From: <chr...@us...> - 2011-03-07 15:09:21
|
Revision: 180 http://bugs-r.svn.sourceforge.net/bugs-r/?rev=180&view=rev Author: chris-jackson Date: 2011-03-07 15:09:12 +0000 (Mon, 07 Mar 2011) Log Message: ----------- Changes to allow BRugs to work seamlessly with an existing installation of OpenBUGS on Linux and Windows. Requires OpenBUGS 3.2.1 or later. Modified Paths: -------------- branches/linux/BRugs/.Rbuildignore branches/linux/BRugs/DESCRIPTION branches/linux/BRugs/NEWS branches/linux/BRugs/R/bugs.data.R branches/linux/BRugs/R/formatdata.R branches/linux/BRugs/R/internal.R branches/linux/BRugs/R/samples.density.R branches/linux/BRugs/R/unix/help.R branches/linux/BRugs/R/windows/help.R branches/linux/BRugs/R/zzz.R branches/linux/BRugs/man/BRugs.Rd branches/linux/BRugs/man/BRugsFit.Rd branches/linux/BRugs/man/bugs.data.Rd branches/linux/BRugs/src/BugsHelper.c branches/linux/BRugs/src/Makevars branches/linux/BRugs/tests/BRugs.R branches/linux/BRugs/tests/examples.R branches/linux/BRugs/tests/functions.R Added Paths: ----------- branches/linux/BRugs/Changelog branches/linux/BRugs/R/unix/internal.R branches/linux/BRugs/R/unix/zzz.R branches/linux/BRugs/R/unix/zzz.R.in branches/linux/BRugs/R/windows/internal.R branches/linux/BRugs/R/windows/zzz.R branches/linux/BRugs/configure branches/linux/BRugs/configure.ac branches/linux/BRugs/configure.win branches/linux/BRugs/src/Makefile.win branches/linux/BRugs/src/Makevars.in Removed Paths: ------------- branches/linux/BRugs/R/internal-linux.R branches/linux/BRugs/R/internal-win.R branches/linux/BRugs/inst/README-inst_OpenBUGS branches/linux/BRugs/src/Makevars.win Modified: branches/linux/BRugs/.Rbuildignore =================================================================== --- branches/linux/BRugs/.Rbuildignore 2010-11-13 17:31:25 UTC (rev 179) +++ branches/linux/BRugs/.Rbuildignore 2011-03-07 15:09:12 UTC (rev 180) @@ -1,2 +1,3 @@ -inst/README-inst_OpenBUGS exec/BugsHelper +exec +.+\.Rout Added: branches/linux/BRugs/Changelog =================================================================== --- branches/linux/BRugs/Changelog (rev 0) +++ branches/linux/BRugs/Changelog 2011-03-07 15:09:12 UTC (rev 180) @@ -0,0 +1 @@ +See "NEWS" Modified: branches/linux/BRugs/DESCRIPTION =================================================================== --- branches/linux/BRugs/DESCRIPTION 2010-11-13 17:31:25 UTC (rev 179) +++ branches/linux/BRugs/DESCRIPTION 2011-03-07 15:09:12 UTC (rev 180) @@ -1,11 +1,12 @@ Package: BRugs -Title: OpenBUGS and its R / S-PLUS interface BRugs -Version: 0.6-1 -Date: 2010-11-03 -Author: OpenBUGS was developed by Andrew Thomas, Dave Lunn, David Spiegelhalter and Nicky Best. R Code modified, extended and packaged for R by Uwe Ligges and Sibylle Sturtz. Some ideas taken from the R2WinBUGS package based on code by Andrew Gelman. With considerable contributions by Gregor Gorjanc. Linux port of BRugs and other developments by Chris Jackson. -Description: An R / S-PLUS package containing OpenBUGS and its R / S-PLUS interface BRugs. -Maintainer: Uwe Ligges <li...@st...> -Depends: R (>= 2.5.0), coda +Title: R interface to the OpenBUGS MCMC software +Version: 0.7 +Date: 2011-03-07 +Author: OpenBUGS was developed by Andrew Thomas, Dave Lunn, David Spiegelhalter and Nicky Best. R interface developed by Uwe Ligges, Sibylle Sturtz, Andrew Gelman, Gregor Gorjanc and Chris Jackson. Linux port and most recent developments by Chris Jackson. +Description: Fully-interactive R interface to the OpenBUGS software for Bayesian analysis using MCMC sampling +Maintainer: Chris Jackson <chr...@mr...> +Depends: R (>= 2.5.0), utils, coda +SystemRequirements: OpenBUGS (>= 3.2.1) Archs: i386 License: GPL-2 URL: http://www.openbugs.info/ Modified: branches/linux/BRugs/NEWS =================================================================== --- branches/linux/BRugs/NEWS 2010-11-13 17:31:25 UTC (rev 179) +++ branches/linux/BRugs/NEWS 2011-03-07 15:09:12 UTC (rev 180) @@ -1,3 +1,38 @@ +Version 0.7 +----------- + +BRugs now works with an existing installation of OpenBUGS (3.2.1 or +later) instead of being distributed with the OpenBUGS library. + +On Windows, the OpenBUGS location is determined by a registry key +which is installed by the OpenBUGS for Windows installation program. + +On Linux, the OpenBUGS shared