|
From: <li...@us...> - 2011-12-30 16:40:39
|
Revision: 235
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=235&view=rev
Author: ligges
Date: 2011-12-30 16:40:33 +0000 (Fri, 30 Dec 2011)
Log Message:
-----------
Windows:
- adaption in Makefile.win to derive path automagically
- hence we can get rid of non empty configure
- get rid of meaningless exec subdir
- avoid copying of dlls into BRugs but always use the OpenBUGS installation
- dirty hack to set the PATH so that the Helper finds the dll under 64-bit
Modified Paths:
--------------
trunk/BRugs/R/windows/zzz.i386.R
trunk/BRugs/R/windows/zzz.x64.R
trunk/BRugs/configure.win
trunk/BRugs/src/Makefile.win
Removed Paths:
-------------
trunk/BRugs/R/windows/zzz.x64.R.in
trunk/BRugs/configure.win.R
trunk/BRugs/exec/
Modified: trunk/BRugs/R/windows/zzz.i386.R
===================================================================
--- trunk/BRugs/R/windows/zzz.i386.R 2011-12-30 16:32:10 UTC (rev 234)
+++ trunk/BRugs/R/windows/zzz.i386.R 2011-12-30 16:40:33 UTC (rev 235)
@@ -1,40 +1,39 @@
-".onLoad.i386" <- function(lib, pkg){
- ob <- findOpenBUGS()
- loadOpenBUGS(ob$dir)
- msg <- paste("Welcome to BRugs connected to OpenBUGS")
- if (!is.na(ob$version))
- msg <- paste(msg, "version", ob$version)
- else msg <- paste(msg, "in directory", ob$dir)
- packageStartupMessage(msg)
-}
-
-".onUnload.i386" <- function(libpath){
- if(is.loaded("CmdInterpreter")) {
- libname <- paste(options()$OpenBUGS, "libOpenBUGS.dll", sep="/")
- dyn.unload(libname)
- }
-}
-
-## Load OpenBUGS from specified location
-loadOpenBUGS <- function(dir) {
- libname <- paste(dir, "libOpenBUGS.dll", sep="/")
- if (!file.exists(libname)) {
- warning("Shared library \"libOpenBUGS.dll\" not found in ", dir)
- return(FALSE)
- }
- options(OpenBUGS = dir)
- dyn.load(libname)
- len <- nchar(dir)
- .C("SetWorkingDir", as.character(dir), len)
- ## Set temporary dir for "buffer.txt" output
- tempDir <- gsub("\\\\", "/", tempdir())
- .C("SetTempDir", as.character(tempDir), nchar(tempDir))
- command <- "BugsMappers.SetDest(2)"
- .CmdInterpreter(command)
- if(is.null(getOption("BRugsVerbose")))
- options("BRugsVerbose" = TRUE)
- .initGlobals()
- options(OpenBUGSExamples = paste(dir, "Examples", sep="/"))
- invisible()
-}
-
+".onLoad.i386" <- function(lib, pkg){
+ ob <- findOpenBUGS()
+ loadOpenBUGS(ob$dir)
+ msg <- paste("Welcome to BRugs connected to OpenBUGS")
+ if (!is.na(ob$version))
+ msg <- paste(msg, "version", ob$version)
+ else msg <- paste(msg, "in directory", ob$dir)
+ packageStartupMessage(msg)
+}
+
+".onUnload.i386" <- function(libpath){
+ if(is.loaded("CmdInterpreter")) {
+ libname <- paste(options()$OpenBUGS, "libOpenBUGS.dll", sep="/")
+ dyn.unload(libname)
+ }
+}
+
+## Load OpenBUGS from specified location
+loadOpenBUGS <- function(dir) {
+ libname <- paste(dir, "libOpenBUGS.dll", sep="/")
+ if (!file.exists(libname)) {
+ warning("Shared library \"libOpenBUGS.dll\" not found in ", dir)
+ return(FALSE)
+ }
+ options(OpenBUGS = dir)
+ dyn.load(libname)
+ len <- nchar(dir)
+ .C("SetWorkingDir", as.character(dir), 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(dir, "Examples", sep="/"))
+ invisible()
+}
Modified: trunk/BRugs/R/windows/zzz.x64.R
===================================================================
--- trunk/BRugs/R/windows/zzz.x64.R 2011-12-30 16:32:10 UTC (rev 234)
+++ trunk/BRugs/R/windows/zzz.x64.R 2011-12-30 16:40:33 UTC (rev 235)
@@ -4,19 +4,23 @@
## TODO any need for these to be user specifiable?
options("BRugsTmpdir" = gsub("\\\\", "/", tempdir()))
options("BRugsExtFile" = paste(basename(tempfile()), ".bug", sep=""))
- options(OpenBUGS = "C:/Program Files (x86)/OpenBUGS/OpenBUGS321")
- options(OpenBUGSdoc = "C:/Program Files (x86)/OpenBUGS/OpenBUGS321")
- options(OpenBUGSExamples = paste(options()$OpenBUGSdoc, "Examples", sep="/"))
+ ob <- findOpenBUGS()
+ options(OpenBUGS = ob$dir)
+ options(OpenBUGSdoc = ob$dir)
+ options(OpenBUGSExamples = paste(ob$dir, "Examples", sep="/"))
if(is.null(getOption("BRugsVerbose")))
options("BRugsVerbose" = TRUE)
.initGlobals()
- ob <- findOpenBUGS()
msg <- paste("Welcome to BRugs connected to OpenBUGS")
if (!is.na(ob$version))
msg <- paste(msg, " version ", ob$version)
else msg <- paste(msg, " in directory ", ob$dir)
packageStartupMessage(msg)
+ pathtoBUGS <- gsub("/", "\\", ob$dir)
+ oldpath <- Sys.getenv("PATH")
+ if(!length(grep(pathtoBUGS, oldpath, fixed=TRUE)))
+ Sys.setenv(PATH=paste(oldpath, pathtoBUGS, sep=";"))
}
".onUnload.x64" <- function(libpath){
Deleted: trunk/BRugs/R/windows/zzz.x64.R.in
===================================================================
--- trunk/BRugs/R/windows/zzz.x64.R.in 2011-12-30 16:32:10 UTC (rev 234)
+++ trunk/BRugs/R/windows/zzz.x64.R.in 2011-12-30 16:40:33 UTC (rev 235)
@@ -1,25 +0,0 @@
-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@")
- options(OpenBUGSdoc = "@OPENBUGSDOC@")
- options(OpenBUGSExamples = paste(options()$OpenBUGSdoc, "Examples", sep="/"))
-
- if(is.null(getOption("BRugsVerbose")))
- options("BRugsVerbose" = TRUE)
- .initGlobals()
- ob <- findOpenBUGS()
- msg <- paste("Welcome to BRugs connected to OpenBUGS")
- if (!is.na(ob$version))
- msg <- paste(msg, "version", ob$version)
- else msg <- paste(msg, "in directory", ob$dir)
- packageStartupMessage(msg)
- }
-
- ".onUnload" <- function(libpath){
- }
-
-}
Modified: trunk/BRugs/configure.win
===================================================================
--- trunk/BRugs/configure.win 2011-12-30 16:32:10 UTC (rev 234)
+++ trunk/BRugs/configure.win 2011-12-30 16:40:33 UTC (rev 235)
@@ -1,13 +0,0 @@
-## Configure script only needed for 64 bit Windows, where BRugs calls
-## the 32-bit OpenBUGS library via a helper application. First find
-## the location of the OpenBUGS installation.
-
-OPENBUGS=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" configure.win.R`
-
-## Install the OpenBUGS DLL into the package. There is no Windows
-## equivalent of $rpath for adding to the dynamic link path, therefore
-## the DLL is installed in the same directory as the helper
-## executable.
-
-OPENBUGSLIB="$OPENBUGS/libOpenBUGS.dll"
-cp "$OPENBUGSLIB" exec
Deleted: trunk/BRugs/configure.win.R
===================================================================
--- trunk/BRugs/configure.win.R 2011-12-30 16:32:10 UTC (rev 234)
+++ trunk/BRugs/configure.win.R 2011-12-30 16:40:33 UTC (rev 235)
@@ -1,20 +0,0 @@
-## Find OpenBUGS installation location
-source("R/windows/findOpenBUGS.R")
-OPENBUGS <- findOpenBUGS()$dir
-OPENBUGS <- gsub("\\\\","/",OPENBUGS)
-
-dummy <- file.copy("src/Makevars.in","src/Makefile.win", overwrite=TRUE)
-x <- readLines("src/Makefile.win")
-x <- gsub("@OPENBUGS@", dQuote(OPENBUGS), x, fixed=TRUE)
-x <- gsub("@DYNLIBEXT@", "dll", x, fixed=TRUE)
-writeLines(x, "src/Makefile.win")
-
-dummy <- file.copy("R/windows/zzz.x64.R.in","R/windows/zzz.x64.R", overwrite=TRUE)
-x <- readLines("R/windows/zzz.x64.R")
-x <- gsub("@OPENBUGS@", OPENBUGS, x, fixed=TRUE)
-x <- gsub("@OPENBUGSDOC@", OPENBUGS, x, fixed=TRUE)
-x <- gsub("\".onLoad\"[[:space:]]*<-[[:space:]]*function", "\".onLoad.x64\" <- function", x)
-x <- gsub("\".onUnload\"[[:space:]]*<-[[:space:]]*function", "\".onUnload.x64\" <- function", x)
-writeLines(x, "R/windows/zzz.x64.R")
-
-cat(OPENBUGS)
Modified: trunk/BRugs/src/Makefile.win
===================================================================
--- trunk/BRugs/src/Makefile.win 2011-12-30 16:32:10 UTC (rev 234)
+++ trunk/BRugs/src/Makefile.win 2011-12-30 16:40:33 UTC (rev 235)
@@ -1,6 +1,7 @@
-BUGS_LIBS = "C:/Program Files (x86)/OpenBUGS/OpenBUGS321"/libOpenBUGS.dll
-BUGS_LDFLAGS = -m32 -Wl,-rpath="C:/Program Files (x86)/OpenBUGS/OpenBUGS321"
+BUGS_PATH = `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "source('../R/windows/findOpenBUGS.R');cat(findOpenBUGS()[['dir']])"`
+BUGS_LIBS = "$(BUGS_PATH)/libOpenBUGS.dll"
+BUGS_LDFLAGS = -m32 -Wl,-rpath="$(BUGS_PATH)"
BugsHelper:
- mkdir -p ../exec
- $(CC) $(CFLAGS) $(LDFLAGS) $(BUGS_LDFLAGS) BugsHelper.c $(BUGS_LIBS) -o ../exec/BugsHelper
+ mkdir -p $(R_PACKAGE_DIR)/exec
+ $(CC) $(CFLAGS) $(LDFLAGS) $(BUGS_LDFLAGS) BugsHelper.c $(BUGS_LIBS) -o $(R_PACKAGE_DIR)/exec/BugsHelper
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|
|
From: <li...@us...> - 2012-01-02 13:24:51
|
Revision: 245
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=245&view=rev
Author: ligges
Date: 2012-01-02 13:24:45 +0000 (Mon, 02 Jan 2012)
Log Message:
-----------
statements: 32-bit Windows is still the most native version, Linux version labeled as "beta"
Modified Paths:
--------------
trunk/BRugs/DESCRIPTION
trunk/BRugs/NEWS
Modified: trunk/BRugs/DESCRIPTION
===================================================================
--- trunk/BRugs/DESCRIPTION 2011-12-30 19:44:11 UTC (rev 244)
+++ trunk/BRugs/DESCRIPTION 2012-01-02 13:24:45 UTC (rev 245)
@@ -3,7 +3,7 @@
Version: 0.7-4
Date: 2011-12-30
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
+Description: Fully-interactive R interface to the OpenBUGS software for Bayesian analysis using MCMC sampling; 32-bit R under Windows is supported "most native", 64-bit R interface under Windows is probably slower, Linux versions are in "beta" status
Maintainer: Uwe Ligges <li...@st...>
Depends: R (>= 2.11.0), coda
Imports: utils, coda
Modified: trunk/BRugs/NEWS
===================================================================
--- trunk/BRugs/NEWS 2011-12-30 19:44:11 UTC (rev 244)
+++ trunk/BRugs/NEWS 2012-01-02 13:24:45 UTC (rev 245)
@@ -1,10 +1,11 @@
Changes to BRugs:
=====================
-Version 0.7.2 (?? September 2011)
+Version 0.7.3 (02 January 2012)
-------------
BRugs now supports 64-bit R on Windows, using the same helper program
as Linux for calling the 32 bit OpenBUGS shared library. Thanks to
-Brian Ripley for the reports.
