Feb 10, 2023
diff --git a/NEWS b/NEWS
@@ -1,3 +1,11 @@
+CHANGES IN VERSION 1.68.0
+-------------------------
+
+NEW FEATURES
+
+    o getPackageNEWS and printNEWS are deprecated from biocViews.
+    See help('biocViews-deprecated') for more details.
+
 CHANGES IN VERSION 1.67.0
 -------------------------
 

diff --git a/R/getPackageNEWS.R b/R/getPackageNEWS.R
@@ -9,13 +9,20 @@
 ## collate package NEWS files using starting version number in
 ## prevRepos, and membership in currRepos as references. Package
 ## source tree rooted at srcDir, possibiblly as tarred files
-
+utils::globalVariables("Version")
 # repo:  bioc data/experiment workflows
 getPackageNEWS <- function(prevRepos="3.6",
                            currRepos="3.7",
                            repo=c("bioc", "data/experiment", "workflows"),
                            srcdir=NULL){
-
+    .Deprecated(
+        "getPackagesNEWS", "ReleaseLaunch",
+        c(
+            "'getPackageNEWS' is deprecated.\n",
+            "Use 'ReleaseLaunch::getPackagesNEWS' instead.\n",
+            "See help(\"biocViews-deprecated\")"
+        )
+    )
     repo <- match.arg(repo)
     URL_BASE <- "http://master.bioconductor.org/packages/"
     VIEWS <- "%s%s/%s/VIEWS"
@@ -73,99 +80,17 @@ getPackageNEWS <- function(prevRepos="3.6",
 
 }
 
-
-## based on tools:::.build_news_db()
-getNEWSFromFile <- function (dir, destfile, format = NULL, reader = NULL,
-    output=c("md", "text"))
-{
-    mdIfy <- function(txt)
-    {
-        lines <- strsplit(txt, "\n")
-        segs <- lines[[1]]
-        segs <- sub("^    o +", "- ", segs)
-        segs <- sub("^\t", "  ", segs)
-        return(paste(segs, collapse="\n"))
-    }
-
-    newsRdFile <- file.path(dir, "NEWS.Rd") ## should never be found
-    newsRdFile2 <- file.path(dir, "inst", "NEWS.Rd")
-
-    if (!file_test("-f", newsRdFile) && !file_test("-f", newsRdFile2)) {
-
-
-        newsMdFile <- file.path(dir, "NEWS.md")
-        newsMdFile2 <- file.path(dir, "inst", "NEWS.md")
-
-        if (!file_test("-f", newsMdFile) && !file_test("-f", newsMdFile2)) {
-
-
-            nfile <- file.path(dir, "NEWS")
-            nfile2 <- file.path(dir, "inst", "NEWS")
-
-
-            if (!file_test("-f", nfile) && !file_test("-f", nfile2))
-                return(invisible())
-
-            nfile <- ifelse(file_test("-f", nfile), nfile, nfile2)
-
-            if (!is.null(format))
-                .NotYetUsed("format", FALSE)
-            if (!is.null(reader))
-                .NotYetUsed("reader", FALSE)
-
-            file <- file(destfile, "w+")
-            on.exit(close(file))
-            news <- paste(readLines(nfile), collapse="\n")
-            if ("md" == output)
-                news = mdIfy(news)
-            cat(news, file=file)
-            return(invisible())
-        }
-
-        newsMdFile <- ifelse(file_test("-f", newsMdFile), newsMdFile,
-                             newsMdFile2)
-        file <- file(destfile, "w+")
-        on.exit(close(file))
-        db <- tools:::.build_news_db_from_package_NEWS_md(newsMdFile)
-        news <- NULL
-        try(news <- capture.output(print(db)))
-        if (is.null(news))
-            {
-                message(sprintf("Error building news database for %s/%s",
-                                dir, destfile))
-                return(invisible())
-            }
-        news <- paste(news, collapse="\n")
-        if ("md" == output)
-            news <- mdIfy(news)
-        cat(news, file=file)
-        return(invisible())
-    }
-
-    newsRdFile <- ifelse(file_test("-f", newsRdFile), newsRdFile, newsRdFile2)
-
-    file <- file(destfile, "w+")
-    on.exit(close(file))
-    db <- tools:::.build_news_db_from_package_NEWS_Rd(newsRdFile)
-    news <- NULL
-    try(news <- capture.output(print(db)))
-    if (is.null(news))
-    {
-        message(sprintf("Error building news database for %s/%s",
-            dir, destfile))
-        return(invisible())
-    }
-    news <- paste(news, collapse="\n")
-    if ("md" == output)
-        news <- mdIfy(news)
-    cat(news, file=file)
-    return(invisible())
-}
-
-
 printNEWS <- function(dbs, destfile, overwrite=FALSE, width=68,
                       output=c("md", "text"), relativeLink=FALSE, ...)
 {
+    .Deprecated(
+        "printNEWS", "ReleaseLaunch",
+        c(
+            "'printNEWS' is deprecated.\n",
+            "Use 'ReleaseLaunch::printNEWS' instead.\n",
+            "See help(\"biocViews-deprecated\")"
+        )
+    )
     output <- match.arg(output)
     dbs <- lapply(dbs, function(db) {
          db[["Text"]] <- sapply(db[["Text"]], function(elt) {

diff --git a/R/repository.R b/R/repository.R
@@ -308,6 +308,94 @@ extractReadmes <- function(reposRoot, srcContrib, destDir) {
     extractTopLevelFiles(reposRoot, srcContrib, destDir, "README")
 }
 