library and documentation are assumed to +be installed together in a library directory. Using the new OpenBUGS +for Linux source package OpenBUGS-3.2.1.tar.gz or later, this library +directory is by default + +/usr/local/lib/OpenBUGS + +In most cases it should be detected automatically when installing, but +it can be changed by running, for instance + +R CMD INSTALL --configure-args='--with-openbugs=/usr/lib/OpenBUGS' + + + +Version 0.61 +------------ +Fix for crash in bugsData + + +Version 0.6 +----------- + +Forked from the version of BRugs (0.5.3) available on CRAN Extras. +This new version supports Linux for the first time, as detailed below. + + CHANGES MADE FOR LINUX PORT OF BRugs * A C program called BugsHelper is used to call the OpenBUGS shared Modified: branches/linux/BRugs/R/bugs.data.R =================================================================== --- branches/linux/BRugs/R/bugs.data.R 2010-11-13 17:31:25 UTC (rev 179) +++ branches/linux/BRugs/R/bugs.data.R 2011-03-07 15:09:12 UTC (rev 180) @@ -1,12 +1,14 @@ "bugsData" <- function(data, fileName = file.path(tempdir(), "data.txt"), format="E", digits = 5){ - if(is.numeric(unlist(data))) + if(is.list(data)) { + data <- lapply(data, function(x){x <- if(is.character(x)||is.factor(x)) match(x, unique(x)) else x}) if(is.R()) { write.datafile(lapply(data, formatC, digits = digits, format = format), fileName) } else { writeDatafileS4(data, towhere = "data.txt") } + } else { if(is.R()) { data.list <- lapply(as.list(data), get, pos = parent.frame(2)) Modified: branches/linux/BRugs/R/formatdata.R =================================================================== --- branches/linux/BRugs/R/formatdata.R 2010-11-13 17:31:25 UTC (rev 179) +++ branches/linux/BRugs/R/formatdata.R 2011-03-07 15:09:12 UTC (rev 180) @@ -6,7 +6,9 @@ datalist.string <- vector(n, mode = "list") datanames <- names(datalist) for (i in 1:n) { - datalist.string[[i]] <- + if (is.factor(datalist[[i]])) + datalist[[i]] <- as.integer(datalist[[i]]) + datalist.string[[i]] <- if (length(datalist[[i]]) == 1) paste(names(datalist)[i], "=", as.character(datalist[[i]]), sep = "") Deleted: branches/linux/BRugs/R/internal-linux.R =================================================================== --- branches/linux/BRugs/R/internal-linux.R 2010-11-13 17:31:25 UTC (rev 179) +++ branches/linux/BRugs/R/internal-linux.R 2011-03-07 15:09:12 UTC (rev 180) @@ -1,36 +0,0 @@ -dquote <- function(x){ - paste("\"", x, "\"", sep="") -} - -.OpenBUGS.Linux <- function(cmds, cmdtypes, args) -{ - ncmds <- length(cmds) - if (ncmds > 99999) stop("Maximum number of OpenBUGS API commands exceeded") - tempDir <- getOption("BRugsTmpdir") - ## Don't want internalize/externalize to overwrite the command - ## output buffer, so redirect its output to a separate trash can. - trashDir <- paste(tempDir, "_trash", sep="") - extFile <- getOption("BRugsExtFile") - pkgPath <- searchpaths()[search()=="package:BRugs"] - bugsPath <- paste(pkgPath, "/exec/BugsHelper", sep="") - shcmd <- paste(bugsPath, dquote(tempDir), dquote(trashDir), dquote(extFile)) - for (i in 1:ncmds) { - if (cmdtypes[i] %in% c("CharArray","RealArray")) - cat(args[[i]], file=paste(tempDir, "/input",i,".txt", sep="")) - cmdtype <- match(cmdtypes[i], .OpenBUGS.cmdtypes) - 1 - shcmd <- paste(shcmd, dquote(cmds[i]), cmdtype) - } - res <- system(shcmd) - handleRes(res) - out <- vector(ncmds, mode="list") - for (i in 1:ncmds) { - if (cmdtypes[i] %in% c("Integer","CharArray","RealArray")) - out[[i]] <- scan(paste(tempDir,"/output",i,".txt",sep=""), - switch(cmdtypes[i], - "Integer" = integer(), - "CharArray" = character(), - "RealArray" = double()), - quiet=TRUE) - } - out -} Deleted: branches/linux/BRugs/R/internal-win.R =================================================================== --- branches/linux/BRugs/R/internal-win.R 2010-11-13 17:31:25 UTC (rev 179) +++ branches/linux/BRugs/R/internal-win.R 2011-03-07 15:09:12 UTC (rev 180) @@ -1,33 +0,0 @@ -### Run a list of OpenBUGS API command strings - -.OpenBUGS.Windows <- function(cmds, cmdtypes, args) -{ - ncmds <- length(cmds) - out <- vector(ncmds, mode="list") - for (i in 1:ncmds) { - out[[i]] <- switch(cmdtypes[i], - "CmdInterpreter" = { - res <- .C("CmdInterpreter", cmds[i], nchar(cmds[i]), integer(1), PACKAGE = "BRugs") - handleRes(res[[3]]) - res - }, - "Integer" = { - values <- .C("Integer", cmds[i], nchar(cmds[i]), integer(1), integer(1), PACKAGE = "BRugs") - handleRes(values[[4]]) - as.integer(values[[3]]) - }, - "CharArray" = { - values <- .C("CharArray", cmds[i], nchar(cmds[i]), args[[i]], nchar(args[[i]]), integer(1), PACKAGE="BRugs") - handleRes(values[[5]]) - values[[3]] - }, - "RealArray" = { - values <- .C("RealArray", cmds[i], nchar(cmds[i]), args[[i]], length(args[[i]]), integer(1), PACKAGE="BRugs") - handleRes(values[[5]]) - values[[3]] - }) - - } - out -} - Modified: branches/linux/BRugs/R/internal.R =================================================================== --- branches/linux/BRugs/R/internal.R 2010-11-13 17:31:25 UTC (rev 179) +++ branches/linux/BRugs/R/internal.R 2011-03-07 15:09:12 UTC (rev 180) @@ -29,10 +29,7 @@ if (is.null(args)) args <- as.list(rep(NA, ncmds)) stopifnot(ncmds==length(cmdtypes)) stopifnot(ncmds==length(args)) - switch(Sys.info()["sysname"], - "Linux" = .OpenBUGS.Linux(cmds, cmdtypes, args), - "Windows" = .OpenBUGS.Windows(cmds, cmdtypes, args), - stop("Only Linux and Windows are supported")) + .OpenBUGS.platform(cmds, cmdtypes, args) } handleRes <- function(res) Modified: branches/linux/BRugs/R/samples.density.R =================================================================== --- branches/linux/BRugs/R/samples.density.R 2010-11-13 17:31:25 UTC (rev 179) +++ branches/linux/BRugs/R/samples.density.R 2011-03-07 15:09:12 UTC (rev 180) @@ -31,10 +31,12 @@ thin <- max(c(thin, 1)) samplesSetThin(thin) mons <- samplesMonitors(node) - if (is.R()) - par(mfrow = mfrow, ask = ask, ann = ann) - else - par(mfrow = mfrow, ask = ask) + if (plot) { + if (is.R()) + par(mfrow = mfrow, ask = ask, ann = ann) + else + par(mfrow = mfrow, ask = ask) + } result <- sapply(mons, plotDensity, plot=plot, ...) if (!is.R()) invisible() Modified: branches/linux/BRugs/R/unix/help.R =================================================================== --- branches/linux/BRugs/R/unix/help.R 2010-11-13 17:31:25 UTC (rev 179) +++ branches/linux/BRugs/R/unix/help.R 2011-03-07 15:09:12 UTC (rev 180) @@ -24,6 +24,6 @@ "switch to its window."), exdent = 4)) writeLines("Otherwise, be patient ...") - browseURL(system.file("OpenBUGS", "Manuals", "Contents.html", package="BRugs")) + browseURL(paste(options()$OpenBUGS, "doc", "Manuals", "Contents.html", sep="/")) invisible("") } Added: branches/linux/BRugs/R/unix/internal.R =================================================================== --- branches/linux/BRugs/R/unix/internal.R (rev 0) +++ branches/linux/BRugs/R/unix/internal.R 2011-03-07 15:09:12 UTC (rev 180) @@ -0,0 +1,36 @@ +dquote <- function(x){ + paste("\"", x, "\"", sep="") +} + +.OpenBUGS.platform <- function(cmds, cmdtypes, args) +{ + ncmds <- length(cmds) + if (ncmds > 99999) stop("Maximum number of OpenBUGS API commands exceeded") + tempDir <- getOption("BRugsTmpdir") + ## Don't want internalize/externalize to overwrite the command + ## output buffer, so redirect its output to a separate trash can. + trashDir <- paste(tempDir, "_trash", sep="") + extFile <- getOption("BRugsExtFile") + pkgPath <- searchpaths()[search()=="package:BRugs"] + bugsPath <- paste(pkgPath, "/exec/BugsHelper", sep="") + shcmd <- paste(bugsPath, dquote(tempDir), dquote(trashDir), dquote(extFile)) + for (i in 1:ncmds) { + if (cmdtypes[i] %in% c("CharArray","RealArray")) + cat(args[[i]], file=paste(tempDir, "/input",i,".txt", sep="")) + cmdtype <- match(cmdtypes[i], .OpenBUGS.cmdtypes) - 1 + shcmd <- paste(shcmd, dquote(cmds[i]), cmdtype) + } + res <- system(shcmd) + handleRes(res) + out <- vector(ncmds, mode="list") + for (i in 1:ncmds) { + if (cmdtypes[i] %in% c("Integer","CharArray","RealArray")) + out[[i]] <- scan(paste(tempDir,"/output",i,".txt",sep=""), + switch(cmdtypes[i], + "Integer" = integer(), + "CharArray" = character(), + "RealArray" = double()), + quiet=TRUE) + } + out +} Added: branches/linux/BRugs/R/unix/zzz.R =================================================================== --- branches/linux/BRugs/R/unix/zzz.R (rev 0) +++ branches/linux/BRugs/R/unix/zzz.R 2011-03-07 15:09:12 UTC (rev 180) @@ -0,0 +1,18 @@ +if (is.R()){ + + ".onLoad" <- function(lib, pkg){ + ## TODO any need for these to be user