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From: <wa...@us...> - 2007-03-24 21:30:28
|
Revision: 1085
http://svn.sourceforge.net/r-gregmisc/?rev=1085&view=rev
Author: warnes
Date: 2007-03-24 14:30:26 -0700 (Sat, 24 Mar 2007)
Log Message:
-----------
Update my email address
Modified Paths:
--------------
trunk/fork/DESCRIPTION
trunk/fork/man/exit.Rd
trunk/fork/man/fork.Rd
trunk/fork/man/getpid.Rd
trunk/fork/man/kill.Rd
trunk/fork/man/signame.Rd
Modified: trunk/fork/DESCRIPTION
===================================================================
--- trunk/fork/DESCRIPTION 2007-03-24 21:27:27 UTC (rev 1084)
+++ trunk/fork/DESCRIPTION 2007-03-24 21:30:26 UTC (rev 1085)
@@ -2,10 +2,13 @@
Title: R functions for handling multiple processes.
Version: 1.2.0
Date: 2007-03-22
-Author: Gregory R. Warnes <wa...@bs...>
+Author: Gregory R. Warnes <gr...@ra...>. Financial
+ support for some aspects of this package provided by Metrum Research Group,
+ LLC <http://www.metrumrg.com>.
Description: These functions provides simple wrappers around the Unix process
management API calls: fork, signal, wait, waitpid, kill, and _exit. This
enables construction of programs that utilize and mange multiple concurrent
- processes.
-Maintainer: Gregory R. Warnes <wa...@bs...>
+ processes. Commercial support for this package available from
+ Random Technologies, LLC <http://www.random-technologies-llc.com>
+Maintainer: Gregory R. Warnes <gr...@ra...>
License: GPL
Modified: trunk/fork/man/exit.Rd
===================================================================
--- trunk/fork/man/exit.Rd 2007-03-24 21:27:27 UTC (rev 1084)
+++ trunk/fork/man/exit.Rd 2007-03-24 21:30:26 UTC (rev 1085)
@@ -25,7 +25,7 @@
argument, so it is usually not necessary to directly call exit().
}
\references{"\_exit" man page}
-\author{ Gregory R. Warnes \email{wa...@bs...}}
+\author{ Gregory R. Warnes \email{gr...@ra...}}
\seealso{\code{\link{fork}}, \code{\link{getpid}}, \code{\link{wait}},
\code{\link{kill}}, \code{\link{killall}} }
\examples{
Modified: trunk/fork/man/fork.Rd
===================================================================
--- trunk/fork/man/fork.Rd 2007-03-24 21:27:27 UTC (rev 1084)
+++ trunk/fork/man/fork.Rd 2007-03-24 21:30:26 UTC (rev 1085)
@@ -88,7 +88,7 @@
function returns 0 to the child process.
}
\references{'fork' man page}
-\author{ Gregory R. Warnes \email{wa...@bs...}}
+\author{ Gregory R. Warnes \email{gr...@ra...}}
\seealso{\code{\link{getpid}}, \code{\link{exit}}, \code{\link{wait}},
\code{\link{kill}}, \code{\link{killall}} }
\examples{
Modified: trunk/fork/man/getpid.Rd
===================================================================
--- trunk/fork/man/getpid.Rd 2007-03-24 21:27:27 UTC (rev 1084)
+++ trunk/fork/man/getpid.Rd 2007-03-24 21:30:26 UTC (rev 1085)
@@ -15,7 +15,7 @@
Integer process id.
}
\references{Unix "getpid" man page}
-\author{ Gregory R. Warnes \email{wa...@bs...}}
+\author{ Gregory R. Warnes \email{gr...@ra...}}
\seealso{\code{\link{fork}}, \code{\link{exit}}, \code{\link{wait}},
\code{\link{kill}}, \code{\link{killall}} }
\examples{
Modified: trunk/fork/man/kill.Rd
===================================================================
--- trunk/fork/man/kill.Rd 2007-03-24 21:27:27 UTC (rev 1084)
+++ trunk/fork/man/kill.Rd 2007-03-24 21:30:26 UTC (rev 1085)
@@ -28,7 +28,7 @@
\code{killall} does not return a value.
}
\references{"kill" and "waitpid" man pages}
-\author{ Gregory R. Warnes \email{wa...@bs...}}
+\author{ Gregory R. Warnes \email{gr...@ra...}}
\seealso{\code{\link{getpid}}, \code{\link{exit}}, \code{\link{wait}},
\code{\link{kill}}, \code{\link{killall}} }
\examples{
Modified: trunk/fork/man/signame.Rd
===================================================================
--- trunk/fork/man/signame.Rd 2007-03-24 21:27:27 UTC (rev 1084)
+++ trunk/fork/man/signame.Rd 2007-03-24 21:30:26 UTC (rev 1085)
@@ -29,7 +29,7 @@
\item{desc}{Description}
}
\references{Unix "signal" man page.}
-\author{ Gregory R. Warnes \email{wa...@bs...}}
+\author{ Gregory R. Warnes \email{gr...@ra...}}
\seealso{\code{\link{getpid}}, \code{\link{exit}}, \code{\link{wait}},
\code{\link{kill}}, \code{\link{killall}} }
\examples{
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|
|
From: <wa...@us...> - 2007-03-24 21:28:24
|
Revision: 1084
http://svn.sourceforge.net/r-gregmisc/?rev=1084&view=rev
Author: warnes
Date: 2007-03-24 14:27:27 -0700 (Sat, 24 Mar 2007)
Log Message:
-----------
Add note of financial support from Metrum
Modified Paths:
--------------
trunk/fork/man/handleSIGCLD.Rd
trunk/fork/man/signal.Rd
Modified: trunk/fork/man/handleSIGCLD.Rd
===================================================================
--- trunk/fork/man/handleSIGCLD.Rd 2007-03-23 22:53:00 UTC (rev 1083)
+++ trunk/fork/man/handleSIGCLD.Rd 2007-03-24 21:27:27 UTC (rev 1084)
@@ -30,7 +30,10 @@
}
\references{W.R. Stevens and S.A. Rago, Advanced Programming in the UNIX
environment, 2nd ed. (c) 2005, Pearson Education, pp 308-310.}
-\author{Gregory R. Warnes \email{gre...@ro...} }
+\author{Gregory R. Warnes \email{gr...@ra...},
+ with financial support from Metrum Research Group, LLC
+ \url{http://www.metrumrg.com}.
+}
\seealso{ \code{\link{fork}}, \code{\link{wait}}, \code{\link{signal}} }
\examples{
Modified: trunk/fork/man/signal.Rd
===================================================================
--- trunk/fork/man/signal.Rd 2007-03-23 22:53:00 UTC (rev 1083)
+++ trunk/fork/man/signal.Rd 2007-03-24 21:27:27 UTC (rev 1084)
@@ -22,7 +22,10 @@
Nothing of interest.
