[Genabel-commits] r833 - in pkg/GenABEL: . R

[noreply at r-forge.r-project.org]

Author: yurii
Date: 2011-12-07 16:56:16 +0100 (Wed, 07 Dec 2011)
New Revision: 833

Modified:
   pkg/GenABEL/DESCRIPTION
   pkg/GenABEL/R/zzz.R
Log:
release candidate for v 1.7-0 passing all checks

Modified: pkg/GenABEL/DESCRIPTION
===================================================================
--- pkg/GenABEL/DESCRIPTION	2011-12-07 15:53:53 UTC (rev 832)
+++ pkg/GenABEL/DESCRIPTION	2011-12-07 15:56:16 UTC (rev 833)
@@ -5,7 +5,7 @@
 Date: 2011-12-05
 Author: GenABEL developers
 Maintainer: GenABEL developers <genabel.project at gmail.com>
-Depends: R (>= 2.10.0), methods, MASS
+Depends: R (>= 2.10.0), methods, MASS, utils
 Suggests: qvalue, genetics, haplo.stats, DatABEL (>= 0.9-0), hglm, MetABEL, PredictABEL
 Description: a package for genome-wide association analysis between 
              quantitative or binary traits and single-nucleotide

Modified: pkg/GenABEL/R/zzz.R
===================================================================
--- pkg/GenABEL/R/zzz.R	2011-12-07 15:53:53 UTC (rev 832)
+++ pkg/GenABEL/R/zzz.R	2011-12-07 15:56:16 UTC (rev 833)
@@ -1,62 +1,65 @@
 .onLoad <- function(lib, pkg) {
-	if (require(utils)) {
-		pkgDescription <- packageDescription(pkg)
-		pkgVersion <- pkgDescription$Version
-		pkgDate <- pkgDescription$Date
-		welcomeMessage <- paste(pkg," v. ",pkgVersion," (",pkgDate,") loaded\n",sep="")
-		# check if CRAN version is the same as loaded
-		cranVersion <- checkPackageVersionOnCRAN(pkg)
-		if (!is.null(cranVersion)) 
-			if (pkgVersion != cranVersion) {
-				welcomeMessage <- paste(welcomeMessage,
-						"\nInstalled ",pkg," version (",pkgVersion,") is not the same as stable\n",
-						"version available from CRAN (",cranVersion,"). Unless used intentionally,\n",
-						"consider updating to the latest CRAN version. For that, use\n",
-						"'install.packages(\"",pkg,"\")', or ask your system administrator\n",
-						"to update the package.\n\n",sep="")
-			}
-	}
-	# check for news
-	address <- c(
-			"http://genabel.r-forge.r-project.org/version_and_news.html",
-			"http://www.genabel.org/sites/default/files/version_and_news.html"
-	)
-	svtmo <- options("timeout")
-	options("timeout"=10)
-	tryRes1 <- 0; class(tryRes1) <- "try-error"
-	curaddr <- 1
-	while (class(tryRes1) == "try-error" && curaddr <= length(address) ) {
-		suppressWarnings(
-				tryRes0 <- try(conn <- url(address[curaddr]),silent=TRUE)
-		)
-		suppressWarnings(
-				tryRes1 <- try(fulltext <- readLines(conn),silent=TRUE)
-		)
-		close(conn)
-		curaddr <- curaddr + 1
-	}
-	if (class(tryRes1) != "try-error") {
-		if (length(fulltext)>0)
-		{
-			# message to all users
-			strnews <- grep("<messagetoall>",tolower(fulltext))
-			endnews <- grep("</messagetoall>",tolower(fulltext))
-			if (length(strnews)>0 && length(endnews)>0) 
-				if ((endnews-1) >= (strnews+1)) {
+}
+
+setHook(packageEvent("GenABEL", "onLoad"),
+		function() {
+			pkgDescription <- packageDescription(pkg)
+			pkgVersion <- pkgDescription$Version
+			pkgDate <- pkgDescription$Date
+			welcomeMessage <- paste(pkg," v. ",pkgVersion," (",pkgDate,") loaded\n",sep="")
+			# check if CRAN version is the same as loaded
+			cranVersion <- checkPackageVersionOnCRAN(pkg)
+			if (!is.null(cranVersion)) 
+				if (pkgVersion != cranVersion) {
 					welcomeMessage <- paste(welcomeMessage,
-							fulltext[(strnews+1):(endnews-1)],sep="\n")
+							"\nInstalled ",pkg," version (",pkgVersion,") is not the same as stable\n",
+							"version available from CRAN (",cranVersion,"). Unless used intentionally,\n",
+							"consider updating to the latest CRAN version. For that, use\n",
+							"'install.packages(\"",pkg,"\")', or ask your system administrator\n",
+							"to update the package.\n\n",sep="")
 				}
-			# check for specific package news
-			strnews <- grep(paste("<",pkg,"news>",sep=""),tolower(fulltext))
-			endnews <- grep(paste("</",pkg,"news>",sep=""),tolower(fulltext))
-			if (length(strnews)>0 && length(endnews)>0) 
-				if ((endnews-1) >= (strnews+1)) {
-					welcomeMessage <- paste(welcomeMessage,
-							fulltext[(strnews+1):(endnews-1)],sep="\n")
+			# check for news
+			address <- c(
+					"http://genabel.r-forge.r-project.org/version_and_news.html",
+					"http://www.genabel.org/sites/default/files/version_and_news.html"
+			)
+			svtmo <- options("timeout")
+			options("timeout"=10)
+			tryRes1 <- 0; class(tryRes1) <- "try-error"
+			curaddr <- 1
+			while (class(tryRes1) == "try-error" && curaddr <= length(address) ) {
+				suppressWarnings(
+						tryRes0 <- try(conn <- url(address[curaddr]),silent=TRUE)
+				)
+				suppressWarnings(
+						tryRes1 <- try(fulltext <- readLines(conn),silent=TRUE)
+				)
+				close(conn)
+				curaddr <- curaddr + 1
+			}
+			if (class(tryRes1) != "try-error") {
+				if (length(fulltext)>0)
+				{
+					# message to all users
+					strnews <- grep("<messagetoall>",tolower(fulltext))
+					endnews <- grep("</messagetoall>",tolower(fulltext))
+					if (length(strnews)>0 && length(endnews)>0) 
+						if ((endnews-1) >= (strnews+1)) {
+							welcomeMessage <- paste(welcomeMessage,
+									fulltext[(strnews+1):(endnews-1)],sep="\n")
+						}
+					# check for specific package news
+					strnews <- grep(paste("<",pkg,"news>",sep=""),tolower(fulltext))
+					endnews <- grep(paste("</",pkg,"news>",sep=""),tolower(fulltext))
+					if (length(strnews)>0 && length(endnews)>0) 
+						if ((endnews-1) >= (strnews+1)) {
+							welcomeMessage <- paste(welcomeMessage,
+									fulltext[(strnews+1):(endnews-1)],sep="\n")
+						}
 				}
+				#rm(a,fulltext,ver)
+			}
+			options("timeout"=svtmo)
+			packageStartupMessage(welcomeMessage)
 		}
-		#rm(a,fulltext,ver)
-	}
-	options("timeout"=svtmo)
-	packageStartupMessage(welcomeMessage)
-}
+)