specifiable? + options("BRugsTmpdir" = gsub("\\\\", "/", tempdir())) + options("BRugsExtFile" = paste(basename(tempfile()), ".bug", sep="")) + options(OpenBUGS = "/home/chris/usr/lib/OpenBUGS") + + if(is.null(getOption("BRugsVerbose"))) + options("BRugsVerbose" = TRUE) + .initGlobals() + options(OpenBUGSExamples = paste(options()$OpenBUGS, "doc", "Examples", sep="/")) + } + + ".onUnload" <- function(libpath){ + } + +} Added: branches/linux/BRugs/R/unix/zzz.R.in =================================================================== --- branches/linux/BRugs/R/unix/zzz.R.in (rev 0) +++ branches/linux/BRugs/R/unix/zzz.R.in 2011-03-07 15:09:12 UTC (rev 180) @@ -0,0 +1,18 @@ +if (is.R()){ + + ".onLoad" <- function(lib, pkg){ + ## TODO any need for these to be user specifiable? + options("BRugsTmpdir" = gsub("\\\\", "/", tempdir())) + options("BRugsExtFile" = paste(basename(tempfile()), ".bug", sep="")) + options(OpenBUGS = "@OPENBUGS@") + + if(is.null(getOption("BRugsVerbose"))) + options("BRugsVerbose" = TRUE) + .initGlobals() + options(OpenBUGSExamples = paste(options()$OpenBUGS, "doc", "Examples", sep="/")) + } + + ".onUnload" <- function(libpath){ + } + +} Modified: branches/linux/BRugs/R/windows/help.R =================================================================== --- branches/linux/BRugs/R/windows/help.R 2010-11-13 17:31:25 UTC (rev 179) +++ branches/linux/BRugs/R/windows/help.R 2011-03-07 15:09:12 UTC (rev 180) @@ -2,7 +2,7 @@ { ## stolen from help.start() # a <- system.file("OpenBUGS", "Manuals", "WinBUGS Manual.html", package="BRugs") - # if (!file.exists(a)) + # if (!file.exists(a)) # stop("I can't find the html help") # a <- chartr("/", "\\", a) # message("If nothing happens, you should open `", a, "' yourself") @@ -15,9 +15,9 @@ help.WinBUGS <- function(browser = getOption("browser")) { # stolen from help.start() - a <- system.file("OpenBUGS", "Manuals", "Contents.html", package="BRugs") - if (!file.exists(a)) - stop("I can't find the html help") + a <- paste(options()$OpenBUGS, "Manuals", "Contents.html", sep="\\") + if (!file.exists(a)) + stop("HTML help not found in file ", a) if (is.R()) a <- chartr("/", "\\", a) else Added: branches/linux/BRugs/R/windows/internal.R =================================================================== --- branches/linux/BRugs/R/windows/internal.R (rev 0) +++ branches/linux/BRugs/R/windows/internal.R 2011-03-07 15:09:12 UTC (rev 180) @@ -0,0 +1,32 @@ +### Run a list of OpenBUGS API command strings + +.OpenBUGS.platform <- function(cmds, cmdtypes, args) +{ + ncmds <- length(cmds) + out <- vector(ncmds, mode="list") + for (i in 1:ncmds) { + out[[i]] <- switch(cmdtypes[i], + "CmdInterpreter" = { + res <- .C("CmdInterpreter", cmds[i], nchar(cmds[i]), integer(1), PACKAGE="libOpenBUGS") + handleRes(res[[3]]) + res + }, + "Integer" = { + values <- .C("Integer", cmds[i], nchar(cmds[i]), integer(1), integer(1), PACKAGE="libOpenBUGS") + handleRes(values[[4]]) + as.integer(values[[3]]) + }, + "CharArray" = { + values <- .C("CharArray", cmds[i], nchar(cmds[i]), args[[i]], nchar(args[[i]]), integer(1), PACKAGE="libOpenBUGS") + handleRes(values[[5]]) + values[[3]] + }, + "RealArray" = { + values <- .C("RealArray", cmds[i], nchar(cmds[i]), args[[i]], length(args[[i]]), integer(1), PACKAGE="libOpenBUGS") + handleRes(values[[5]]) + values[[3]] + }) + + } + out +} Added: branches/linux/BRugs/R/windows/zzz.R =================================================================== --- branches/linux/BRugs/R/windows/zzz.R (rev 0) +++ branches/linux/BRugs/R/windows/zzz.R 2011-03-07 15:09:12 UTC (rev 180) @@ -0,0 +1,44 @@ +if (is.R()){ + + ".onLoad" <- function(lib, pkg){ + ob.reg <- try(utils:::readRegistry("Software\\OpenBUGS","HLM")) + if (inherits(ob.reg, "try-error")) stop("OpenBUGS 3.2.1 or greater must be installed") + rnames <- names(ob.reg) + ver <- gsub("OpenBUGS ", "", rnames) + ver <- gsub("(.+)e$","\\1", ver) + version.inst <- as.numeric(paste(substr(ver, 1, 2), gsub("\\.","",substr(ver, 3, nchar(ver))), sep="")) + deps <- utils:::packageDescription("BRugs", fields="SystemRequirements") + ver <- gsub(".*OpenBUGS ?\\(>= ?(.+)\\).