}
\references{ See the unix man page for "signal" for more information}
-\author{Gregory R. Warnes \email{gre...@ro...} }
+\author{Gregory R. Warnes \email{gr...@ra...},
+ with financial support from Metrum Research Group, LLC
+ \url{http://www.metrumrg.com}.
+}
\note{
Be very careful with this function. It can be used to totally
confuse the R process.
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|
|
From: <wa...@us...> - 2007-03-23 22:53:06
|
Revision: 1083
http://svn.sourceforge.net/r-gregmisc/?rev=1083&view=rev
Author: warnes
Date: 2007-03-23 15:53:00 -0700 (Fri, 23 Mar 2007)
Log Message:
-----------
Allow permutations for r>n provided repeats.allowed=TRUE
Modified Paths:
--------------
trunk/gtools/R/combinations.R
Modified: trunk/gtools/R/combinations.R
===================================================================
--- trunk/gtools/R/combinations.R 2007-03-22 17:12:16 UTC (rev 1082)
+++ trunk/gtools/R/combinations.R 2007-03-23 22:53:00 UTC (rev 1083)
@@ -62,8 +62,8 @@
|| r < 1 || (r %% 1) != 0) stop("bad value of r")
if(!is.atomic(v) || length(v) < n)
stop("v is either non-atomic or too short")
- if( (r > n) ) #& repeats.allowed==FALSE)
- stop("r > n") # and repeats.allowed=FALSE")
+ if( (r > n) & repeats.allowed==FALSE)
+ stop("r > n and repeats.allowed=FALSE")
if(set) {
v <- unique(sort(v))
if (length(v) < n) stop("too few different elements")
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|
From: <wa...@us...> - 2007-03-22 17:12:21
|
Revision: 1082
http://svn.sourceforge.net/r-gregmisc/?rev=1082&view=rev
Author: warnes
Date: 2007-03-22 10:12:16 -0700 (Thu, 22 Mar 2007)
Log Message:
-----------
Add NEWS file
Added Paths:
-----------
trunk/fork/NEWS
Added: trunk/fork/NEWS
===================================================================
--- trunk/fork/NEWS (rev 0)
+++ trunk/fork/NEWS 2007-03-22 17:12:16 UTC (rev 1082)
@@ -0,0 +1,12 @@
+
+Version: 1.2.0 - 2007-03-22
+===========================
+
+ - Added new function handleSIGCLD/restoreSIGCLD for setting
+ up/removing a SIGCLD handler so that fork'ed processes can safely be
+ ignored without becoming zombies. See ?handleSIGCLD for details.
+
+ - Added regression tests for SysV and BSD style signal handling that
+ checks for zombie process creation & tests that signal("SIGCHLD","ignore")
+ and/or handleSIGCLD() prevents zombie process creation.
+
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|
|
From: <wa...@us...> - 2007-03-22 17:12:07
|
Revision: 1081
http://svn.sourceforge.net/r-gregmisc/?rev=1081&view=rev
Author: warnes
Date: 2007-03-22 10:12:02 -0700 (Thu, 22 Mar 2007)
Log Message:
-----------
Add date to DESCRIPTION file
Modified Paths:
--------------
trunk/fork/DESCRIPTION
Modified: trunk/fork/DESCRIPTION
===================================================================
--- trunk/fork/DESCRIPTION 2007-03-14 17:21:41 UTC (rev 1080)
+++ trunk/fork/DESCRIPTION 2007-03-22 17:12:02 UTC (rev 1081)
@@ -1,6 +1,7 @@
Package: fork
Title: R functions for handling multiple processes.
Version: 1.2.0
+Date: 2007-03-22
Author: Gregory R. Warnes <wa...@bs...>
Description: These functions provides simple wrappers around the Unix process
management API calls: fork, signal, wait, waitpid, kill, and _exit. This
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|
From: <wa...@us...> - 2007-03-14 17:21:43
|
Revision: 1080
http://svn.sourceforge.net/r-gregmisc/?rev=1080&view=rev
Author: warnes
Date: 2007-03-14 10:21:41 -0700 (Wed, 14 Mar 2007)
Log Message:
-----------
Add Barrets LOH data set
Added Paths:
-----------
trunk/RMCMC/data/
trunk/RMCMC/data/BarrettsLOH.txt
trunk/RMCMC/data/loh.R
Added: trunk/RMCMC/data/BarrettsLOH.txt
===================================================================
--- trunk/RMCMC/data/BarrettsLOH.txt (rev 0)
+++ trunk/RMCMC/data/BarrettsLOH.txt 2007-03-14 17:21:41 UTC (rev 1080)
@@ -0,0 +1,41 @@
+ loh n
+1p 7 17
+1q 3 15
+2p 4 17
+2q 3 18
+3p 5 15
+3q 4 15
+4p 5 15
+4q 3 19
+5p 6 16
+5q 12 15
+6p 5 18
+6q 3 19
+7p 1 18
+7q 3 19
+8p 5 19
+8q 3 21
+9p 11 17
+9q 2 16
+10p 2 12
+10q 2 17
+11p 3 18
+11q 5 18
+12p 3 19
+12q 4 19
+13q 6 14
+14q 3 12
+15q 1 16
+16p 4 19
+16q 5 16
+17p 19 19
+17q 5 21
+18p 5 15
+18q 6 13
+19p 5 20
+19q 6 16
+20p 2 17
+20q 0 8
+21p 0 7
+21q 6 18
+22q 4 15
Property changes on: trunk/RMCMC/data/BarrettsLOH.txt
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/RMCMC/data/loh.R
===================================================================
--- trunk/RMCMC/data/loh.R (rev 0)
+++ trunk/RMCMC/data/loh.R 2007-03-14 17:21:41 UTC (rev 1080)
@@ -0,0 +1 @@
+loh <- read.table("BarrettsLOH.txt")
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|
From: <wa...@us...> - 2007-03-09 22:35:14
|
Revision: 1079
http://svn.sourceforge.net/r-gregmisc/?rev=1079&view=rev
Author: warnes
Date: 2007-03-09 14:35:13 -0800 (Fri, 09 Mar 2007)
Log Message:
-----------
Remove stray character
Modified Paths:
--------------
trunk/gmodels/R/ci.R
Modified: trunk/gmodels/R/ci.R
===================================================================
--- trunk/gmodels/R/ci.R 2007-03-09 20:10:58 UTC (rev 1078)
+++ trunk/gmodels/R/ci.R 2007-03-09 22:35:13 UTC (rev 1079)
@@ -49,7 +49,7 @@
"Std. Error"= coef(x)[,2],
"p-value" = coef(x)[,4])
- reqtval
+ retval
}
ci.lme <- function(x,confidence=0.95,alpha=1-confidence,...)
