Merge pull request #18 from iagomosqueira/master

Added check.software to compare pkg versions with SOFTWARE,bib

DESCRIPTION

@@ -23,5 +23,5 @@ Description: General framework to organize data, methods, and results used in
 License: GPL-3
 URL: https://github.com/ices-tools-prod/TAF
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(old_usage=TRUE)

NAMESPACE

@@ -5,6 +5,7 @@ export(already.in.taf.library)
 export(boot.dir)
 export(boot.dir.inside)
 export(boot.exists)
+export(check.software)
 export(clean)
 export(clean.boot)
 export(clean.data)

R/check.software.R

@@ -0,0 +1,59 @@
+#' Check versions with those in SOFTWARE.bib
+#' 
+#' Compare installed and required package versions
+#'
+#' @details
+#' A SOFTWARE.bib file can be use to record what package versions a certain
+#' analysis expects. Those available in the running session can be compared
+#' with those listed in the file. A warning is printed if the former are
+#' earlier that the later.
+#'
+#' @return TRUE or FALSE if available packages match those required or not.
+#'
+#' @name check.software
+#' @rdname check.software
+#'
+#' @seealso [draft.software()]
+#' @keywords classes
+#' @export
+
+check.software <- function() {
+
+  # GET bib file                         
+  bibfile <- (file.path(boot.dir(), "SOFTWARE.bib"))
+
+  # CHECK file exists
+  if(!file.exists(bibfile))
+    stop(paste0("File ", boot.dir(), "/SOFTWARE.bib does not exist"))
+
+  # READ bib file
+  entries <- taf.sources("software")
+
+  # EXTRACT versions
+  versions <- sapply(entries, '[[', 'version')
+
+  # COMPARE with available in session: 0 if equal, -1 is too old, 1 if newer
+  comparison <- unlist(lapply(setNames(nm=names(versions)), function(x)
+    compareVersion(as.character(packageVersion(x)), versions[x])))
+
+  # FIND those too old
+  toold <- comparison == -1
+
+  # WARN if any SOFTWARE.bib:versions > available
+  if(any(toold)) {
+
+    msg <- lapply(names(toold)[toold], function(x)
+      paste0(x, ": ", packageVersion(x), " installed but ", versions[x],
+      " required\n"))
+
+    warning(strwrap(msg, prefix="; ", initial=""))
+
+    invisible(FALSE)
+
+  } else {
+    invisible(TRUE)
+  }
+}
+
+
+