*", "\\1", deps) + version.req <- as.numeric(paste(substr(ver, 1, 2), gsub("\\.","",substr(ver, 3, nchar(ver))), sep="")) + if (max(version.inst) < version.req) + stop("Found OpenBUGS version ", version.inst, ". Requires ", version.req, " or greater") + ## OpenBUGS installation location + options(OpenBUGS = utils:::readRegistry(paste("Software","OpenBUGS",rnames[which.max(version.inst)],sep="\\"),"HLM")$InstallPath) + libname <- paste(options()$OpenBUGS, "libOpenBUGS.dll", sep="/") + if (!file.exists(libname)) { + stop("Shared library \"libOpenBUGS.dll\" not found in ", options()$OpenBUGS) + } + ## All checks passed - load the DLL + dyn.load(libname) + len <- nchar(options()$OpenBUGS) + .C("SetWorkingDir", as.character(options()$OpenBUGS), len, PACKAGE="libOpenBUGS") + ## Set temporary dir for "buffer.txt" output + tempDir <- gsub("\\\\", "/", tempdir()) + .C("SetTempDir", as.character(tempDir), nchar(tempDir), PACKAGE="libOpenBUGS") + command <- "BugsMappers.SetDest(2)" + .CmdInterpreter(command) + + if(is.null(getOption("BRugsVerbose"))) + options("BRugsVerbose" = TRUE) + .initGlobals() + options(OpenBUGSExamples = paste(options()$OpenBUGS, "Examples", sep="/")) + } + + ".onUnload" <- function(libpath){ + if(is.loaded("CmdInterpreter")) { + libname <- paste(options()$OpenBUGS, "libOpenBUGS.dll", sep="/") + dyn.unload(libname) + } + } + +} Modified: branches/linux/BRugs/R/zzz.R =================================================================== --- branches/linux/BRugs/R/zzz.R 2010-11-13 17:31:25 UTC (rev 179) +++ branches/linux/BRugs/R/zzz.R 2011-03-07 15:09:12 UTC (rev 180) @@ -1,3 +1,5 @@ +## See unix/zzz.R, windows/zzz.R for platform specific .onLoad functions + if (is.R()){ .initGlobals <- function(){ @@ -7,61 +9,19 @@ options("BRugsSamplesLastChain" = 1) options("BRugsSamplesThin" = 1) options("BRugsSamplesVariable" = "*") - options("BRugsNextChain" = 1) # index of chain which needs to be initialized next + options("BRugsNextChain" = 1) # index of chain which needs to be initialized next options("BRugsPrec" = 4) } - - .onLoad <- function(...) { - switch(Sys.info()["sysname"], - "Linux" = .onLoad.Linux(...), - "Windows" = .onLoad.Windows(...), - stop("Only Linux and Windows are supported")) - if(is.null(getOption("BRugsVerbose"))) - options("BRugsVerbose" = TRUE) - .initGlobals() - } - - ".onLoad.Windows" <- function(lib, pkg){ - ## sets path / file variables and initializes subsystems - root <- file.path(system.file("OpenBUGS", package=pkg)) - library.dynam("BRugs", pkg, lib) - len <- nchar(root) - tempDir <- gsub("\\\\", "/", tempdir()) - .C("SetWorkingDir", as.character(root), len, PACKAGE="BRugs") - .C("SetTempDir", as.character(tempDir), nchar(tempDir), PACKAGE="BRugs") - command <- "BugsMappers.SetDest(2)" - .CmdInterpreter(command) - } - ".onLoad.Linux" <- function(lib, pkg){ - ## TODO any need for these to be user specifiable? - options("BRugsTmpdir" = gsub("\\\\", "/", tempdir())) - options("BRugsExtFile" = paste(basename(tempfile()), ".bug", sep="")) - } - ".onAttach" <- function(lib, pkg){ message("Welcome to BRugs running on OpenBUGS version 3.1.2") } - .onUnload <- function(...) { - switch(Sys.info()["sysname"], - "Linux" = .onUnload.Linux(...), - "Windows" = .onUnload.Windows(...), - stop("Only Linux and Windows are supported")) - } - - ".onUnload.Windows" <- function(libpath){ - library.dynam.unload("BRugs", libpath) - } - - ".onUnload.Linux" <- function(libpath){ - } - ## Overwriting new (from R-2.6.0) sQuote (for typing human readable text) in R within the BRugs Namespace! ## we cannot use sQuote that uses fancy quotes! sQuote <- function(x) paste("'", x, "'", sep="") - + } else { # ends if (is.R()) ".First.lib" <- function(lib.loc, section) @@ -76,12 +36,12 @@ command <- "BugsMappers.SetDest(2)" .C("CmdInterpreter", as.character(command), nchar(command), integer(1)) if(is.null(getOption("BRugsVerbose"))) - options("BRugsVerbose" = TRUE) + options("BRugsVerbose" = TRUE) invisible() } - + .tempDir <- getwd() - + tempdir <- function(){ .tempDir } } # ends else Added: branches/linux/BRugs/configure =================================================================== --- branches/linux/BRugs/configure (rev 0) +++ branches/linux/BRugs/configure 2011-03-07 15:09:12 UTC (rev 180) @@ -0,0 +1,5000 @@ +#! /bin/sh +# Guess values for system-dependent variables and create Makefiles. +# Generated by GNU Autoconf 2.65 for BRugs 0.7. +# +# +# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001, +# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, +# Inc. +# +# +# This