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From: <wa...@us...> - 2007-03-09 20:11:30
|
Revision: 1078
http://svn.sourceforge.net/r-gregmisc/?rev=1078&view=rev
Author: warnes
Date: 2007-03-09 12:10:58 -0800 (Fri, 09 Mar 2007)
Log Message:
-----------
Update NEWS file.
Modified Paths:
--------------
trunk/gmodels/NEWS
Modified: trunk/gmodels/NEWS
===================================================================
--- trunk/gmodels/NEWS 2007-03-09 20:07:20 UTC (rev 1077)
+++ trunk/gmodels/NEWS 2007-03-09 20:10:58 UTC (rev 1078)
@@ -1,3 +1,14 @@
+Version 2.13.2
+--------------
+
+Bug Fixes:
+
+- Lower and upper end of confidence interval for lmer objects were
+ reversed in est.lmer().
+
+- Correct Greg's email address in two help files.
+
+
Version 2.13.1
--------------
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|
|
From: <wa...@us...> - 2007-03-09 20:07:43
|
Revision: 1077
http://svn.sourceforge.net/r-gregmisc/?rev=1077&view=rev
Author: warnes
Date: 2007-03-09 12:07:20 -0800 (Fri, 09 Mar 2007)
Log Message:
-----------
Update version number
Modified Paths:
--------------
trunk/gmodels/DESCRIPTION
Modified: trunk/gmodels/DESCRIPTION
===================================================================
--- trunk/gmodels/DESCRIPTION 2007-03-09 20:06:36 UTC (rev 1076)
+++ trunk/gmodels/DESCRIPTION 2007-03-09 20:07:20 UTC (rev 1077)
@@ -1,5 +1,5 @@
Package: gmodels
-Version: 2.13.1
+Version: 2.13.2
Title: Various R programming tools for model fitting
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker, Thomas Lumley, and Randall C Johnson.
@@ -16,3 +16,4 @@
URL: http://cran.r-project.org/src/contrib/PACKAGES.html
http://www.sf.net/projects/r-gregmisc
Packaged: Mon Jun 5 16:19:14 2006; root
+Date: 2007-03-09
\ No newline at end of file
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|
|
From: <wa...@us...> - 2007-03-09 20:07:05
|
Revision: 1076
http://svn.sourceforge.net/r-gregmisc/?rev=1076&view=rev
Author: warnes
Date: 2007-03-09 12:06:36 -0800 (Fri, 09 Mar 2007)
Log Message:
-----------
Minor code formatting changes
Modified Paths:
--------------
trunk/gmodels/R/ci.R
Modified: trunk/gmodels/R/ci.R
===================================================================
--- trunk/gmodels/R/ci.R 2007-03-09 20:06:05 UTC (rev 1075)
+++ trunk/gmodels/R/ci.R 2007-03-09 20:06:36 UTC (rev 1076)
@@ -3,21 +3,22 @@
ci <- function(x, confidence=0.95,alpha=1-confidence,...)
UseMethod("ci")
-ci.default <- function(x, confidence=0.95,alpha=1-confidence,na.rm=FALSE,...) {
- est <- mean(x, na.rm=na.rm)
- stderr <- sd(x, na.rm=na.rm)/sqrt(nobs(x));
- ci.low <- est + qt(alpha/2, nobs(x)-1) * stderr
- ci.high <- est - qt(alpha/2, nobs(x)-1) * stderr
- retval <- c(
- Estimate=est,
- "CI lower"=ci.low,
- "CI upper"=ci.high,
- "Std. Error"=stderr
- )
+ci.default <- function(x, confidence=0.95,alpha=1-confidence,na.rm=FALSE,...)
+ {
+ est <- mean(x, na.rm=na.rm)
+ stderr <- sd(x, na.rm=na.rm)/sqrt(nobs(x));
+ ci.low <- est + qt(alpha/2, nobs(x)-1) * stderr
+ ci.high <- est - qt(alpha/2, nobs(x)-1) * stderr
+ retval <- c(
+ Estimate=est,
+ "CI lower"=ci.low,
+ "CI upper"=ci.high,
+ "Std. Error"=stderr
+ )
+
+ retval
+ }
- retval
-}
-
ci.binom <- function(x, confidence=0.95,alpha=1-confidence,...)
{
if( !(all(x) %in% c(0,1)) ) stop("Binomial values must be either 0 or 1.")
@@ -37,48 +38,55 @@
}
ci.lm <- function(x,confidence=0.95,alpha=1-confidence,...)
-{
- x <- summary(x)
- est <- coef(x)[,1] ;
- ci.low <- est + qt(alpha/2, x$df[2]) * coef(x)[,2] ;
- ci.high <- est - qt(alpha/2, x$df[2]) * coef(x)[,2] ;
- retval <- cbind(Estimate=est,
- "CI lower"=ci.low,
- "CI upper"=ci.high,
- "Std. Error"= coef(x)[,2],
- "p-value" = coef(x)[,4])
+ {
+ x <- summary(x)
+ est <- coef(x)[,1] ;
+ ci.low <- est + qt(alpha/2, x$df[2]) * coef(x)[,2] ;
+ ci.high <- est - qt(alpha/2, x$df[2]) * coef(x)[,2] ;
+ retval <- cbind(Estimate=est,
+ "CI lower"=ci.low,
+ "CI upper"=ci.high,
+ "Std. Error"= coef(x)[,2],
+ "p-value" = coef(x)[,4])
+
+ reqtval
+ }
- retval
-}
-
ci.lme <- function(x,confidence=0.95,alpha=1-confidence,...)
{
- x <- summary(x)
- est <- x$tTable[,"Value"] ;
- ci.low <- est + qt(alpha/2, x$tTable[,"DF"]) * x$tTable[,"Std.Error"] ;
- ci.high <- est - qt(alpha/2, x$tTable[,"DF"]) * x$tTable[,"Std.Error"] ;
- retval <- cbind(Estimate=est,
- "CI lower"=ci.low,
- "CI upper"=ci.high,
- "Std. Error"= x$tTable[,"Std.Error"],
- "DF" = x$tTable[,"DF"],
- "p-value" = x$tTable[,"p-value"])
- rownames(retval) <- rownames(x$tTable)
- retval
-}
+ x <- summary(x)
+ est <- x$tTable[,"Value"] ;
+ ci.low <- est + qt(alpha/2, x$tTable[,"DF"]) * x$tTable[,"Std.Error"] ;
+ ci.high <- est - qt(alpha/2, x$tTable[,"DF"]) * x$tTable[,"Std.Error"] ;
+ retval <- cbind(Estimate=est,
+ "CI lower"=ci.low,
+ "CI upper"=ci.high,
+ "Std. Error"= x$tTable[,"Std.Error"],
+ "DF" = x$tTable[,"DF"],
+ "p-value" = x$tTable[,"p-value"])
+ rownames(retval) <- rownames(x$tTable)
+ retval
+ }
-ci.lmer <- function(x, confidence=0.95, alpha=1-confidence, sim.lmer=TRUE, n.sim=1000, ...) ################### changed this function
+ci.lmer <- function(x,
+ confidence=0.95,
+ alpha=1-confidence,
+ sim.lmer=TRUE,
+ n.sim=1000,
+ ...