+Brian Ripley for the reports. This is typically slower than the more
+native interface used for 32-bit R on Windows.
On Linux, when the OpenBUGS library call terminates with a "trap"
error, the trap message is now shown. Thanks to Alexandre Villers.
@@ -26,7 +27,11 @@
BugsCmd API function is now supported by BugsHelper, but this is not
used.
+Some minor bug and documentation fixes.
+First CRAN version for OpenBUGS 3.2.1.
+
+
Version 0.7.1 (19 April 2011)
-------------
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|
|
From: Uwe L. <li...@st...> - 2012-01-02 13:52:58
|
I am about to release this as soon as Kurt is back from vacation and handles CRAN submissions. Any objections? Uwe On 02.01.2012 14:24, li...@us... wrote: > Revision: 245 > http://bugs-r.svn.sourceforge.net/bugs-r/?rev=245&view=rev > Author: ligges > Date: 2012-01-02 13:24:45 +0000 (Mon, 02 Jan 2012) > Log Message: > ----------- > statements: 32-bit Windows is still the most native version, Linux version labeled as "beta" > > Modified Paths: > -------------- > trunk/BRugs/DESCRIPTION > trunk/BRugs/NEWS > > Modified: trunk/BRugs/DESCRIPTION > =================================================================== > --- trunk/BRugs/DESCRIPTION 2011-12-30 19:44:11 UTC (rev 244) > +++ trunk/BRugs/DESCRIPTION 2012-01-02 13:24:45 UTC (rev 245) > @@ -3,7 +3,7 @@ > Version: 0.7-4 > Date: 2011-12-30 > 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 > +Description: Fully-interactive R interface to the OpenBUGS software for Bayesian analysis using MCMC sampling; 32-bit R under Windows is supported "most native", 64-bit R interface under Windows is probably slower, Linux versions are in "beta" status > Maintainer: Uwe Ligges<li...@st...> > Depends: R (>= 2.11.0), coda > Imports: utils, coda > > Modified: trunk/BRugs/NEWS > =================================================================== > --- trunk/BRugs/NEWS 2011-12-30 19:44:11 UTC (rev 244) > +++ trunk/BRugs/NEWS 2012-01-02 13:24:45 UTC (rev 245) > @@ -1,10 +1,11 @@ > Changes to BRugs: > ===================== > -Version 0.7.2 (?? September 2011) > +Version 0.7.3 (02 January 2012) > ------------- > BRugs now supports 64-bit R on Windows, using the same helper program > as Linux for calling the 32 bit OpenBUGS shared library. Thanks to > -Brian Ripley for the reports. > +Brian Ripley for the reports. This is typically slower than the more > +native interface used for 32-bit R on Windows. > > On Linux, when the OpenBUGS library call terminates with a "trap" > error, the trap message is now shown. Thanks to Alexandre Villers. > @@ -26,7 +27,11 @@ > BugsCmd API function is now supported by BugsHelper, but this is not > used. > > +Some minor bug and documentation fixes. > > +First CRAN version for OpenBUGS 3.2.1. > + > + > Version 0.7.1 (19 April 2011) > ------------- > > > This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. > > > ------------------------------------------------------------------------------ > Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex > infrastructure or vast IT resources to deliver seamless, secure access to > virtual desktops. With this all-in-one solution, easily deploy virtual > desktops for less than the cost of PCs and save 60% on VDI infrastructure > costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox > _______________________________________________ > Bugs-r-devel mailing list > Bug...@li... > https://lists.sourceforge.net/lists/listinfo/bugs-r-devel |
|
From: <li...@us...> - 2012-01-06 09:50:54
|
Revision: 248
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=248&view=rev
Author: ligges
Date: 2012-01-06 09:50:47 +0000 (Fri, 06 Jan 2012)
Log Message:
-----------
bugfix release: we generated a $TEMPDIR_trash directory that was not cleaned up, now trash is a subdir of tempdir()
Modified Paths:
--------------
trunk/BRugs/DESCRIPTION
trunk/BRugs/R/internal.R
trunk/BRugs/src/BugsHelper.c
Modified: trunk/BRugs/DESCRIPTION
===================================================================
--- trunk/BRugs/DESCRIPTION 2012-01-03 09:57:39 UTC (rev 247)
+++ trunk/BRugs/DESCRIPTION 2012-01-06 09:50:47 UTC (rev 248)
@@ -1,7 +1,7 @@
Package: BRugs
Title: R interface to the OpenBUGS MCMC software
-Version: 0.7-4
-Date: 2011-12-30
+Version: 0.7-5
+Date: 2012-01-06
Author: OpenBUGS was developed by Andrew Thomas, Dave Lunn, David Spiegelhalter and Nicky Best. R interface developed by Uwe Ligges, Sibylle Sturtz, Andrew Gelman, Gregor Gorjanc and Chris Jackson. Linux port and most recent developments by Chris Jackson.
Description: Fully-interactive R interface to the OpenBUGS software for Bayesian analysis using MCMC sampling. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.
Maintainer: Uwe Ligges <li...@st...>
Modified: trunk/BRugs/R/internal.R
===================================================================
--- trunk/BRugs/R/internal.R 2012-01-03 09:57:39 UTC (rev 247)
+++ trunk/BRugs/R/internal.R 2012-01-06 09:50:47 UTC (rev 248)
@@ -47,7 +47,7 @@
tempDir <- getOption("BRugsTmpdir")
## Don't want internalize/externalize to overwrite the command
## output buffer, so redirect its output to a separate trash can.
- trashDir <- paste(tempDir, "_trash", sep="")
+ trashDir <- file.path(tempDir, "trash", fsep="/")
extFile <- getOption("BRugsExtFile")
cmdFile <- paste(tempDir, "cmds.txt", sep="/")
bugsPath <- system.file("exec", paste("BugsHelper", if(.Platform$OS.type == "windows") ".exe", sep=""), package="BRugs")
Modified: trunk/BRugs/src/BugsHelper.c
===================================================================
--- trunk/BRugs/src/BugsHelper.c 2012-01-03 09:57:39 UTC (rev 247)
+++ trunk/BRugs/src/BugsHelper.c 2012-01-06 09:50:47 UTC (rev 248)
@@ -49,7 +49,7 @@
"BugsEmbed.SetFilePath('/scratch/chris/lib/R/BRugs/OpenBUGS/Examples/Ratsdata.txt');BugsEmbed.LoadDataGuard;BugsEmbed.LoadData" 0
- /path/to/BugsHelper "/tmp/RtmpaRQois" "/tmp/RtmpaRQois_trash" "file327b23c6.bug" "BugsEmbed.SetFilePath('/path/to/Examples/Ratsmodel.txt');BugsEmbed.ParseGuard;BugsEmbed.Parse" 0 "BugsEmbed.SetFilePath('/path/to/Examples/Ratsdata.txt');BugsEmbed.LoadDataGuard;BugsEmbed.LoadData" 0
+ /path/to/BugsHelper "/tmp/RtmpaRQois" "/tmp/RtmpaRQois/trash" "file327b23c6.bug" "BugsEmbed.SetFilePath('/path/to/Examples/Ratsmodel.txt');BugsEmbed.ParseGuard;BugsEmbed.Parse" 0 "BugsEmbed.SetFilePath('/path/to/Examples/Ratsdata.txt');BugsEmbed.LoadDataGuard;BugsEmbed.LoadData" 0
TODO
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|
|
From: <li...@us...> - 2012-07-23 17:47:56
|
Revision: 254
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=254&view=rev
Author: ligges
Date: 2012-07-23 17:47:46 +0000 (Mon, 23 Jul 2012)
Log Message:
-----------
make BRugs OpenBUGS 3.2.2 compatible (and drop back compatibility) and some more fixes for R >= 2.15.1; bump version number
Modified Paths:
--------------
trunk/BRugs/DESCRIPTION
trunk/BRugs/NEWS
trunk/BRugs/R/info.modules.R
trunk/BRugs/R/info.node.R
trunk/BRugs/R/info.updaters.R
trunk/BRugs/R/model.setWD.R
trunk/BRugs/tests/BRugs.Rout.save
trunk/BRugs/tests/examples.Rout.save
trunk/BRugs/tests/functions.Rout.save
Modified: trunk/BRugs/DESCRIPTION
===================================================================
--- trunk/BRugs/DESCRIPTION 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/DESCRIPTION 2012-07-23 17:47:46 UTC (rev 254)
@@ -1,12 +1,12 @@
Package: BRugs
Title: R interface to the OpenBUGS MCMC software
-Version: 0.7-5
-Date: 2012-01-06
+Version: 0.8-0
+Date: 2012-07-23
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. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.