configure script is free software; the Free Software Foundation +# gives unlimited permission to copy, distribute and modify it. +## -------------------- ## +## M4sh Initialization. ## +## -------------------- ## + +# Be more Bourne compatible +DUALCASE=1; export DUALCASE # for MKS sh +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : + emulate sh + NULLCMD=: + # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which + # is contrary to our usage. Disable this feature. + alias -g '${1+"$@"}'='"$@"' + setopt NO_GLOB_SUBST +else + case `(set -o) 2>/dev/null` in #( + *posix*) : + set -o posix ;; #( + *) : + ;; +esac +fi + + +as_nl=' +' +export as_nl +# Printing a long string crashes Solaris 7 /usr/bin/printf. +as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' +as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo +as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo +# Prefer a ksh shell builtin over an external printf program on Solaris, +# but without wasting forks for bash or zsh. +if test -z "$BASH_VERSION$ZSH_VERSION" \ + && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='print -r --' + as_echo_n='print -rn --' +elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='printf %s\n' + as_echo_n='printf %s' +else + if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then + as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"' + as_echo_n='/usr/ucb/echo -n' + else + as_echo_body='eval expr "X$1" : "X\\(.*\\)"' + as_echo_n_body='eval + arg=$1; + case $arg in #( + *"$as_nl"*) + expr "X$arg" : "X\\(.*\\)$as_nl"; + arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; + esac; + expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl" + ' + export as_echo_n_body + as_echo_n='sh -c $as_echo_n_body as_echo' + fi + export as_echo_body + as_echo='sh -c $as_echo_body as_echo' +fi + +# The user is always right. +if test "${PATH_SEPARATOR+set}" != set; then + PATH_SEPARATOR=: + (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && { + (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 || + PATH_SEPARATOR=';' + } +fi + + +# IFS +# We need space, tab and new line, in precisely that order. Quoting is +# there to prevent editors from complaining about space-tab. +# (If _AS_PATH_WALK were called with IFS unset, it would disable word +# splitting by setting IFS to empty value.) +IFS=" "" $as_nl" + +# Find who we are. Look in the path if we contain no directory separator. +case $0 in #(( + *[\\/]* ) as_myself=$0 ;; + *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break + done +IFS=$as_save_IFS + + ;; +esac +# We did not find ourselves, most probably we were run as `sh COMMAND' +# in which case we are not to be found in the path. +if test "x$as_myself" = x; then + as_myself=$0 +fi +if test ! -f "$as_myself"; then + $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 + exit 1 +fi + +# Unset variables that we do not need and which cause bugs (e.g. in +# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" +# suppresses any "Segmentation fault" message there. '((' could +# trigger a bug in pdksh 5.2.14. +for as_var in BASH_ENV ENV MAIL MAILPATH +do eval test x\${$as_var+set} = xset \ + && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : +done +PS1='$ ' +PS2='> ' +PS4='+ ' + +# NLS nuisances. +LC_ALL=C +export LC_ALL +LANGUAGE=C +export LANGUAGE + +# CDPATH. +(unset CDPATH) >/dev/null 2>&1 && unset CDPATH + +if test "x$CONFIG_SHELL" = x; then + as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then : + emulate sh + NULLCMD=: + # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which + # is contrary to our usage. Disable this feature. + alias -g '\${1+\"\$@\"}'='\"\$@\"' + setopt NO_GLOB_SUBST +else + case \`(set -o) 2>/dev/null\` in #( + *posix*) : + set -o posix ;; #( + *) : + ;; +esac +fi +" + as_required="as_fn_return () { (exit \$1); } +as_fn_success () { as_fn_return 0; } +as_fn_failure () { as_fn_return 1; } +as_fn_ret_success () { return 0; } +as_fn_ret_failure () { return 1; } + +exitcode=0 +as_fn_success || { exitcode=1; echo as_fn_success failed.; } +as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; } +as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; } +as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; } +if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then : + +else + exitcode=1; echo positional parameters were not saved. +fi +test x\$exitcode = x0 || exit 1" + as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO + as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO + eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" && + test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1" + if (eval "$as_required") 2>/dev/null; then : + as_have_required=yes +else + as_have_required=no +fi + if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then : + +else + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +as_found=false +for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + as_found=: + case $as_dir in #( + /*) + for as_base in sh bash ksh sh5; do + # Try only shells that exist, to save several forks. + as_shell=$as_dir/$as_base + if { test -f "$as_shell" || test -f "$as_shell.exe"; } && + { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then : + CONFIG_SHELL=$as_shell as_have_required=yes + if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then : + break 2 +fi +fi + done;; + esac + as_found=false +done +$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } && + { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then : + CONFIG_SHELL=$SHELL as_have_required=yes +fi; } +IFS=$as_save_IFS + + + if test "x$CONFIG_SHELL" != x; then : + # We cannot yet assume a decent shell, so we have to provide a + # neutralization value for shells without unset; and this also + # works around shells that cannot unset nonexistent variables. + BASH_ENV=/dev/null + ENV=/dev/null + (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV + export CONFIG_SHELL + exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"} +fi + + if test x$as_have_required = xno; then : + $as_echo "$0: This script requires a shell more modern than all" + $as_echo "$0: the shells that I found on your system." + if test x${ZSH_VERSION+set} = xset ; then + $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should" + $as_echo "$0: be upgraded to zsh 4.3.4 or later." + else + $as_echo "$0: Please tell bug...@gn... about your system, +$0: including any error possibly output before this +$0: message. Then install a modern shell, or manually run +$0: the script under such a shell if you do have one." + fi + exit 1 +fi +fi +fi +SHELL=${CONFIG_SHELL-/bin/sh} +export SHELL +# Unset more variables known to interfere with behavior of common tools. +CLICOLOR_FORCE= GREP_OPTIONS= +unset CLICOLOR_FORCE GREP_OPTIONS + +## --------------------- ## +## M4sh Shell Functions. ## +## --------------------- ## +# as_fn_unset VAR +# --------------- +# Portably unset VAR. +as_fn_unset () +{ + { eval $1=; unset $1;} +} +as_unset=as_fn_unset + +# as_fn_set_status STATUS +# ----------------------- +# Set $? to STATUS, without forking. +as_fn_set_status () +{ + return $1 +} # as_fn_set_status + +# as_fn_exit STATUS +# ----------------- +# Exit the shell with STATUS, even in a "trap 0" or "set -e" context. +as_fn_exit () +{ + set +e + as_fn_set_status $1 + exit $1 +} # as_fn_exit + +# as_fn_mkdir_p +# ------------- +# Create "$as_dir" as a directory, including parents if necessary. +as_fn_mkdir_p () +{ + + case $as_dir in #( + -*) as_dir=./$as_dir;; + esac + test -d "$as_dir" || eval $as_mkdir_p || { + as_dirs= + while :; do + case $as_dir in #( + *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( + *) as_qdir=$as_dir;; + esac + as_dirs="'$as_qdir' $as_dirs" + as_dir=`$as_dirname -- "$as_dir" || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + test -d "$as_dir" && break + done + test -z "$as_dirs" || eval "mkdir $as_dirs" + } || test -d "$as_dir" || as_fn_error "cannot create directory $as_dir" + + +} # as_fn_mkdir_p +# as_fn_append VAR VALUE +# ---------------------- +# Append the text in VALUE to the end of the definition contained in VAR. Take +# advantage of any shell optimizations that allow amortized linear growth over +# repeated appends, instead of the typical quadratic growth present in naive +# implementations. +if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : + eval 'as_fn_append () + { + eval $1+=\$2 + }' +else + as_fn_append () + { + eval $1=\$$1\$2 + } +fi # as_fn_append + +# as_fn_arith ARG... +# ------------------ +# Perform arithmetic evaluation on the ARGs, and store the