+ )
{
if(!(require(coda, quietly=TRUE) & require(Matrix, quietly=TRUE)))
stop("coda and Matrix packages required for ci.lmer")
x.effects <- fixef(x)
n <- length(x.effects)
-
+
retval <- est.lmer(obj = x, cm = diag(n), beta0 = rep(0, n),
conf.int = confidence, show.beta0 = FALSE,
- n.sim = n.sim)[,c("Estimate", "Lower.CI", "Upper.CI", "Std. Error", "p value")]
-
+ n.sim = n.sim)[,c("Estimate", "Lower.CI", "Upper.CI",
+ "Std. Error", "p value")]
+
colnames(retval)[c(2:3, 5)] <- c("CI lower", "CI upper", "p-value")
rownames(retval) <- names(x.effects)
retval
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From: <wa...@us...> - 2007-03-09 20:06:36
|
Revision: 1075
http://svn.sourceforge.net/r-gregmisc/?rev=1075&view=rev
Author: warnes
Date: 2007-03-09 12:06:05 -0800 (Fri, 09 Mar 2007)
Log Message:
-----------
Flip lower and upper interval in ci.lmer(). Add example to man page.
Modified Paths:
--------------
trunk/gmodels/R/est.lmer.R
trunk/gmodels/man/ci.Rd
Modified: trunk/gmodels/R/est.lmer.R
===================================================================
--- trunk/gmodels/R/est.lmer.R 2007-03-09 19:43:05 UTC (rev 1074)
+++ trunk/gmodels/R/est.lmer.R 2007-03-09 20:06:05 UTC (rev 1075)
@@ -24,7 +24,8 @@
est <- drop(cm %*% samp.summ$statistics[1:n,1])
stderr <- sd(samp.cm)
- pval <- sapply(1:length(beta0), function(i){percentile(beta0[i], samp.cm[,i])})
+ pval <- sapply(1:length(beta0),
+ function(i){percentile(beta0[i], samp.cm[,i])})
pval <- ifelse(pval <= .5, 2*pval, 2*(1-pval))
if(is.null(conf.int))
@@ -33,10 +34,15 @@
upper.ci <- NULL
}else{
alpha <- 1-conf.int
- samp.ci <- sapply(1:length(beta0), function(i){quantile(samp.cm[,i], probs=c(alpha/2, 1-alpha/2))})
+ samp.ci <- sapply(1:length(beta0),
+ function(i)
+ {
+ quantile(samp.cm[,i], probs=c(alpha/2, 1-alpha/2))
+ }
+ )
- lower.ci <- samp.ci[2,]
- upper.ci <- samp.ci[1,]
+ lower.ci <- samp.ci[1,]
+ upper.ci <- samp.ci[2,]
}
# return results
Modified: trunk/gmodels/man/ci.Rd
===================================================================
--- trunk/gmodels/man/ci.Rd 2007-03-09 19:43:05 UTC (rev 1074)
+++ trunk/gmodels/man/ci.Rd 2007-03-09 20:06:05 UTC (rev 1075)
@@ -66,5 +66,13 @@
reg <- lm(Area ~ Population, data=as.data.frame(state.x77))
ci(reg)
+\dontrun{
+# lmer example
+library(lme4)
+fm2 <- lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject), sleepstudy)
+ci(fm2)
}
+
+
+}
\keyword{ regression }
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|
|
From: <wa...@us...> - 2007-03-09 19:43:58
|
Revision: 1074
http://svn.sourceforge.net/r-gregmisc/?rev=1074&view=rev
Author: warnes
Date: 2007-03-09 11:43:05 -0800 (Fri, 09 Mar 2007)
Log Message:
-----------
Fix some old email addressses that got missed
Modified Paths:
--------------
trunk/gmodels/man/ci.Rd
trunk/gmodels/man/estimable.Rd
Modified: trunk/gmodels/man/ci.Rd
===================================================================
--- trunk/gmodels/man/ci.Rd 2007-03-09 09:05:00 UTC (rev 1073)
+++ trunk/gmodels/man/ci.Rd 2007-03-09 19:43:05 UTC (rev 1074)
@@ -42,7 +42,7 @@
\code{Estimate}, \code{CI lower}, \code{CI upper}, \code{Std. Error},
\code{DF} (for lme objects only), and \code{p-value}.
}
-\author{ Gregory R. Warnes \email{Gregory\_R\_Warnes\@groton.pfizer.com}
+\author{ Gregory R. Warnes \email{wa...@bs...}
}
\seealso{
\code{\link[stats]{confint}},
Modified: trunk/gmodels/man/estimable.Rd
===================================================================
--- trunk/gmodels/man/estimable.Rd 2007-03-09 09:05:00 UTC (rev 1073)
+++ trunk/gmodels/man/estimable.Rd 2007-03-09 19:43:05 UTC (rev 1074)
@@ -93,7 +93,7 @@
}
\author{
BXC (Bendix Carstensen) \email{bxc\@novonordisk.com},
- Gregory R. Warnes \email{Gregory\_R\_Warnes\@groton.pfizer.com},
+ Gregory R. Warnes \email{wa...@bs...},
S\xF8ren H\xF8jsgaard \email{so...@ag...}, and
Randall C Johnson \email{rjo...@nc...}
}
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|
|
From: <gg...@us...> - 2007-03-09 09:05:02
|
Revision: 1073
http://svn.sourceforge.net/r-gregmisc/?rev=1073&view=rev
Author: ggorjan
Date: 2007-03-09 01:05:00 -0800 (Fri, 09 Mar 2007)
Log Message:
-----------
use of \method in Rd markup - issues a warning with _R_CHECK_RD_STYLE_=TRUE env. variable with R 2.5.0
Modified Paths:
--------------
trunk/gplots/man/ooplot.Rd
Modified: trunk/gplots/man/ooplot.Rd
===================================================================
--- trunk/gplots/man/ooplot.Rd 2007-03-06 23:37:37 UTC (rev 1072)
+++ trunk/gplots/man/ooplot.Rd 2007-03-09 09:05:00 UTC (rev 1073)
@@ -9,7 +9,7 @@
}
\usage{
ooplot(data, ...)