Maintainer: Uwe Ligges <li...@st...>
Depends: R (>= 2.11.0), coda
Imports: utils, coda
-SystemRequirements: OpenBUGS (>= 3.2.1), hence Windows or Linux
+SystemRequirements: OpenBUGS (>= 3.2.2), hence Windows or Linux
License: GPL-2
URL: http://www.openbugs.info/
Modified: trunk/BRugs/NEWS
===================================================================
--- trunk/BRugs/NEWS 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/NEWS 2012-07-23 17:47:46 UTC (rev 254)
@@ -1,5 +1,20 @@
Changes to BRugs:
=====================
+
+Version 0.8.0 (23 July 2012)
+-------------
+BRugs now works with an existing installation of OpenBUGS (>?)= 3.2.2.
+
+modelSetWD is exported from the NAMESPACE
+
+bugfixed to find examples on various Linux installations
+
+
+Version 0.7.4, 0.7.5
+--------------------
+bugfix releases
+
+
Version 0.7.3 (02 January 2012)
-------------
BRugs now supports 64-bit R on Windows, using the same helper program
Modified: trunk/BRugs/R/info.modules.R
===================================================================
--- trunk/BRugs/R/info.modules.R 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/R/info.modules.R 2012-07-23 17:47:46 UTC (rev 254)
@@ -5,7 +5,7 @@
command <- "BugsEmbed.Modules"
.CmdInterpreter(command)
buffer <- file.path(tempdir(), "buffer.txt")
- result <- read.fwf(buffer, c(50, 12, 12, 12, 12, 10), skip = 1, as.is=TRUE)
+ result <- read.table(buffer, skip = 1, as.is=TRUE, sep="\t")[,-1]
for(i in c(1,4,5,6))
result[,i] <- gsub(" ", "", result[,i])
names(result) <- c("Module", "Clients", "Version", "Maintainer", "Compiled", "Loaded")
Modified: trunk/BRugs/R/info.node.R
===================================================================
--- trunk/BRugs/R/info.node.R 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/R/info.node.R 2012-07-23 17:47:46 UTC (rev 254)
@@ -1,42 +1,42 @@
-"infoNodeValues" <-
-function(nodeLabel)
-# Get current value of node
-{
- nodeLabel <- as.character(nodeLabel)
- out <- .OpenBUGS(c("BugsRobjects.SetVariable", "BugsRobjects.GetSize"),
- c("CharArray","Integer"),
- list(nodeLabel, NA))
- nodeSize <- out[[2]]
- if(nodeSize == -1)
- stop(nodeLabel, " is not a node in BUGS model")
- numChains <- getNumChains()
- out <- .OpenBUGS(c("BugsRobjects.SetVariable", "BugsRobjects.GetValues"),
- c("CharArray","RealArray"),
- list(nodeLabel, double(nodeSize*numChains)))
- values <- matrix(out[[2]], nrow=nodeSize, ncol=numChains)
- values
-}
-
-infoNodeMethods <- function(nodeLabel)
-{
- nodeName <- sQuote(nodeLabel)
- command <- paste("BugsEmbed.SetNode(",nodeName,"); BugsEmbed.Methods");
- .CmdInterpreter(command)
- buffer <- file.path(tempdir(), "buffer.txt")
- result <- read.fwf(buffer, c(25, 25, 25, 25), skip = 1, as.is=TRUE, col.names=c("Node","Type", "Size", "Depth"))
- for (i in 1:2)
- result[,i] <- gsub(" ", "", result[,i])
- result
-}
-
-infoNodeTypes <- function(nodeLabel)
-{
- nodeName <- sQuote(nodeLabel)
- command <- paste("BugsEmbed.SetNode(",nodeName,"); BugsEmbed.Types");
- .CmdInterpreter(command)
- buffer <- file.path(tempdir(), "buffer.txt")
- result <- read.fwf(buffer, c(25, 25), skip = 1, as.is=TRUE, col.names=c("Node","Type"))
- for (i in 1:2)
- result[,i] <- gsub(" ", "", result[,i])
- result
-}
+"infoNodeValues" <-
+function(nodeLabel)
+# Get current value of node
+{
+ nodeLabel <- as.character(nodeLabel)
+ out <- .OpenBUGS(c("BugsRobjects.SetVariable", "BugsRobjects.GetSize"),
+ c("CharArray","Integer"),
+ list(nodeLabel, NA))
+ nodeSize <- out[[2]]
+ if(nodeSize == -1)
+ stop(nodeLabel, " is not a node in BUGS model")
+ numChains <- getNumChains()
+ out <- .OpenBUGS(c("BugsRobjects.SetVariable", "BugsRobjects.GetValues"),
+ c("CharArray","RealArray"),
+ list(nodeLabel, double(nodeSize*numChains)))
+ values <- matrix(out[[2]], nrow=nodeSize, ncol=numChains)
+ values
+}
+
+infoNodeMethods <- function(nodeLabel)
+{
+ nodeName <- sQuote(nodeLabel)
+ command <- paste("BugsEmbed.SetNode(",nodeName,"); BugsEmbed.Methods");
+ .CmdInterpreter(command)
+ buffer <- file.path(tempdir(), "buffer.txt")
+ result <- read.table(buffer, sep="\t", skip = 1, as.is=TRUE, col.names=c("empty", "Node", "Type", "Size", "Depth"))[,-1]
+ for (i in 1:2)
+ result[,i] <- gsub(" ", "", result[,i])
+ result
+}
+
+infoNodeTypes <- function(nodeLabel)
+{
+ nodeName <- sQuote(nodeLabel)
+ command <- paste("BugsEmbed.SetNode(",nodeName,"); BugsEmbed.Types");
+ .CmdInterpreter(command)
+ buffer <- file.path(tempdir(), "buffer.txt")
+ result <- read.table(buffer, sep="\t", skip = 1, as.is=TRUE, col.names=c("empty", "Node", "Type"))[,-1]
+ for (i in 1:2)
+ result[,i] <- gsub(" ", "", result[,i])
+ result
+}
Modified: trunk/BRugs/R/info.updaters.R
===================================================================
--- trunk/BRugs/R/info.updaters.R 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/R/info.updaters.R 2012-07-23 17:47:46 UTC (rev 254)
@@ -8,8 +8,8 @@
if (readLines(buffer)[1]=="BugsCmds:NotCompiled")
stop("Model not compiled")
buffer <- file.path(tempdir(), "Updater types.txt")
- result <- read.fwf(buffer, c(25, 50, 10, 10), skip = 1, as.is=TRUE,
- row.names=1, col.names=c("Node","Type", "Size","Depth"))
+ result <- read.table(buffer, sep="\t", skip=1, as.is=TRUE,
+ row.names=2, col.names=c("empty", "Node", "Type", "Size", "Depth"))[,-1]
## strip leading and trailing spaces
for (i in 1:2) {
result[,i] <- gsub("^ +", "\\1", result[,i])
@@ -30,8 +30,8 @@
if (readLines(buffer)[1]=="BugsCmds:NotCompiled")
stop("Model not compiled")
buffer <- file.path(tempdir(), "Updater types.txt")
- result <- read.fwf(buffer, c(25, 50, 10, 10), skip = 1, as.is=TRUE,
- row.names=1, col.names=c("Node","Type", "Size","Depth"))
+ result <- read.table(buffer, sep="\t", skip=1, as.is=TRUE,
+ row.names=2, col.names=c("empty", "Node", "Type", "Size", "Depth"))[,-1]
## strip leading and trailing spaces
for (i in 1:2) {
result[,i] <- gsub("^ +", "\\1", result[,i])
Modified: trunk/BRugs/R/model.setWD.R
===================================================================
--- trunk/BRugs/R/model.setWD.R 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/R/model.setWD.R 2012-07-23 17:47:46 UTC (rev 254)
@@ -1,3 +1,3 @@
## Simple alias to mimic the OpenBUGS script command
-"modelSetWD" <- setwd
+"modelSetWD" <- function(dir) setwd(dir)
Modified: trunk/BRugs/tests/BRugs.Rout.save
===================================================================
--- trunk/BRugs/tests/BRugs.Rout.save 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/tests/BRugs.Rout.save 2012-07-23 17:47:46 UTC (rev 254)
@@ -80,7 +80,7 @@
+ }
Loading required package: coda
Loading required package: lattice
-Welcome to BRugs connected to OpenBUGS version 3.2.1
+Welcome to BRugs connected to OpenBUGS version 3.2.2
model is syntactically correct
data loaded
model compiled
Modified: trunk/BRugs/tests/examples.Rout.save
===================================================================
--- trunk/BRugs/tests/examples.Rout.save 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/tests/examples.Rout.save 2012-07-23 17:47:46 UTC (rev 254)
@@ -68,7 +68,7 @@
+ }
Loading required package: coda
Loading required package: lattice
-Welcome to BRugs connected to OpenBUGS version 3.2.1
+Welcome to BRugs connected to OpenBUGS version 3.2.2
model is syntactically correct
data loaded
model compiled
@@ -89,7 +89,7 @@
model is initialized
model is already initialized
5000 updates took 0 s
-can not calculate deviance for this model
+can not calculate DIC for this model
monitor set for variable 'bronchitis'
monitor set for variable 'either'
monitor set for variable 'lung.cancer'
@@ -128,7 +128,7 @@
model is initialized
model is already initialized
5000 updates took 0 s
-can not calculate deviance for this model
+can not calculate DIC for this model
monitor set for variable 'Sigma2'
monitor set for variable 'rho'
monitor set for variable 'tau'
@@ -187,7 +187,7 @@
initial values loaded but chain contain uninitialized variables
initial values generated, model initialized
5000 updates took 0 s
-can not calculate deviance for this model
+can not calculate DIC for this model
monitor set for variable 'P'
monitor set for variable 'lambda'
monitor set for variable 'sigma'
Modified: trunk/BRugs/tests/functions.Rout.save
===================================================================
--- trunk/BRugs/tests/functions.Rout.save 2012-07-12 02:22:12 UTC (rev 253)
+++ trunk/BRugs/tests/functions.Rout.save 2012-07-23 17:47:46 UTC (rev 254)
@@ -151,7 +151,7 @@
+ }
Loading required package: coda
Loading required package: lattice
-Welcome to BRugs connected to OpenBUGS version 3.2.1
+Welcome to BRugs connected to OpenBUGS version 3.2.2
model is syntactically correct
data loaded
model compiled
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <chr...@us...> - 2012-07-24 08:42:24
|
Revision: 255
http://bugs-r.svn.sourceforge.net/bugs-r/?rev=255&view=rev
Author: chris-jackson
Date: 2012-07-24 08:42:13 +0000 (Tue, 24 Jul 2012)
Log Message:
-----------
Depend on OpenBUGS 3.2.2, and find documentation from both source and binary installations.