result in the +# global $as_val. Take advantage of shells that can avoid forks. The arguments +# must be portable across $(()) and expr. +if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : + eval 'as_fn_arith () + { + as_val=$(( $* )) + }' +else + as_fn_arith () + { + as_val=`expr "$@" || test $? -eq 1` + } +fi # as_fn_arith + + +# as_fn_error ERROR [LINENO LOG_FD] +# --------------------------------- +# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are +# provided, also output the error to LOG_FD, referencing LINENO. Then exit the +# script with status $?, using 1 if that was 0. +as_fn_error () +{ + as_status=$?; test $as_status -eq 0 && as_status=1 + if test "$3"; then + as_lineno=${as_lineno-"$2"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + $as_echo "$as_me:${as_lineno-$LINENO}: error: $1" >&$3 + fi + $as_echo "$as_me: error: $1" >&2 + as_fn_exit $as_status +} # as_fn_error + +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then + as_expr=expr +else + as_expr=false +fi + +if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then + as_basename=basename +else + as_basename=false +fi + +if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then + as_dirname=dirname +else + as_dirname=false +fi + +as_me=`$as_basename -- "$0" || +$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ + X"$0" : 'X\(//\)$' \| \ + X"$0" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ + s//\1/ + q + } + /^X\/\(\/\/\)$/{ + s//\1/ + q + } + /^X\/\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + + + as_lineno_1=$LINENO as_lineno_1a=$LINENO + as_lineno_2=$LINENO as_lineno_2a=$LINENO + eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" && + test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || { + # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-) + sed -n ' + p + /[$]LINENO/= + ' <$as_myself | + sed ' + s/[$]LINENO.*/&-/ + t lineno + b + :lineno + N + :loop + s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/ + t loop + s/-\n.*// + ' >$as_me.lineno && + chmod +x "$as_me.lineno" || + { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; } + + # Don't try to exec as it changes $[0], causing all sort of problems + # (the dirname of $[0] is not the place where we might find the + # original and so on. Autoconf is especially sensitive to this). + . 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then + srcdir=. +fi +# Remove unnecessary trailing slashes from srcdir. +# Double slashes in file names in object file debugging info +# mess up M-x gdb in Emacs. +case $srcdir in +*/) srcdir=`expr "X$srcdir" : 'X\(.*[^/]\)' \| "X$srcdir" : 'X\(.*\)'`;; +esac +for ac_var in $ac_precious_vars; do + eval ac_env_${ac_var}_set=\${${ac_var}+set} + eval ac_env_${ac_var}_value=\$${ac_var} + eval ac_cv_env_${ac_var}_set=\${${ac_var}+set} + eval ac_cv_env_${ac_var}_value=\$${ac_var} +done + +# +# Report the --help message. +# +if test "$ac_init_help" = "long"; then + # Omit some internal or obsolete options to make the list less imposing. + # This message is too long to be a string in the A/UX 3.1 sh. + cat <<_ACEOF +\`configure' configures BRugs 0.7 to adapt to many kinds of systems. + +Usage: $0 [OPTION]... [VAR=VALUE]... + +To assign environment variables (e.g., CC, CFLAGS...), specify them as +VAR=VALUE. See below for descriptions of some of the useful variables. + +Defaults for the options are specified in brackets. + +Configuration: + -h, --help display this help and exit + --help=short display options specific to this package + --help=recursive display the short help of all the included packages + -V, --version display version information and exit + -q, --quiet, --silent do not print \`checking...' messages + --cache-file=FILE cache test results in FILE [disabled] + -C, --config-cache alias for \`--cache-file=config.cache' + -n, --no-create do not create output files + --srcdir=DIR find the sources in DIR [configure dir or \`..'] + +Installation directories: + --prefix=PREFIX install architecture-independent files in PREFIX + [$ac_default_prefix] + --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX + [PREFIX] + +By default, \`make install' will install all the files in +\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify +an installation prefix ... 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