-ooplot.default(data, width=1, space=NULL, names.arg=NULL,
+\method{ooplot}{default}(data, width=1, space=NULL, names.arg=NULL,
legend.text=NULL, horiz=FALSE,
density=NULL, angle=45, kmg="fpnumkMGTP",
kmglim=TRUE,
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From: <wa...@us...> - 2007-03-06 23:37:39
|
Revision: 1072
http://svn.sourceforge.net/r-gregmisc/?rev=1072&view=rev
Author: warnes
Date: 2007-03-06 15:37:37 -0800 (Tue, 06 Mar 2007)
Log Message:
-----------
Update version number and description
Modified Paths:
--------------
trunk/fork/DESCRIPTION
Modified: trunk/fork/DESCRIPTION
===================================================================
--- trunk/fork/DESCRIPTION 2007-03-06 23:29:46 UTC (rev 1071)
+++ trunk/fork/DESCRIPTION 2007-03-06 23:37:37 UTC (rev 1072)
@@ -1,10 +1,10 @@
Package: fork
Title: R functions for handling multiple processes.
-Version: 1.1.1
+Version: 1.2.0
Author: Gregory R. Warnes <wa...@bs...>
Description: These functions provides simple wrappers around the Unix process
- management API calls: fork, wait, waitpid, kill, and _exit. This
- enables construction of programs that utilize multiple concurrent
+ management API calls: fork, signal, wait, waitpid, kill, and _exit. This
+ enables construction of programs that utilize and mange multiple concurrent
processes.
Maintainer: Gregory R. Warnes <wa...@bs...>
License: GPL
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|
|
From: <wa...@us...> - 2007-03-06 23:29:47
|
Revision: 1071
http://svn.sourceforge.net/r-gregmisc/?rev=1071&view=rev
Author: warnes
Date: 2007-03-06 15:29:46 -0800 (Tue, 06 Mar 2007)
Log Message:
-----------
Fix syntax error in example due to incomplete code deletion.
Modified Paths:
--------------
trunk/fork/man/handleSIGCLD.Rd
Modified: trunk/fork/man/handleSIGCLD.Rd
===================================================================
--- trunk/fork/man/handleSIGCLD.Rd 2007-03-06 23:29:12 UTC (rev 1070)
+++ trunk/fork/man/handleSIGCLD.Rd 2007-03-06 23:29:46 UTC (rev 1071)
@@ -46,8 +46,6 @@
## don't do anything useful
exit()
}
- else
- pidList[i] <- pid
}
## remove the dummy signal handler
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|
|
From: <wa...@us...> - 2007-03-06 23:29:17
|
Revision: 1070
http://svn.sourceforge.net/r-gregmisc/?rev=1070&view=rev
Author: warnes
Date: 2007-03-06 15:29:12 -0800 (Tue, 06 Mar 2007)
Log Message:
-----------
Add 'PACKAGE=' argument to '.C' calls to make 'R CMD check' happy
Modified Paths:
--------------
trunk/fork/R/handleSIGCLD.R
trunk/fork/R/restoreSIGCLD.R
Modified: trunk/fork/R/handleSIGCLD.R
===================================================================
--- trunk/fork/R/handleSIGCLD.R 2007-03-06 23:28:27 UTC (rev 1069)
+++ trunk/fork/R/handleSIGCLD.R 2007-03-06 23:29:12 UTC (rev 1070)
@@ -5,6 +5,6 @@
handleSIGCLD <- function()
{
- .C("R_install_sigcld_handler")
+ .C("R_install_sigcld_handler", PACKAGE="fork")
invisible(NULL)
}
Modified: trunk/fork/R/restoreSIGCLD.R
===================================================================
--- trunk/fork/R/restoreSIGCLD.R 2007-03-06 23:28:27 UTC (rev 1069)
+++ trunk/fork/R/restoreSIGCLD.R 2007-03-06 23:29:12 UTC (rev 1070)
@@ -1,6 +1,6 @@
# Restore the original SIGCLD hander. This reverses the action of 'handleSIGCLD'.
restoreSIGCLD <- function()
{
- .C("R_restore_sigcld_handler")
+ .C("R_restore_sigcld_handler", PACKAGE="fork")
invisible(NULL)
}
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|
|
From: <wa...@us...> - 2007-03-06 23:28:29
|
Revision: 1069
http://svn.sourceforge.net/r-gregmisc/?rev=1069&view=rev
Author: warnes
Date: 2007-03-06 15:28:27 -0800 (Tue, 06 Mar 2007)
Log Message:
-----------
Improve regression tests, add saved .Rout files for doing regression testing.
Modified Paths:
--------------
trunk/fork/tests/checkZombies.R
trunk/fork/tests/test_many_fork_BSD.R
trunk/fork/tests/test_many_fork_SysV.R
trunk/fork/tests/test_many_fork_broken.R
Added Paths:
-----------
trunk/fork/tests/test_many_fork_BSD.Rout.save
trunk/fork/tests/test_many_fork_SysV.Rout.save
trunk/fork/tests/test_many_fork_broken.Rout.save
Modified: trunk/fork/tests/checkZombies.R
===================================================================
--- trunk/fork/tests/checkZombies.R 2007-03-06 23:17:34 UTC (rev 1068)
+++ trunk/fork/tests/checkZombies.R 2007-03-06 23:28:27 UTC (rev 1069)
@@ -32,6 +32,7 @@
if(length(zombies)>50)
{
retval = TRUE
+ warning(length(zombies), " Zombie Processes Present!\n")
cat(length(zombies), " Zombie Processes Present!\n")
}
else
Modified: trunk/fork/tests/test_many_fork_BSD.R
===================================================================
--- trunk/fork/tests/test_many_fork_BSD.R 2007-03-06 23:17:34 UTC (rev 1068)
+++ trunk/fork/tests/test_many_fork_BSD.R 2007-03-06 23:28:27 UTC (rev 1069)
@@ -12,11 +12,5 @@
nZombies <- checkZombies()
-if(nZombies) {
- stop("Zombie processes created")
-} else {
- cat("Success!\n")
-}
-
# remove signal handler
restoreSIGCLD()
Added: trunk/fork/tests/test_many_fork_BSD.Rout.save
===================================================================
--- trunk/fork/tests/test_many_fork_BSD.Rout.save (rev 0)
+++ trunk/fork/tests/test_many_fork_BSD.Rout.save 2007-03-06 23:28:27 UTC (rev 1069)
@@ -0,0 +1,40 @@
+
+R version 2.4.1 (2006-12-18)
+Copyright (C) 2006 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ## This script starts child processes, and sets up a 'dummy' SIGCLD
+> ## hander to handle child process notifications. Hopefully on both BSD
+> ## and Sys5 derived systems, this should cause child processes to exit
+> ## and die cleanly, IE without becoming zombies.