Modified Paths:
--------------
trunk/BRugs/configure
trunk/BRugs/configure.ac
Modified: trunk/BRugs/configure
===================================================================
--- trunk/BRugs/configure 2012-07-23 17:47:46 UTC (rev 254)
+++ trunk/BRugs/configure 2012-07-24 08:42:13 UTC (rev 255)
@@ -1,11 +1,11 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.65 for BRugs 0.7.
+# Generated by GNU Autoconf 2.68 for BRugs 0.8.
#
#
# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
-# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-# Inc.
+# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
+# Foundation, Inc.
#
#
# This configure script is free software; the Free Software Foundation
@@ -89,6 +89,7 @@
IFS=" "" $as_nl"
# Find who we are. Look in the path if we contain no directory separator.
+as_myself=
case $0 in #((
*[\\/]* ) as_myself=$0 ;;
*) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
@@ -213,11 +214,18 @@
# We cannot yet assume a decent shell, so we have to provide a
# neutralization value for shells without unset; and this also
# works around shells that cannot unset nonexistent variables.
+ # Preserve -v and -x to the replacement shell.
BASH_ENV=/dev/null
ENV=/dev/null
(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
export CONFIG_SHELL
- exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"}
+ case $- in # ((((
+ *v*x* | *x*v* ) as_opts=-vx ;;
+ *v* ) as_opts=-v ;;
+ *x* ) as_opts=-x ;;
+ * ) as_opts= ;;
+ esac
+ exec "$CONFIG_SHELL" $as_opts "$as_myself" ${1+"$@"}
fi
if test x$as_have_required = xno; then :
@@ -315,7 +323,7 @@
test -d "$as_dir" && break
done
test -z "$as_dirs" || eval "mkdir $as_dirs"
- } || test -d "$as_dir" || as_fn_error "cannot create directory $as_dir"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
} # as_fn_mkdir_p
@@ -355,19 +363,19 @@
fi # as_fn_arith
-# as_fn_error ERROR [LINENO LOG_FD]
-# ---------------------------------
+# as_fn_error STATUS 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 $?, using 1 if that was 0.
+# script with STATUS, using 1 if that was 0.
as_fn_error ()
{
- as_status=$?; 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
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
fi
- $as_echo "$as_me: error: $1" >&2
+ $as_echo "$as_me: error: $2" >&2
as_fn_exit $as_status
} # as_fn_error
@@ -529,7 +537,7 @@
exec 6>&1
# Name of the host.
-# hostname on some systems (SVR3.2, Linux) returns a bogus exit status,
+# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status,
# so uname gets run too.
ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
@@ -548,8 +556,8 @@
# Identity of this package.
PACKAGE_NAME='BRugs'
PACKAGE_TARNAME='brugs'
-PACKAGE_VERSION='0.7'
-PACKAGE_STRING='BRugs 0.7'
+PACKAGE_VERSION='0.8'
+PACKAGE_STRING='BRugs 0.8'
PACKAGE_BUGREPORT=''
PACKAGE_URL=''
@@ -680,8 +688,9 @@
fi
case $ac_option in
- *=*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
- *) ac_optarg=yes ;;
+ *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
+ *=) ac_optarg= ;;
+ *) ac_optarg=yes ;;
esac
# Accept the important Cygnus configure options, so we can diagnose typos.
@@ -726,7 +735,7 @@
ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
# Reject names that are not valid shell variable names.
expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
- as_fn_error "invalid feature name: $ac_useropt"
+ as_fn_error $? "invalid feature name: $ac_useropt"
ac_useropt_orig=$ac_useropt
ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
case $ac_user_opts in
@@ -752,7 +761,7 @@
ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
# Reject names that are not valid shell variable names.
expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
- as_fn_error "invalid feature name: $ac_useropt"
+ as_fn_error $? "invalid feature name: $ac_useropt"
ac_useropt_orig=$ac_useropt
ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
case $ac_user_opts in
@@ -956,7 +965,7 @@
ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
# Reject names that are not valid shell variable names.
expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
- as_fn_error "invalid package name: $ac_useropt"
+ as_fn_error $? "invalid package name: $ac_useropt"
ac_useropt_orig=$ac_useropt
ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
case $ac_user_opts in
@@ -972,7 +981,7 @@
ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'`
# Reject names that are not valid shell variable names.
expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
- as_fn_error "invalid package name: $ac_useropt"
+ as_fn_error $? "invalid package name: $ac_useropt"
ac_useropt_orig=$ac_useropt
ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
case $ac_user_opts in
@@ -1002,8 +1011,8 @@
| --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*)
x_libraries=$ac_optarg ;;
- -*) as_fn_error "unrecognized option: \`$ac_option'
-Try \`$0 --help' for more information."
+ -*) as_fn_error $? "unrecognized option: \`$ac_option'
+Try \`$0 --help' for more information"
;;
*=*)
@@ -1011,7 +1020,7 @@
# Reject names that are not valid shell variable names.
case $ac_envvar in #(
'' | [0-9]* | *[!_$as_cr_alnum]* )
- as_fn_error "invalid variable name: \`$ac_envvar'" ;;
+ as_fn_error $? "invalid variable name: \`$ac_envvar'" ;;
esac
eval $ac_envvar=\$ac_optarg
export $ac_envvar ;;
@@ -1021,7 +1030,7 @@
$as_echo "$as_me: WARNING: you should use --build, --host, --target" >&2
expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null &&
$as_echo "$as_me: WARNING: invalid host type: $ac_option" >&2
- : ${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}
+ : "${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}"
;;
esac
@@ -1029,13 +1038,13 @@
if test -n "$ac_prev"; then
ac_option=--`echo $ac_prev | sed 's/_/-/g'`
- as_fn_error "missing argument to $ac_option"
+ as_fn_error $? "missing argument to $ac_option"
fi
if test -n "$ac_unrecognized_opts"; then
case $enable_option_checking in
no) ;;
- fatal) as_fn_error "unrecognized options: $ac_unrecognized_opts" ;;
+ fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;;
*) $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;;
esac
fi
@@ -1058,7 +1067,7 @@
[\\/$]* | ?:[\\/]* ) continue;;
NONE | '' ) case $ac_var in *prefix ) continue;; esac;;
esac
- as_fn_error "expected an absolute directory name for --$ac_var: $ac_val"
+ as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val"
done
# There might be people who depend on the old broken behavior: `$host'
@@ -1072,8 +1081,8 @@
if test "x$host_alias" != x; then
if test "x$build_alias" = x; then
cross_compiling=maybe
- $as_echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host.
- If a cross compiler is detected then cross compile mode will be used." >&2
+ $as_echo "$as_me: WARNING: if you wanted to set the --build type, don't use --host.
+ If a cross compiler is detected then cross compile mode will be used" >&2
elif test "x$build_alias" != "x$host_alias"; then
cross_compiling=yes
fi
@@ -1088,9 +1097,9 @@
ac_pwd=`pwd` && test -n "$ac_pwd" &&
ac_ls_di=`ls -di .` &&
ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` ||
- as_fn_error "working directory cannot be determined"
+ as_fn_error $? "working directory cannot be determined"
test "X$ac_ls_di" = "X$ac_pwd_ls_di" ||
- as_fn_error "pwd does not report name of working directory"
+ as_fn_error $? "pwd does not report name of working directory"
# Find the source files, if location was not specified.
@@ -1129,11 +1138,11 @@
fi
if test ! -r "$srcdir/$ac_unique_file"; then
test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .."
- as_fn_error "cannot find sources ($ac_unique_file) in $srcdir"
+ as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir"
fi
ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work"
ac_abs_confdir=`(
- cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error "$ac_msg"
+ cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg"
pwd)`
# When building in place, set srcdir=.
if test "$ac_abs_confdir" = "$ac_pwd"; then
@@ -1159,7 +1168,7 @@
# 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.
+\`configure' configures BRugs 0.8 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1173,7 +1182,7 @@
--help=short display options specific to this package
--help=recursive display the short help of all the included packages
-V, --version display version information and exit
- -q, --quiet, --silent do not print \`checking...' messages
+ -q, --quiet, --silent do not print \`checking ...' messages
--cache-file=FILE cache test results in FILE [disabled]
-C, --config-cache alias for \`--cache-file=config.cache'
-n, --no-create do not create output files
@@ -1220,15 +1229,15 @@
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of BRugs 0.7:";;
+ short | recursive ) echo "Configuration of BRugs 0.8:";;
esac
cat <<\_ACEOF
Optional Packages:
--with-PACKAGE[=ARG] use PACKAGE [ARG=yes]
--without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no)
- --with-openbugs=PATH the location of OpenBUGS installed from the source
- package, by default /usr/local/lib/OpenBUGS
+ --with-openbugs=PATH the location of the OpenBUGS installation, by
+ default /usr/local
Some influential environment variables:
CC C compiler command
@@ -1305,10 +1314,10 @@
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-BRugs configure 0.7
-generated by GNU Autoconf 2.65
+BRugs configure 0.8
+generated by GNU Autoconf 2.68
-Copyright (C) 2009 Free Software Foundation, Inc.
+Copyright (C) 2010 Free Software Foundation, Inc.
This configure script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it.
