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

[Yury Aulchenko]

Dear All,

I consider this (SVN rev 833, see commit details below) version of GenABEL as a release candidate for v. 1.7-0 -- it passes all checks on latest R-devel (2011-12-04 r57813) without any problems, at least on Mac OS X Lion. I am going to think if I can add some more easy fixes tomorrow, check under Debian, and submit to CRAN late tomorrow or early Fri. 

best wishes,
Yurii
-------------------------------------------------------
Yurii Aulchenko, PhD, Dr. Habil.
Independent researcher and consultant
yurii [dot] aulchenko [at] gmail [dot] com

On Dec 7, 2011, at 4:56 PM, noreply at r-forge.wu-wien.ac.at wrote:

> 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)
> -}
> +) 
> 
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