+>
+> library(fork)
+>
+> ## start signal handler
+> handleSIGCLD()
+Installing SIGCHLD signal handler...Done.
+>
+> source("checkZombies.R")
+>
+> nZombies <- checkZombies()
+Generating 100 child processes (to become zombies)...
+Give them 10 seconds to die and exit..
+Check the process table to see if there are any zombies...
+Done. No Zombies present.
+>
+> # remove signal handler
+> restoreSIGCLD()
+Restoring original SIGCHLD signal handler...Done.
+>
Modified: trunk/fork/tests/test_many_fork_SysV.R
===================================================================
--- trunk/fork/tests/test_many_fork_SysV.R 2007-03-06 23:17:34 UTC (rev 1068)
+++ trunk/fork/tests/test_many_fork_SysV.R 2007-03-06 23:28:27 UTC (rev 1069)
@@ -12,8 +12,3 @@
nZombies <- checkZombies()
-if(nZombies)
- stop("Zombie processes created")
-else
- cat("Success!\n")
-
Added: trunk/fork/tests/test_many_fork_SysV.Rout.save
===================================================================
--- trunk/fork/tests/test_many_fork_SysV.Rout.save (rev 0)
+++ trunk/fork/tests/test_many_fork_SysV.Rout.save 2007-03-06 23:28:27 UTC (rev 1069)
@@ -0,0 +1,36 @@
+
+R version 2.4.1 (2006-12-18)
+Copyright (C) 2006 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ## This script starts child processes, and sets the SIGCHLD hander to
+> ## "ignore". On Sys5 derived systems, this should cause child
+> ## processes to exit and die cleanly without the parent process
+> ## querying the exit state. IE, no zombie processes will be created.
+>
+> library(fork)
+>
+> ## ignore sigchld signals so child processes will die cleanly
+> signal("SIGCHLD","ignore")
+>
+> source("checkZombies.R")
+>
+> nZombies <- checkZombies()
+Generating 100 child processes (to become zombies)...
+Give them 10 seconds to die and exit..
+Check the process table to see if there are any zombies...
+Done. No Zombies present.
+>
+>
Modified: trunk/fork/tests/test_many_fork_broken.R
===================================================================
--- trunk/fork/tests/test_many_fork_broken.R 2007-03-06 23:17:34 UTC (rev 1068)
+++ trunk/fork/tests/test_many_fork_broken.R 2007-03-06 23:28:27 UTC (rev 1069)
@@ -8,7 +8,3 @@
nZombies <- checkZombies()
-if(nZombies)
- stop("Zombie processes created")
-else
- cat("Success!\n")
Added: trunk/fork/tests/test_many_fork_broken.Rout.save
===================================================================
--- trunk/fork/tests/test_many_fork_broken.Rout.save (rev 0)
+++ trunk/fork/tests/test_many_fork_broken.Rout.save 2007-03-06 23:28:27 UTC (rev 1069)
@@ -0,0 +1,35 @@
+
+R version 2.4.1 (2006-12-18)
+Copyright (C) 2006 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ## This script starts child processes, but doesn't do anything about
+> ## collecting or ignoring child process return status. Consequently, it should
+> ## generate zombie child processes.
+>
+> library(fork)
+>
+> source("checkZombies.R")
+>
+> nZombies <- checkZombies()
+Generating 100 child processes (to become zombies)...
+Give them 10 seconds to die and exit..
+Check the process table to see if there are any zombies...
+100 Zombie Processes Present!
+Warning message:
+100 Zombie Processes Present!
+ in: checkZombies()
+>
+>
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|
From: <wa...@us...> - 2007-03-06 23:17:35
|
Revision: 1068
http://svn.sourceforge.net/r-gregmisc/?rev=1068&view=rev
Author: warnes
Date: 2007-03-06 15:17:34 -0800 (Tue, 06 Mar 2007)
Log Message:
-----------
Add a helpful comment
Modified Paths:
--------------
trunk/fork/src/sigchld_handler.c
Modified: trunk/fork/src/sigchld_handler.c
===================================================================
--- trunk/fork/src/sigchld_handler.c 2007-03-06 23:15:31 UTC (rev 1067)
+++ trunk/fork/src/sigchld_handler.c 2007-03-06 23:17:34 UTC (rev 1068)
@@ -20,6 +20,7 @@
void sigchld_handler(int dummy)
{
int st;
+ // wait3 returns 0 when no signal is present to retrieve
while (wait3(&st, WNOHANG, NULL) > 0);
}
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|
From: <wa...@us...> - 2007-03-06 23:15:33
|
Revision: 1067
http://svn.sourceforge.net/r-gregmisc/?rev=1067&view=rev
Author: warnes
Date: 2007-03-06 15:15:31 -0800 (Tue, 06 Mar 2007)
Log Message:
-----------
Create manual pages for handleSIGCLD() and restoreSIGCLD(), as well as appropriately modifying the pages for fork() and signal()
Modified Paths:
--------------
trunk/fork/man/fork.Rd
trunk/fork/man/signal.Rd
Added Paths:
-----------
trunk/fork/man/handleSIGCLD.Rd
Modified: trunk/fork/man/fork.Rd
===================================================================
--- trunk/fork/man/fork.Rd 2007-03-06 22:47:29 UTC (rev 1066)
+++ trunk/fork/man/fork.Rd 2007-03-06 23:15:31 UTC (rev 1067)
@@ -162,12 +162,11 @@
close(con2)
}
-\dontrun{
-# Important: if we aren't going to explicitly wait() for the child
-# process to exit, we need to tell the OS that we are ignoring child
-# process signals so it will let us die cleanly.
-signal("SIGCHLD","ignore")
-}
+## Important: if we aren't going to explicitly wait() for the child
+## process to exit, we need to set up a dummy signal handler to collect
+## (and then throw away) the exit status so that child processes will not
+## become zombies when they exit
+handleSIGCLD()
# fork off the process
pid <- fork(recieve)
@@ -175,6 +174,9 @@
# start sending...
send()
}
+
+## restore SIGCLD signal handling to the previous state
+restoreSIGCLD()
}
\keyword{programming}
Added: trunk/fork/man/handleSIGCLD.Rd
===================================================================
--- trunk/fork/man/handleSIGCLD.Rd (rev 0)
+++ trunk/fork/man/handleSIGCLD.Rd 2007-03-06 23:15:31 UTC (rev 1067)
@@ -0,0 +1,57 @@
+\name{handleSIGCLD}
+\alias{handleSIGCLD}
+\alias{restoreSIGCLD}
+\title{Establish or remove a dummy handler for SIGCLD signals}
+\description{
+ Establish \code{handleSIGCLD} or remove \code{ignoreSIGCLD} a dummy
+ handler for SIGCLD signals
+}
+\usage{
+handleSIGCLD()
+restoreSIGCLD()
+}
+\details{
+ The \code{handleSIGCLD} function establishes a 'dummy' handler for
+ SIGCLD signals. It accepts signals from exiting child processes
+ created by \code{fork} and ignores them. This prevents child
+ processes from becoming 'zombies', which would occurs when the parent
+ process does not handle this signal.