_ACEOF
@@ -1352,7 +1361,7 @@
ac_retval=1
fi
- eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
as_fn_set_status $ac_retval
} # ac_fn_c_try_compile
@@ -1398,7 +1407,7 @@
# interfere with the next link command; also delete a directory that is
# left behind by Apple's compiler. We do this before executing the actions.
rm -rf conftest.dSYM conftest_ipa8_conftest.oo
- eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
as_fn_set_status $ac_retval
} # ac_fn_c_try_link
@@ -1406,8 +1415,8 @@
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by BRugs $as_me 0.7, which was
-generated by GNU Autoconf 2.65. Invocation command line was
+It was created by BRugs $as_me 0.8, which was
+generated by GNU Autoconf 2.68. Invocation command line was
$ $0 $@
@@ -1517,11 +1526,9 @@
{
echo
- cat <<\_ASBOX
-## ---------------- ##
+ $as_echo "## ---------------- ##
## Cache variables. ##
-## ---------------- ##
-_ASBOX
+## ---------------- ##"
echo
# The following way of writing the cache mishandles newlines in values,
(
@@ -1555,11 +1562,9 @@
)
echo
- cat <<\_ASBOX
-## ----------------- ##
+ $as_echo "## ----------------- ##
## Output variables. ##
-## ----------------- ##
-_ASBOX
+## ----------------- ##"
echo
for ac_var in $ac_subst_vars
do
@@ -1572,11 +1577,9 @@
echo
if test -n "$ac_subst_files"; then
- cat <<\_ASBOX
-## ------------------- ##
+ $as_echo "## ------------------- ##
## File substitutions. ##
-## ------------------- ##
-_ASBOX
+## ------------------- ##"
echo
for ac_var in $ac_subst_files
do
@@ -1590,11 +1593,9 @@
fi
if test -s confdefs.h; then
- cat <<\_ASBOX
-## ----------- ##
+ $as_echo "## ----------- ##
## confdefs.h. ##
-## ----------- ##
-_ASBOX
+## ----------- ##"
echo
cat confdefs.h
echo
@@ -1649,7 +1650,12 @@
ac_site_file1=NONE
ac_site_file2=NONE
if test -n "$CONFIG_SITE"; then
- ac_site_file1=$CONFIG_SITE
+ # We do not want a PATH search for config.site.
+ case $CONFIG_SITE in #((
+ -*) ac_site_file1=./$CONFIG_SITE;;
+ */*) ac_site_file1=$CONFIG_SITE;;
+ *) ac_site_file1=./$CONFIG_SITE;;
+ esac
elif test "x$prefix" != xNONE; then
ac_site_file1=$prefix/share/config.site
ac_site_file2=$prefix/etc/config.site
@@ -1664,7 +1670,11 @@
{ $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5
$as_echo "$as_me: loading site script $ac_site_file" >&6;}
sed 's/^/| /' "$ac_site_file" >&5
- . "$ac_site_file"
+ . "$ac_site_file" \
+ || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "failed to load site script $ac_site_file
+See \`config.log' for more details" "$LINENO" 5; }
fi
done
@@ -1740,7 +1750,7 @@
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
{ $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
$as_echo "$as_me: error: changes in the environment can compromise the build" >&2;}
- as_fn_error "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
+ as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5
fi
## -------------------- ##
## Main body of script. ##
@@ -1754,16 +1764,6 @@
-## Work around the inconsistency between the installation destinations of the 3.2.1 source and binary packages.
-## Source installs library in $prefix/lib/OpenBUGS/lib, doc in $prefix/lib/OpenBUGS/doc.
-## Binaries install in standards-compliant locations $prefix/lib and $prefix/share/doc/openbugs-version respectively.
-## Look in all of these places.
-## Return OPENBUGS = $prefix/lib/OpenBUGS for source installations, and
-## OPENBUGS = $prefix for binary installations.
-## Return OPENBUGSDOC = $prefix/lib/OpenBUGS/doc for source installations,
-## and OPENBUGSDOC = $prefix/share/doc/openbugs-version for binary installations.
-## If user specifies -with-openbugs, this is interpreted for a source installation.
-
## TODO only runs on x86 Linux - give error on other unixes.
@@ -1773,7 +1773,7 @@
set dummy OpenBUGS; ac_word=$2
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_path_ac_prefix_program+set}" = set; then :
+if ${ac_cv_path_ac_prefix_program+:} false; then :
$as_echo_n "(cached) " >&6
else
case $ac_prefix_program in
@@ -1869,21 +1869,29 @@
if test -n "$openbugs_path" ; then
OPENBUGS=${openbugs_path}
- SOURCEINST=true
else
if test "$prefix" = "NONE" ; then
- as_fn_error "OpenBUGS not found. Install OpenBUGS 3.2.1 or later, or specify its location using, for example, R CMD INSTALL BRugs --configure-args='--with-openbugs=/usr/local/lib/OpenBUGS' " "$LINENO" 5
+ as_fn_error $? "OpenBUGS 3.2.2 or later not found. Install it, or specify its location using, for example, R CMD INSTALL BRugs --configure-args='--with-openbugs=/usr/local' " "$LINENO" 5
else
- if test -e ${prefix}/lib/OpenBUGS/lib/libOpenBUGS.so ; then
- OPENBUGS=${prefix}/lib/OpenBUGS
- SOURCEINST=true
- else
+ if test -e ${prefix}/lib/libOpenBUGS.so ; then
OPENBUGS=${prefix}
- SOURCEINST=false
+ elif test -e ${prefix}/lib/OpenBUGS/lib/libOpenBUGS.so ; then # for 3.2.1
+ OPENBUGS=${prefix}
fi
fi
fi
+VERSION=`echo "modelQuit()" | ${OPENBUGS}/bin/OpenBUGS | sed -ne "s/OpenBUGS version \(.*\) rev \(.*\)/\1/p"`
+if test `echo ${VERSION} |cut -d. -f1` -lt 3; then
+ as_fn_error $? "Requires OpenBUGS version 3.2.2 or greater" "$LINENO" 5
+fi
+if test `echo ${VERSION} |cut -d. -f1` -eq 3 -a `echo ${VERSION} |cut -d. -f2` -lt 2 ; then
+ as_fn_error $? "Requires OpenBUGS version 3.2.2 or greater" "$LINENO" 5
+fi
+if test `echo ${VERSION} |cut -d. -f1` -eq 3 -a `echo ${VERSION} |cut -d. -f2` -eq 2 -a `echo ${VERSION} |cut -d. -f3` -lt 2 ; then
+ as_fn_error $? "Requires OpenBUGS version 3.2.2 or greater" "$LINENO" 5
+fi
+
OLDFLAGS=${LDFLAGS}
LDFLAGS="-L${OPENBUGS}/lib -m32"
ac_ext=c
@@ -1896,7 +1904,7 @@
set dummy ${ac_tool_prefix}gcc; ac_word=$2
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_CC+set}" = set; then :
+if ${ac_cv_prog_CC+:} false; then :
$as_echo_n "(cached) " >&6
else
if test -n "$CC"; then
@@ -1936,7 +1944,7 @@
set dummy gcc; ac_word=$2
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_ac_ct_CC+set}" = set; then :
+if ${ac_cv_prog_ac_ct_CC+:} false; then :
$as_echo_n "(cached) " >&6
else
if test -n "$ac_ct_CC"; then
@@ -1989,7 +1997,7 @@
set dummy ${ac_tool_prefix}cc; ac_word=$2
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_CC+set}" = set; then :
+if ${ac_cv_prog_CC+:} false; then :
$as_echo_n "(cached) " >&6
else
if test -n "$CC"; then
@@ -2029,7 +2037,7 @@
set dummy cc; ac_word=$2
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_CC+set}" = set; then :
+if ${ac_cv_prog_CC+:} false; then :
$as_echo_n "(cached) " >&6
else
if test -n "$CC"; then
@@ -2088,7 +2096,7 @@
set dummy $ac_tool_prefix$ac_prog; ac_word=$2
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_CC+set}" = set; then :
+if ${ac_cv_prog_CC+:} false; then :
$as_echo_n "(cached) " >&6
else
if test -n "$CC"; then
@@ -2132,7 +2140,7 @@
set dummy $ac_prog; ac_word=$2
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_ac_ct_CC+set}" = set; then :
+if ${ac_cv_prog_ac_ct_CC+:} false; then :
$as_echo_n "(cached) " >&6
else
if test -n "$ac_ct_CC"; then
@@ -2186,8 +2194,8 @@
test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error "no acceptable C compiler found in \$PATH
-See \`config.log' for more details." "$LINENO" 5; }
+as_fn_error $? "no acceptable C compiler found in \$PATH
+See \`config.log' for more details" "$LINENO" 5; }
# Provide some information about the compiler.
$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
@@ -2301,9 +2309,8 @@
{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ as_fn_set_status 77
-as_fn_error "C compiler cannot create executables
-See \`config.log' for more details." "$LINENO" 5; }; }
+as_fn_error 77 "C compiler cannot create executables
+See \`config.log' for more details" "$LINENO" 5; }
else
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
$as_echo "yes" >&6; }
@@ -2345,8 +2352,8 @@
else
{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error "cannot compute suffix of executables: cannot compile and link
-See \`config.log' for more details." "$LINENO" 5; }
+as_fn_error $? "cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details" "$LINENO" 5; }
fi
rm -f conftest conftest$ac_cv_exeext
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5
@@ -2403,9 +2410,9 @@
else
{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error "cannot run C compiled programs.
+as_fn_error $? "cannot run C compiled programs.
If you meant to cross compile, use \`--host'.