+## based on tools:::.build_news_db()
+getNEWSFromFile <- function (dir, destfile, format = NULL, reader = NULL,
+    output=c("md", "text"))
+{
+    mdIfy <- function(txt)
+    {
+        lines <- strsplit(txt, "\n")
+        segs <- lines[[1]]
+        segs <- sub("^    o +", "- ", segs)
+        segs <- sub("^\t", "  ", segs)
+        return(paste(segs, collapse="\n"))
+    }
+
+    newsRdFile <- file.path(dir, "NEWS.Rd") ## should never be found
+    newsRdFile2 <- file.path(dir, "inst", "NEWS.Rd")
+
+    if (!file_test("-f", newsRdFile) && !file_test("-f", newsRdFile2)) {
+
+
+        newsMdFile <- file.path(dir, "NEWS.md")
+        newsMdFile2 <- file.path(dir, "inst", "NEWS.md")
+
+        if (!file_test("-f", newsMdFile) && !file_test("-f", newsMdFile2)) {
+
+
+            nfile <- file.path(dir, "NEWS")
+            nfile2 <- file.path(dir, "inst", "NEWS")
+
+
+            if (!file_test("-f", nfile) && !file_test("-f", nfile2))
+                return(invisible())
+
+            nfile <- ifelse(file_test("-f", nfile), nfile, nfile2)
+
+            if (!is.null(format))
+                .NotYetUsed("format", FALSE)
+            if (!is.null(reader))
+                .NotYetUsed("reader", FALSE)
+
+            file <- file(destfile, "w+")
+            on.exit(close(file))
+            news <- paste(readLines(nfile), collapse="\n")
+            if ("md" == output)
+                news = mdIfy(news)
+            cat(news, file=file)
+            return(invisible())
+        }
+
+        newsMdFile <- ifelse(file_test("-f", newsMdFile), newsMdFile,
+                             newsMdFile2)
+        file <- file(destfile, "w+")
+        on.exit(close(file))
+        db <- tools:::.build_news_db_from_package_NEWS_md(newsMdFile)
+        news <- NULL
+        try(news <- capture.output(print(db)))
+        if (is.null(news))
+            {
+                message(sprintf("Error building news database for %s/%s",
+                                dir, destfile))
+                return(invisible())
+            }
+        news <- paste(news, collapse="\n")
+        if ("md" == output)
+            news <- mdIfy(news)
+        cat(news, file=file)
+        return(invisible())
+    }
+
+    newsRdFile <- ifelse(file_test("-f", newsRdFile), newsRdFile, newsRdFile2)
+
+    file <- file(destfile, "w+")
+    on.exit(close(file))
+    db <- tools:::.build_news_db_from_package_NEWS_Rd(newsRdFile)
+    news <- NULL
+    try(news <- capture.output(print(db)))
+    if (is.null(news))
+    {
+        message(sprintf("Error building news database for %s/%s",
+            dir, destfile))
+        return(invisible())
+    }
+    news <- paste(news, collapse="\n")
+    if ("md" == output)
+        news <- mdIfy(news)
+    cat(news, file=file)
+    return(invisible())
+}
+
 extractNEWS <- function(reposRoot, srcContrib, destDir) {
 
     if (missing(destDir))

diff --git a/man/getPackageNEWS.Rd → man/biocViews-deprecated.Rd b/man/getPackageNEWS.Rd → man/biocViews-deprecated.Rd
@@ -1,24 +1,28 @@
-\name{getPackageNEWS}
+\name{biocViews-deprecated}
+
 \alias{getPackageNEWS}
 \alias{printNEWS}
-\title{
-  Retrieve and print package NEWS
-}
-\description{
+\alias{biocViews-deprecated}
 
-  These functions visit two Bioconductor releases, identifying
-  packages that are present in the \sQuote{current} repository and have
-  NEWS since the base version of the same package in the
-  \sQuote{previous} release. All NEWS is reported for packages only
-  in the current repository.
+\title{Deprecated NEWS functions in biocViews}
+
+\description{
+    Functions working with a package's NEWS file have been moved out of the
+    package. These include \code{getPackageNEWS}, and \code{printNEWS}.
+    Please see the \code{ReleaseLaunch} package.
 }
+
 \usage{
-getPackageNEWS(prevRepos="3.6",
-	       currRepos="3.7",
-	       repo=c("bioc", "data/experiment", "workflows"),
-	       srcdir = NULL)
-printNEWS(dbs, destfile, overwrite = FALSE, width = 68,
-	  output=c("md", "text"), relativeLink=FALSE, ...)
+getPackageNEWS(
+    prevRepos="3.6",
+	currRepos="3.7",
+	repo=c("bioc", "data/experiment", "workflows"),
+	srcdir = NULL
+)
+printNEWS(
+    dbs, destfile, overwrite = FALSE, width = 68, output=c("md", "text"),
+    relativeLink=FALSE, ...
+)
 }
 
 \arguments{
@@ -53,8 +57,8 @@ printNEWS(dbs, destfile, overwrite = FALSE, width = 68,
   'https//bioconductor.org'. default: FALSE is full url.}
 
   \item{...}{additional arguments, unused.}
-
 }
+
 \value{
   A list of \code{news_db} files, as returned by \code{utils::news},
   for each package for which relevant NEWS is available.
@@ -63,4 +67,6 @@ printNEWS(dbs, destfile, overwrite = FALSE, width = 68,
   Martin Morgan \url{[email protected]} and Lori Shepherd
 }
 
+\seealso{\url{https://github.com/Bioconductor/ReleaseLaunch}}
+
 \keyword{manip}% __ONLY ONE__ keyword per line