+
+ The \code{restoreSIGCLD} function restores the previous (lack of)
+ signal handler.
+}
+\value{
+ No return value.
+}
+\note{
+ The SIGCLD handling mechanism implemented by \code{handleSIGCLD}
+ should prevent zombie process creation on systems derived from both
+ SYSV and BSD UNIX, including Linux, Mac OSX, NetBSD, and Solaris.
+ }
+\references{W.R. Stevens and S.A. Rago, Advanced Programming in the UNIX
+ environment, 2nd ed. (c) 2005, Pearson Education, pp 308-310.}
+\author{Gregory R. Warnes \email{gre...@ro...} }
+\seealso{ \code{\link{fork}}, \code{\link{wait}}, \code{\link{signal}} }
+\examples{
+
+## set up the dummy signal hander
+handleSIGCLD()
+
+## Generate 100 child processes
+for(i in 1:100)
+ {
+ pid = fork(slave=NULL)
+ if(pid==0)
+ {
+ ## don't do anything useful
+ exit()
+ }
+ else
+ pidList[i] <- pid
+ }
+
+## remove the dummy signal handler
+restoreSIGCLD()
+}
+\keyword{programming}
+
Modified: trunk/fork/man/signal.Rd
===================================================================
--- trunk/fork/man/signal.Rd 2007-03-06 22:47:29 UTC (rev 1066)
+++ trunk/fork/man/signal.Rd 2007-03-06 23:15:31 UTC (rev 1067)
@@ -26,11 +26,23 @@
\note{
Be very careful with this function. It can be used to totally
confuse the R process.
+
+ On sytems derived from BSD UNIX, setting the SIGCHLD signal to
+ 'ignore' will allow child processes to exit cleanly without becoming
+ zombies. This also prevents the parent process from checking the exit
+ status of children, since this information is no longer available once
+ child process disappears. On systems derived from SysV UNIX, setting
+ SIGCHLD to 'ignore' has no effect on the status of child processes
+ that exit, and they will still become zombies unless the exit status
+ is checked. See the \code{handleSIGCLD} function for a mechanism that
+ will prevent child processes from becoming zombies on both SYSV and
+ (hopefully) BSD-derived systems.
}
-\seealso{ \code{\link{sigval}}, \code{\link{fork}} }
+\seealso{ \code{\link{sigval}}, \code{\link{fork}}, \code{\link{handleSIGCLD}} }
\examples{
\dontrun{
-# Ignore child termination signals for forked processes
+## Ignore child termination signals for forked processes NOTE: This
+## mechanism only works on UNIX SYSV-derived systems. See Note above.
signal("SIGCHLD","ignore")
# Fork off a child process to say "Hi!".
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|
|
From: <wa...@us...> - 2007-03-06 22:48:42
|
Revision: 1066
http://svn.sourceforge.net/r-gregmisc/?rev=1066&view=rev
Author: warnes
Date: 2007-03-06 14:47:29 -0800 (Tue, 06 Mar 2007)
Log Message:
-----------
Create SysV and BSD tests for code to prevent zombie process creation, update code that intentionally creates zombies. Move sub-process creation and zombie test code to a function for use by all three test files
Added Paths:
-----------
trunk/fork/tests/test_many_fork_BSD.R
Added: trunk/fork/tests/test_many_fork_BSD.R
===================================================================
--- trunk/fork/tests/test_many_fork_BSD.R (rev 0)
+++ trunk/fork/tests/test_many_fork_BSD.R 2007-03-06 22:47:29 UTC (rev 1066)
@@ -0,0 +1,22 @@
+## This script starts child processes, and sets up a 'dummy' SIGCLD
+## hander to handle child process notifications. Hopefully on both BSD
+## and Sys5 derived systems, this should cause child processes to exit
+## and die cleanly, IE without becoming zombies.
+
+library(fork)
+
+## start signal handler
+handleSIGCLD()
+
+source("checkZombies.R")
+
+nZombies <- checkZombies()
+
+if(nZombies) {
+ stop("Zombie processes created")
+} else {
+ cat("Success!\n")
+}
+
+# remove signal handler
+restoreSIGCLD()
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|
From: <wa...@us...> - 2007-03-06 22:48:36
|
Revision: 1065
http://svn.sourceforge.net/r-gregmisc/?rev=1065&view=rev
Author: warnes
Date: 2007-03-06 14:47:07 -0800 (Tue, 06 Mar 2007)
Log Message:
-----------
Create SysV and BSD tests for code to prevent zombie process creation, update code that intentionally creates zombies. Move sub-process creation and zombie test code to a function for use by all three test files
Modified Paths:
--------------
trunk/fork/tests/test_many_fork_broken.R
Added Paths:
-----------
trunk/fork/tests/checkZombies.R
trunk/fork/tests/test_many_fork_SysV.R
Removed Paths:
-------------
trunk/fork/tests/test_many_fork.R
Added: trunk/fork/tests/checkZombies.R
===================================================================
--- trunk/fork/tests/checkZombies.R (rev 0)
+++ trunk/fork/tests/checkZombies.R 2007-03-06 22:47:07 UTC (rev 1065)
@@ -0,0 +1,48 @@
+checkZombies <- function()
+ {
+ cat("Generating 100 child processes (to become zombies)...\n")
+ pidList <- integer(100)
+ for(i in 1:100)
+ {
+ pid = fork(slave=NULL)
+ if(pid==0)
+ {
+ ##cat("Hi from child process",getpid(),".\n");
+ ##Sys.sleep(10);
+ ##cat("Bye from child process",getpid(),".\n");
+ exit()
+ }
+ else
+ pidList[i] <- pid
+ }
+
+ cat("Give them 10 seconds to die and exit..\n")
+ Sys.sleep(10)
+
+ cat("Check the process table to see if there are any zombies...\n")
+ if(TRUE) # BSD-style 'ps' command (Linux, Mac OSX, NetBSD)
+ {
+ statusList = system("ps -o stat", intern=TRUE)[-1]
+ } else # SysV-style 'ps' command (Solaris)
+ {
+ statusList = system("ps -o s", intern=TRUE)[-1]
+ }
+
+ zombies = grep("[Zz]", statusList, value=TRUE)
+ if(length(zombies)>50)
+ {
+ retval = TRUE
+ cat(length(zombies), " Zombie Processes Present!\n")
+ }
+ else
+ {
+ retval = FALSE
+ cat("Done. No Zombies present.\n")
+ }
+
+
+ for(i in 1:100)
+ wait(pidList[i], nohang=FALSE)
+
+ return(retval)
+}
Deleted: trunk/fork/tests/test_many_fork.R
===================================================================
--- trunk/fork/tests/test_many_fork.R 2007-03-06 22:44:25 UTC (rev 1064)
+++ trunk/fork/tests/test_many_fork.R 2007-03-06 22:47:07 UTC (rev 1065)
@@ -1,27 +0,0 @@
-library(fork)
-
-# ignore sigchld signals so child processes will die cleanly
-#signal("SIGCHLD","ignore")
-
-# start signal handler
-.C("R_install_sigcld_handler")
-
-cat("Hi from the parent process\n");
-
-for(i in 1:100)
- {
- pid = fork(slave=NULL)
- if(pid==0)
- {
- cat("Hi from child process",getpid(),".\n");
- Sys.sleep(10);
- cat("Bye from child process",getpid(),".\n");
- exit()
- }
- }
-
-Sys.sleep(300)
-cat("Bye from the parent process",pid,".\n");
-
-# remove signal handler
-.C("R_restore_sigcld_handler")
Added: trunk/fork/tests/test_many_fork_SysV.R
===================================================================
--- trunk/fork/tests/test_many_fork_SysV.R (rev 0)
+++ trunk/fork/tests/test_many_fork_SysV.R 2007-03-06 22:47:07 UTC (rev 1065)
@@ -0,0 +1,19 @@
+## This script starts child processes, and sets the SIGCHLD hander to
+## "ignore". On Sys5 derived systems, this should cause child
+## processes to exit and die cleanly without the parent process
+## querying the exit state. IE, no zombie processes will be created.