-See \`config.log' for more details." "$LINENO" 5; }
+See \`config.log' for more details" "$LINENO" 5; }
fi
fi
fi
@@ -2416,7 +2423,7 @@
ac_clean_files=$ac_clean_files_save
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5
$as_echo_n "checking for suffix of object files... " >&6; }
-if test "${ac_cv_objext+set}" = set; then :
+if ${ac_cv_objext+:} false; then :
$as_echo_n "(cached) " >&6
else
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
@@ -2456,8 +2463,8 @@
{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-as_fn_error "cannot compute suffix of object files: cannot compile
-See \`config.log' for more details." "$LINENO" 5; }
+as_fn_error $? "cannot compute suffix of object files: cannot compile
+See \`config.log' for more details" "$LINENO" 5; }
fi
rm -f conftest.$ac_cv_objext conftest.$ac_ext
fi
@@ -2467,7 +2474,7 @@
ac_objext=$OBJEXT
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5
$as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
-if test "${ac_cv_c_compiler_gnu+set}" = set; then :
+if ${ac_cv_c_compiler_gnu+:} false; then :
$as_echo_n "(cached) " >&6
else
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
@@ -2504,7 +2511,7 @@
ac_save_CFLAGS=$CFLAGS
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5
$as_echo_n "checking whether $CC accepts -g... " >&6; }
-if test "${ac_cv_prog_cc_g+set}" = set; then :
+if ${ac_cv_prog_cc_g+:} false; then :
$as_echo_n "(cached) " >&6
else
ac_save_c_werror_flag=$ac_c_werror_flag
@@ -2582,7 +2589,7 @@
fi
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5
$as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
-if test "${ac_cv_prog_cc_c89+set}" = set; then :
+if ${ac_cv_prog_cc_c89+:} false; then :
$as_echo_n "(cached) " >&6
else
ac_cv_prog_cc_c89=no
@@ -2680,7 +2687,7 @@
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for CmdInterpreter in -lOpenBUGS" >&5
$as_echo_n "checking for CmdInterpreter in -lOpenBUGS... " >&6; }
-if test "${ac_cv_lib_OpenBUGS_CmdInterpreter+set}" = set; then :
+if ${ac_cv_lib_OpenBUGS_CmdInterpreter+:} false; then :
$as_echo_n "(cached) " >&6
else
ac_check_lib_save_LIBS=$LIBS
@@ -2714,7 +2721,7 @@
fi
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_OpenBUGS_CmdInterpreter" >&5
$as_echo "$ac_cv_lib_OpenBUGS_CmdInterpreter" >&6; }
-if test "x$ac_cv_lib_OpenBUGS_CmdInterpreter" = x""yes; then :
+if test "x$ac_cv_lib_OpenBUGS_CmdInterpreter" = xyes; then :
cat >>confdefs.h <<_ACEOF
#define HAVE_LIBOPENBUGS 1
_ACEOF
@@ -2722,27 +2729,19 @@
LIBS="-lOpenBUGS $LIBS"
else
- as_fn_error "\"Cannot load OpenBUGS library in ${OPENBUGS}/lib. Run R CMD INSTALL BRugs --configure-args='--with-openbugs=...'\"" "$LINENO" 5
+ as_fn_error $? "\"Cannot load OpenBUGS library in ${OPENBUGS}/lib. Run R CMD INSTALL BRugs --configure-args='--with-openbugs=...'\"" "$LINENO" 5
fi
LDFLAGS=${OLDFLAGS}
-VERSION=`echo "modelQuit()" | ${OPENBUGS}/bin/OpenBUGS | sed -ne "s/OpenBUGS version \(.*\) rev \(.*\)/\1/p"`
-if test `echo ${VERSION} |cut -d. -f1` -lt 3; then
- as_fn_error "Requires OpenBUGS version 3.2.1 or greater" "$LINENO" 5
-fi
-if test `echo ${VERSION} |cut -d. -f1` -eq 3 -a `echo ${VERSION} |cut -d. -f2` -lt 2 ; then
- as_fn_error "Requires OpenBUGS version 3.2.1 or greater" "$LINENO" 5
-fi
-
-if ${SOURCEINST} ; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: Found OpenBUGS installation from source package " >&5
-$as_echo "$as_me: Found OpenBUGS installation from source package " >&6;}
- OPENBUGSDOC=${OPENBUGS}/doc
+if test -d "${OPENBUGS}/share/doc/openbugs-${VERSION}" ; then
+ OPENBUGSDOC=${OPENBUGS}/share/doc/openbugs-${VERSION}
else
- { $as_echo "$as_me:${as_lineno-$LINENO}: Found OpenBUGS installation from binary package " >&5
-$as_echo "$as_me: Found OpenBUGS installation from binary package " >&6;}
- OPENBUGSDOC=${OPENBUGS}/share/doc/openbugs-${VERSION}
+ if test -d "${OPENBUGS}/share/doc/openbugs" ; then
+ OPENBUGSDOC=${OPENBUGS}/share/doc/openbugs
+ else
+ as_fn_error $? "OpenBUGS documentation directory not found in ${OPENBUGS}/share/doc" "$LINENO" 5
+ fi
fi
OPENBUGS=${OPENBUGS}/lib
@@ -2817,10 +2816,21 @@
:end' >>confcache
if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
if test -w "$cache_file"; then
- test "x$cache_file" != "x/dev/null" &&
+ if test "x$cache_file" != "x/dev/null"; then
{ $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
$as_echo "$as_me: updating cache $cache_file" >&6;}
- cat confcache >$cache_file
+ if test ! -f "$cache_file" || test -h "$cache_file"; then
+ cat confcache >"$cache_file"
+ else
+ case $cache_file in #(
+ */* | ?:*)
+ mv -f confcache "$cache_file"$$ &&
+ mv -f "$cache_file"$$ "$cache_file" ;; #(
+ *)
+ mv -f confcache "$cache_file" ;;
+ esac
+ fi
+ fi
else
{ $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
@@ -2872,6 +2882,7 @@
ac_libobjs=
ac_ltlibobjs=
+U=
for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
# 1. Remove the extension, and $U if already installed.
ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
@@ -2887,7 +2898,7 @@
-: ${CONFIG_STATUS=./config.status}
+: "${CONFIG_STATUS=./config.status}"
ac_write_fail=0
ac_clean_files_save=$ac_clean_files
ac_clean_files="$ac_clean_files $CONFIG_STATUS"
@@ -2988,6 +2999,7 @@
IFS=" "" $as_nl"
# Find who we are. Look in the path if we contain no directory separator.
+as_myself=
case $0 in #((
*[\\/]* ) as_myself=$0 ;;
*) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
@@ -3033,19 +3045,19 @@
(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
-# as_fn_error ERROR [LINENO LOG_FD]
-# ---------------------------------
+# as_fn_error STATUS 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 $?, using 1 if that was 0.
+# script with STATUS, using 1 if that was 0.
as_fn_error ()
{
- as_status=$?; 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
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
fi
- $as_echo "$as_me: error: $1" >&2
+ $as_echo "$as_me: error: $2" >&2
as_fn_exit $as_status
} # as_fn_error
@@ -3241,7 +3253,7 @@
test -d "$as_dir" && break
done
test -z "$as_dirs" || eval "mkdir $as_dirs"
- } || test -d "$as_dir" || as_fn_error "cannot create directory $as_dir"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
} # as_fn_mkdir_p
@@ -3294,8 +3306,8 @@
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by BRugs $as_me 0.7, which was
-generated by GNU Autoconf 2.65. Invocation command line was
+This file was extended by BRugs $as_me 0.8, which was
+generated by GNU Autoconf 2.68. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
CONFIG_HEADERS = $CONFIG_HEADERS
@@ -3347,11 +3359,11 @@
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-BRugs config.status 0.7
-configured by $0, generated by GNU Autoconf 2.65,
+BRugs config.status 0.8
+configured by $0, generated by GNU Autoconf 2.68,
with options \\"\$ac_cs_config\\"
-Copyright (C) 2009 Free Software Foundation, Inc.
+Copyright (C) 2010 Free Software Foundation, Inc.
This config.status script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it."
@@ -3366,11 +3378,16 @@
while test $# != 0
do
case $1 in
- --*=*)
+ --*=?*)
ac_option=`expr "X$1" : 'X\...
[truncated message content] |
|
From: <li...@us...> - 2013-05-26 16:05:20
|
Revision: 265
http://sourceforge.net/p/bugs-r/code/265
Author: ligges
Date: 2013-05-26 16:05:18 +0000 (Sun, 26 May 2013)
Log Message:
-----------
Bugfix: samplesStats(node) did not work on node vectors of length > 1
Modified Paths:
--------------
trunk/BRugs/DESCRIPTION
trunk/BRugs/NEWS
trunk/BRugs/R/samples.stats.R
Modified: trunk/BRugs/DESCRIPTION
===================================================================
--- trunk/BRugs/DESCRIPTION 2013-04-10 20:33:41 UTC (rev 264)
+++ trunk/BRugs/DESCRIPTION 2013-05-26 16:05:18 UTC (rev 265)
@@ -1,7 +1,7 @@
Package: BRugs
Title: R interface to the OpenBUGS MCMC software
-Version: 0.8-0
-Date: 2012-07-23
+Version: 0.8-1
+Date: 2013-05-26
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. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.
Maintainer: Uwe Ligges <li...@st...>
Modified: trunk/BRugs/NEWS
===================================================================
--- trunk/BRugs/NEWS 2013-04-10 20:33:41 UTC (rev 264)
+++ trunk/BRugs/NEWS 2013-05-26 16:05:18 UTC (rev 265)
@@ -1,6 +1,11 @@
Changes to BRugs:
=====================
+Version 0.8.1 (26 May 2013)
+-------------
+Bugfix: samplesStats(node) did not work on node vectors of length > 1
+
+
Version 0.8.0 (23 July 2012)
-------------
BRugs now works with an existing installation of OpenBUGS (>?)= 3.2.2.
Modified: trunk/BRugs/R/samples.stats.R
===================================================================
--- trunk/BRugs/R/samples.stats.R 2013-04-10 20:33:41 UTC (rev 264)
+++ trunk/BRugs/R/samples.stats.R 2013-05-26 16:05:18 UTC (rev 265)
@@ -33,7 +33,7 @@
}
for(i in seq(along=node)){
- command <- paste(.SamplesGlobalsCmd(node), "SamplesEmbed.StatsGuard;SamplesEmbed.Stats")
+ command <- paste(.SamplesGlobalsCmd(node[i]), "SamplesEmbed.StatsGuard;SamplesEmbed.Stats")
.CmdInterpreter(command)
buffer <- file.path(tempdir(), "buffer.txt")
rlb <- readLines(buffer)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <li...@us...> - 2013-08-18 16:54:58
|
Revision: 266
http://sourceforge.net/p/bugs-r/code/266
Author: ligges
Date: 2013-08-18 16:54:53 +0000 (Sun, 18 Aug 2013)
Log Message:
-----------
Remove utils from Depends and make proper imports so ":::" usage is no longer necessary, as requested by CRAN maintainers.
Modified Paths:
--------------
trunk/BRugs/DESCRIPTION
trunk/BRugs/NAMESPACE
trunk/BRugs/NEWS
trunk/BRugs/R/buildMCMC.R
trunk/BRugs/R/windows/findOpenBUGS.R
Modified: trunk/BRugs/DESCRIPTION
===================================================================
--- trunk/BRugs/DESCRIPTION 2013-05-26 16:05:18 UTC (rev 265)
+++ trunk/BRugs/DESCRIPTION 2013-08-18 16:54:53 UTC (rev 266)
@@ -1,11 +1,11 @@
Package: BRugs
Title: R interface to the OpenBUGS MCMC software
-Version: 0.8-1
-Date: 2013-05-26
+Version: 0.8-2
+Date: 2013-08-18
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. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.
Maintainer: Uwe Ligges <li...@st...>
-Depends: R (>= 2.11.0), coda
+Depends: R (>= 2.11.0)
Imports: utils, coda
SystemRequirements: OpenBUGS (>= 3.2.2), hence Windows or Linux
License: GPL-2
Modified: trunk/BRugs/NAMESPACE
===================================================================
--- trunk/BRugs/NAMESPACE 2013-05-26 16:05:18 UTC (rev 265)
+++ trunk/BRugs/NAMESPACE 2013-08-18 16:54:53 UTC (rev 266)
@@ -1,5 +1,5 @@
importFrom(coda, mcmc, mcmc.list)
-importFrom(utils, compareVersion, maintainer)
+importFrom(utils, compareVersion, maintainer, packageDescription, readRegistry)
export(BRugsFit, bugsData, bugsInits, buildMCMC,
dicClear, dicSet, dicStats,
getNumChains, help.BRugs, help.WinBUGS,
Modified: trunk/BRugs/NEWS
===================================================================
--- trunk/BRugs/NEWS 2013-05-26 16:05:18 UTC (rev 265)
+++ trunk/BRugs/NEWS 2013-08-18 16:54:53 UTC (rev 266)
@@ -1,6 +1,12 @@
Changes to BRugs:
=====================
+Version 0.8.2 (18 August 2013)
+-------------
+Bugfix: remove coda from"Depends:" as "Imports:" is sufficient.
+Bugfix: Remove ":::" constructs to access function from utils that are imported.
+
+
Version 0.8.1 (26 May 2013)
-------------
Bugfix: samplesStats(node) did not work on node vectors of length > 1
Modified: trunk/BRugs/R/buildMCMC.R
===================================================================
--- trunk/BRugs/R/buildMCMC.R 2013-05-26 16:05:18 UTC (rev 265)
+++ trunk/BRugs/R/buildMCMC.R 2013-08-18 16:54:53 UTC (rev 266)
@@ -2,10 +2,6 @@
firstChain = samplesGetFirstChain(), lastChain = samplesGetLastChain(),
thin = samplesGetThin()){
- if(!is.R() && !require("coda"))
- stop("package 'coda' is required to use this function")
-
-
oldBeg <- samplesGetBeg()
oldEnd <- samplesGetEnd()
oldFirstChain <- samplesGetFirstChain()
Modified: trunk/BRugs/R/windows/findOpenBUGS.R
===================================================================
--- trunk/BRugs/R/windows/findOpenBUGS.R 2013-05-26 16:05:18 UTC (rev 265)
+++ trunk/BRugs/R/windows/findOpenBUGS.R 2013-08-18 16:54:53 UTC (rev 266)
@@ -2,10 +2,10 @@
{
dir <- Sys.getenv("OpenBUGS_PATH")
if(!nchar(dir)){
- deps <- utils:::packageDescription("BRugs", fields="SystemRequirements")
+ deps <- packageDescription("BRugs", fields="SystemRequirements")
version.req <- gsub(".*OpenBUGS ?\\(>= ?(.+)\\).*", "\\1", deps)
- ob.reg <- try(utils:::readRegistry("Software\\OpenBUGS", "HLM", view = "32-bit"), silent = TRUE)
+ ob.reg <- try(readRegistry("Software\\OpenBUGS", "HLM", view = "32-bit"), silent = TRUE)
if (inherits(ob.reg, "try-error")) {
warning("OpenBUGS ", version.req, " or greater must be installed\n(if so, this indicates missing registry keys of OpenBUGS).\nSetting the environment variable 'OpenBUGS_PATH' in advance of loading 'BRugs' overwrites the path.\nSee ?loadOpenBUGS in order to load OpenBUGS manually.")
return()
@@ -29,7 +29,7 @@
}
## OpenBUGS installation location
- dir <- utils:::readRegistry(paste("Software","OpenBUGS",rnames,sep="\\"), "HLM", view = "32-bit")[["InstallPath"]]
+ dir <- readRegistry(paste("Software","OpenBUGS",rnames,sep="\\"), "HLM", view = "32-bit")[["InstallPath"]]
} else {
if(!file.exists(file.path(dir, "libOpenBUGS.dll"))){
warning("Environment variable OpenBUGS_PATH found but cannot access ", file.path(dir, "libOpenBUGS.dll"))
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From: <li...@us...> - 2013-08-18 22:31:19
|
Revision: 267
http://sourceforge.net/p/bugs-r/code/267
Author: ligges
Date: 2013-08-18 22:31:14 +0000 (Sun, 18 Aug 2013)
Log Message:
-----------
"hotfix": some functions can only be imported under Windows
Modified Paths:
--------------
trunk/BRugs/DESCRIPTION
trunk/BRugs/NAMESPACE
Modified: trunk/BRugs/DESCRIPTION
===================================================================
--- trunk/BRugs/DESCRIPTION 2013-08-18 16:54:53 UTC (rev 266)
+++ trunk/BRugs/DESCRIPTION 2013-08-18 22:31:14 UTC (rev 267)
@@ -1,6 +1,6 @@
Package: BRugs
Title: R interface to the OpenBUGS MCMC software
-Version: 0.8-2
+Version: 0.8-3
Date: 2013-08-18
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. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.
Modified: trunk/BRugs/NAMESPACE
===================================================================
--- trunk/BRugs/NAMESPACE 2013-08-18 16:54:53 UTC (rev 266)
+++ trunk/BRugs/NAMESPACE 2013-08-18 22:31:14 UTC (rev 267)
@@ -1,5 +1,6 @@
importFrom(coda, mcmc, mcmc.list)
-importFrom(utils, compareVersion, maintainer, packageDescription, readRegistry)
+importFrom(utils, compareVersion, maintainer, packageDescription)
+if(tools:::.OStype() == "windows") importFrom(utils, readRegistry)
export(BRugsFit, bugsData, bugsInits, buildMCMC,
dicClear, dicSet, dicStats,
getNumChains, help.BRugs, help.WinBUGS,
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From: <li...@us...> - 2015-05-31 15:27:29
|
Revision: 269
http://sourceforge.net/p/bugs-r/code/269
Author: ligges
Date: 2015-05-31 15:27:27 +0000 (Sun, 31 May 2015)
Log Message:
-----------
bugfix release
Modified Paths:
--------------
trunk/BRugs/DESCRIPTION
trunk/BRugs/NEWS
trunk/BRugs/R/windows/findOpenBUGS.R
Modified: trunk/BRugs/DESCRIPTION
===================================================================
--- trunk/BRugs/DESCRIPTION 2015-04-07 19:05:12 UTC (rev 268)
+++ trunk/BRugs/DESCRIPTION 2015-05-31 15:27:27 UTC (rev 269)
@@ -1,7 +1,7 @@
Package: BRugs
Title: R interface to the OpenBUGS MCMC software
-Version: 0.8-3
-Date: 2013-08-18
+Version: 0.8-4
+Date: 2015-05-31
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. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.
Maintainer: Uwe Ligges <li...@st...>
Modified: trunk/BRugs/NEWS
===================================================================
--- trunk/BRugs/NEWS 2015-04-07 19:05:12 UTC (rev 268)
+++ trunk/BRugs/NEWS 2015-05-31 15:27:27 UTC (rev 269)
@@ -1,6 +1,13 @@
Changes to BRugs:
=====================
+
+Version 0.8.4 (31 May 2015)
+-------------
+problem when Openbugs_PATH environment variable was set but version did not
+get propagated correctly
+
+
Version 0.8.2 (18 August 2013)
-------------
Bugfix: remove coda from"Depends:" as "Imports:" is sufficient.
Modified: trunk/BRugs/R/windows/findOpenBUGS.R
===================================================================
--- trunk/BRugs/R/windows/findOpenBUGS.R 2015-04-07 19:05:12 UTC (rev 268)
+++ trunk/BRugs/R/windows/findOpenBUGS.R 2015-05-31 15:27:27 UTC (rev 269)
@@ -35,7 +35,7 @@
warning("Environment variable OpenBUGS_PATH found but cannot access ", file.path(dir, "libOpenBUGS.dll"))
return()
}
- version.inst <- NA
+ version.inst <- version.full <- NA
}
list(dir=dir, version=version.full)
}
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From: <li...@us...> - 2015-07-29 21:47:53
|
Revision: 272
http://sourceforge.net/p/bugs-r/code/272
Author: ligges
Date: 2015-07-29 21:47:51 +0000 (Wed, 29 Jul 2015)
Log Message:
-----------
import from base package, fix URLs, ...
Modified Paths:
--------------
trunk/BRugs/DESCRIPTION
trunk/BRugs/NAMESPACE
trunk/BRugs/NEWS
trunk/BRugs/man/BRugs.Rd
trunk/BRugs/man/model.factory.Rd
Modified: trunk/BRugs/DESCRIPTION
===================================================================
--- trunk/BRugs/DESCRIPTION 2015-07-29 21:13:08 UTC (rev 271)
+++ trunk/BRugs/DESCRIPTION 2015-07-29 21:47:51 UTC (rev 272)
@@ -1,12 +1,12 @@
Package: BRugs
-Title: R interface to the OpenBUGS MCMC software
-Version: 0.8-4
-Date: 2015-05-31
+Title: Interface to the 'OpenBUGS' MCMC Software
+Version: 0.8-5
+Date: 2015-07-29
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. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.
+Description: Fully-interactive R interface to the 'OpenBUGS' software for Bayesian analysis using MCMC sampling. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.
Maintainer: Uwe Ligges <li...@st...>
Depends: R (>= 2.11.0)
-Imports: utils, coda
+Imports: utils, coda, grDevices, graphics, stats
SystemRequirements: OpenBUGS (>= 3.2.2), hence Windows or Linux
License: GPL-2
-URL: http://www.openbugs.info/
+URL: http://www.openbugs.net/
Modified: trunk/BRugs/NAMESPACE
===================================================================
--- trunk/BRugs/NAMESPACE 2015-07-29 21:13:08 UTC (rev 271)
+++ trunk/BRugs/NAMESPACE 2015-07-29 21:47:51 UTC (rev 272)
@@ -1,6 +1,10 @@
importFrom(coda, mcmc, mcmc.list)
-importFrom(utils, compareVersion, maintainer, packageDescription)
+importFrom(utils, compareVersion, maintainer, packageDescription, browseURL, read.table)
if(tools:::.OStype() == "windows") importFrom(utils, readRegistry)
+importFrom("grDevices", "dev.cur", "dev.interactive")
+importFrom("graphics", "lines", "par")
+importFrom("stats", "acf", "density", "quantile", "sd")
+
export(BRugsFit, bugsData, bugsInits, buildMCMC,
dicClear, dicSet, dicStats,
getNumChains, help.BRugs, help.WinBUGS,
Modified: trunk/BRugs/NEWS
===================================================================
--- trunk/BRugs/NEWS 2015-07-29 21:13:08 UTC (rev 271)
+++ trunk/BRugs/NEWS 2015-07-29 21:47:51 UTC (rev 272)
@@ -1,6 +1,9 @@
Changes to BRugs:
=====================
+Version 0.8.5 (29 July 2015)
+-------------
+import from base packages, fix URLs
Version 0.8.4 (31 May 2015)
-------------
Modified: trunk/BRugs/man/BRugs.Rd
===================================================================
--- trunk/BRugs/man/BRugs.Rd 2015-07-29 21:13:08 UTC (rev 271)
+++ trunk/BRugs/man/BRugs.Rd 2015-07-29 21:47:51 UTC (rev 272)
@@ -28,7 +28,7 @@
}
\section{Permission and Disclaimer}{
BRugs is released under the GNU GENERAL PUBLIC LICENSE.
- For details see \url{http://openbugs.info/} or type \code{help.BRugs()}.
+ For details see \url{http://www.openbugs.net/} or type \code{help.BRugs()}.
More informally, potential users are reminded to be extremely careful if using this program for serious
statistical analysis. We have tested the program on quite a wide set of examples, but be particularly careful
@@ -40,7 +40,7 @@
within the Windows interface to OpenBUGS. This should give a "Trap"
window, which indicates an internal problem with OpenBUGS. See
- \url{http://www.openbugs.info/Manuals/TipsTroubleshooting.html#TrapMessages}
+ \url{http://www.openbugs.net/Manuals/TipsTroubleshooting.html#TrapMessages}
for suggestions for how to interpret these problematic error
messages.
Modified: trunk/BRugs/man/model.factory.Rd
===================================================================
--- trunk/BRugs/man/model.factory.Rd 2015-07-29 21:13:08 UTC (rev 271)
+++ trunk/BRugs/man/model.factory.Rd 2015-07-29 21:47:51 UTC (rev 272)
@@ -14,7 +14,7 @@
\item{factory}{Character (length 1) name of the factory to be
disabled/enabled, for example \code{"conjugate gamma"}. See
- \url{http://www.openbugs.info/Manuals/ModelMenu.html#Updateroptions}
+ \url{http://www.openbugs.net/Manuals/ModelMenu.html#Updateroptions}
for more information. A list of the currently-used updaters
in a compiled model is given by \code{\link{infoUpdatersbyName}} or
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From: <li...@us...> - 2015-12-16 08:11:10
|
Revision: 273
http://sourceforge.net/p/bugs-r/code/273
Author: ligges
Date: 2015-12-16 08:11:09 +0000 (Wed, 16 Dec 2015)
Log Message:
-----------
adapt tests for changes in file.copy() results
Modified Paths:
--------------
trunk/BRugs/DESCRIPTION
trunk/BRugs/NEWS
trunk/BRugs/tests/examples.R
Modified: trunk/BRugs/DESCRIPTION
===================================================================
--- trunk/BRugs/DESCRIPTION 2015-07-29 21:47:51 UTC (rev 272)
+++ trunk/BRugs/DESCRIPTION 2015-12-16 08:11:09 UTC (rev 273)
@@ -1,7 +1,7 @@
Package: BRugs
Title: Interface to the 'OpenBUGS' MCMC Software
-Version: 0.8-5
-Date: 2015-07-29
+Version: 0.8-6
+Date: 2015-12-16
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. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.
Maintainer: Uwe Ligges <li...@st...>
Modified: trunk/BRugs/NEWS
===================================================================
--- trunk/BRugs/NEWS 2015-07-29 21:47:51 UTC (rev 272)
+++ trunk/BRugs/NEWS 2015-12-16 08:11:09 UTC (rev 273)
@@ -1,6 +1,10 @@
Changes to BRugs:
=====================
+Version 0.8.6 (16 Dec 2015)
+-------------
+adapt tests for changes in file.copy() results
+
Version 0.8.5 (29 July 2015)
-------------
import from base packages, fix URLs
Modified: trunk/BRugs/tests/examples.R
===================================================================
--- trunk/BRugs/tests/examples.R 2015-07-29 21:47:51 UTC (rev 272)
+++ trunk/BRugs/tests/examples.R 2015-12-16 08:11:09 UTC (rev 273)
@@ -35,11 +35,13 @@
### Test for posterior means within 10 percent of previously saved values
res.true <- dget(file="examples.stats.R")
+
+exfiles <- unlist(lapply(test.pattern, function(tp) dir(options()$OpenBUGSExamples, pattern=tp, full.names=TRUE)))
+ok <- file.copy(unique(exfiles), tempdir())
+if(!all(ok))
+ stop("Some files could not be copied from OpenBUGS examples to the temporary directory")
+
for (i in seq(along=test.models)) {
- exfiles <- dir(options()$OpenBUGSExamples, pattern=test.pattern[i], full.names=TRUE)
- ok <- file.copy(exfiles, tempdir())
- if(!all(ok))
- stop("Some files could not be copied from OpenBUGS examples to the temporary directory")
fit <- BRugsFit(data=test.datafile[i], inits=test.inits[i],
modelFile=test.modelfile[i], para=test.params[[test.models[i]]],
nBurnin=5000, nIter=20000, nThin=1, numChains=1, seed=1,
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From: <li...@us...> - 2017-06-26 14:57:58
|
Revision: 276
http://sourceforge.net/p/bugs-r/code/276
Author: ligges
Date: 2017-06-26 14:57:56 +0000 (Mon, 26 Jun 2017)
Log Message:
-----------
adapt for new toolchain (we have to compile with 32-bit compiler / linker)
Modified Paths:
--------------
trunk/BRugs/DESCRIPTION
trunk/BRugs/NEWS
trunk/BRugs/src/Makefile.win
Modified: trunk/BRugs/DESCRIPTION
===================================================================
--- trunk/BRugs/DESCRIPTION 2017-06-26 13:59:22 UTC (rev 275)
+++ trunk/BRugs/DESCRIPTION 2017-06-26 14:57:56 UTC (rev 276)
@@ -5,7 +5,7 @@
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. Runs natively and stably in 32-bit R under Windows. Versions running on Linux and on 64-bit R under Windows are in "beta" status and less efficient.
Maintainer: Uwe Ligges <li...@st...>
-Depends: R (>= 2.11.0)
+Depends: R (>= 3.3.0)
Imports: utils, coda, grDevices, graphics, stats
SystemRequirements: OpenBUGS (>= 3.2.2), hence Windows or Linux
License: GPL-2
Modified: trunk/BRugs/NEWS
===================================================================
--- trunk/BRugs/NEWS 2017-06-26 13:59:22 UTC (rev 275)
+++ trunk/BRugs/NEWS 2017-06-26 14:57:56 UTC (rev 276)
@@ -1,6 +1,10 @@
Changes to BRugs:
=====================
+Version 0.9.0 (26 Jun 2017)
+-------------
+fixes for new Windows toolchain
+
Version 0.8.6 (16 Dec 2015)
-------------
adapt tests for changes in file.copy() results
Modified: trunk/BRugs/src/Makefile.win
===================================================================
--- trunk/BRugs/src/Makefile.win 2017-06-26 13:59:22 UTC (rev 275)
+++ trunk/BRugs/src/Makefile.win 2017-06-26 14:57:56 UTC (rev 276)
@@ -1,3 +1,4 @@
+include $(R_HOME)/etc/i386/Makeconf
BUGS_PATH = `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "source('../R/windows/findOpenBUGS.R');cat(findOpenBUGS()[['dir']])"`
BUGS_LIBS = "$(BUGS_PATH)/libOpenBUGS.dll"
BUGS_LDFLAGS = -m32 -Wl,-rpath="$(BUGS_PATH)"
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From: <li...@us...> - 2017-06-26 15:27:59
|
Revision: 278
http://sourceforge.net/p/bugs-r/code/278
Author: ligges
Date: 2017-06-26 15:27:57 +0000 (Mon, 26 Jun 2017)
Log Message:
-----------
try to make GCC7 happy
Modified Paths:
--------------
trunk/BRugs/NEWS
trunk/BRugs/src/BugsHelper.c
Modified: trunk/BRugs/NEWS
===================================================================
--- trunk/BRugs/NEWS 2017-06-26 14:59:17 UTC (rev 277)
+++ trunk/BRugs/NEWS 2017-06-26 15:27:57 UTC (rev 278)
@@ -3,7 +3,7 @@
Version 0.9.0 (26 Jun 2017)
-------------
-fixes for new Windows toolchain
+fixes for new Windows toolchain and GCC7
Version 0.8.6 (16 Dec 2015)
-------------
Modified: trunk/BRugs/src/BugsHelper.c
===================================================================
--- trunk/BRugs/src/BugsHelper.c 2017-06-26 14:59:17 UTC (rev 277)
+++ trunk/BRugs/src/BugsHelper.c 2017-06-26 15:27:57 UTC (rev 278)
@@ -89,7 +89,7 @@
void read_input_real(char *tmpdir, double **out, int *len, int cmdno) {
char *fname;
- struct stat buf;
+ struct stat buf={.st_dev = 0};
FILE *ifp;
double tmp;
fname = (char *) malloc(strlen(tmpdir) + 16);
@@ -115,7 +115,7 @@
void read_input_char(char *tmpdir, char **out, int *len, int cmdno) {
char *fname;
- struct stat buf;
+ struct stat buf={.st_dev = 0};
FILE *ifp;
fname = (char *) malloc(strlen(tmpdir) + 16);
sprintf(fname, "%s/input%d.txt", tmpdir, cmdno);
@@ -252,7 +252,7 @@
int do_Internalize(char *tmpdir, char *extfile){
char *extpath, *int_cmd;
- struct stat buf;
+ struct stat buf={.st_dev = 0};
int res;
extpath = (char *) malloc(strlen(tmpdir) + 2 + strlen(extfile));
sprintf(extpath, "%s/%s", tmpdir, extfile);
@@ -289,7 +289,7 @@
char *cmd, cmd_type;
char *output_to_buffer_cmd = "BugsMappers.SetDest(2)";
FILE *ifp;
- struct stat buf;
+ struct stat buf={.st_dev = 0};
do_Cmd(output_to_buffer_cmd);
do_TempDir(trashdir);
do_Internalize(tmpdir, extfile);
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