+
+library(fork)
+
+## ignore sigchld signals so child processes will die cleanly
+signal("SIGCHLD","ignore")
+
+source("checkZombies.R")
+
+nZombies <- checkZombies()
+
+if(nZombies)
+ stop("Zombie processes created")
+else
+ cat("Success!\n")
+
Modified: trunk/fork/tests/test_many_fork_broken.R
===================================================================
--- trunk/fork/tests/test_many_fork_broken.R 2007-03-06 22:44:25 UTC (rev 1064)
+++ trunk/fork/tests/test_many_fork_broken.R 2007-03-06 22:47:07 UTC (rev 1065)
@@ -4,33 +4,11 @@
library(fork)
-cat("Generating 100 child processes (to become zombies)...\n")
-for(i in 1:100)
- {
- pid = fork(slave=NULL)
- if(pid==0)
- {
- #cat("Hi from child process",getpid(),".\n");
- #Sys.sleep(10);
- #cat("Bye from child process",getpid(),".\n");
- exit()
- }
- }
+source("checkZombies.R")
-cat("Give them 10 seconds to die and exit..\n")
-Sys.sleep(10)
+nZombies <- checkZombies()
-cat("Check the process table to see if there are any zombies...\n")
-if(TRUE) # BSD-style PS command (Linux, Mac OSX, NetBSD)
-{
- statusList = system("ps -o stat", intern=TRUE)[-1]
-} else
-{
- statusList = system("ps -o s", intern=TRUE)[-1]
-}
-
-zombies = grep("[Zz]", statusList, value=TRUE)
-if(length(zombies)>50)
- stop(length(zombies), " Zombie Processes Present!")
+if(nZombies)
+ stop("Zombie processes created")
else
- cat("Done. No Zombies present.\n")
+ cat("Success!\n")
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|
|
From: <wa...@us...> - 2007-03-06 22:44:27
|
Revision: 1064
http://svn.sourceforge.net/r-gregmisc/?rev=1064&view=rev
Author: warnes
Date: 2007-03-06 14:44:25 -0800 (Tue, 06 Mar 2007)
Log Message:
-----------
Add wrappers for C functions to control setting/restoring child
process signal handler.
Added Paths:
-----------
trunk/fork/R/handleSIGCLD.R
trunk/fork/R/restoreSIGCLD.R
Added: trunk/fork/R/handleSIGCLD.R
===================================================================
--- trunk/fork/R/handleSIGCLD.R (rev 0)
+++ trunk/fork/R/handleSIGCLD.R 2007-03-06 22:44:25 UTC (rev 1064)
@@ -0,0 +1,10 @@
+# setup a a 'dummy' SIGCLD hander to handle child process
+# notifications. Hopefully on both BSD and Sys5 derived systems, this
+# should cause child processes to exit and die cleanly, IE without
+# becoming zombies.
+
+handleSIGCLD <- function()
+ {
+ .C("R_install_sigcld_handler")
+ invisible(NULL)
+ }
Added: trunk/fork/R/restoreSIGCLD.R
===================================================================
--- trunk/fork/R/restoreSIGCLD.R (rev 0)
+++ trunk/fork/R/restoreSIGCLD.R 2007-03-06 22:44:25 UTC (rev 1064)
@@ -0,0 +1,6 @@
+# Restore the original SIGCLD hander. This reverses the action of 'handleSIGCLD'.
+restoreSIGCLD <- function()
+ {
+ .C("R_restore_sigcld_handler")
+ invisible(NULL)
+ }
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|
|
From: <wa...@us...> - 2007-03-06 22:11:06
|
Revision: 1063
http://svn.sourceforge.net/r-gregmisc/?rev=1063&view=rev
Author: warnes
Date: 2007-03-06 14:10:24 -0800 (Tue, 06 Mar 2007)
Log Message:
-----------
Modify script to check for the presence of zombie processes
Added Paths:
-----------
trunk/fork/tests/test_many_fork_broken.R
Added: trunk/fork/tests/test_many_fork_broken.R
===================================================================
--- trunk/fork/tests/test_many_fork_broken.R (rev 0)
+++ trunk/fork/tests/test_many_fork_broken.R 2007-03-06 22:10:24 UTC (rev 1063)
@@ -0,0 +1,36 @@
+## This script starts child processes, but doesn't do anything about
+## collecting or ignoring child process return status. Consequently, it should
+## generate zombie child processes.
+
+library(fork)
+
+cat("Generating 100 child processes (to become zombies)...\n")
+for(i in 1:100)
+ {
+ pid = fork(slave=NULL)
+ if(pid==0)
+ {
+ #cat("Hi from child process",getpid(),".\n");
+ #Sys.sleep(10);
+ #cat("Bye from child process",getpid(),".\n");
+ exit()
+ }
+ }
+
+cat("Give them 10 seconds to die and exit..\n")
+Sys.sleep(10)
+
+cat("Check the process table to see if there are any zombies...\n")
+if(TRUE) # BSD-style PS command (Linux, Mac OSX, NetBSD)
+{
+ statusList = system("ps -o stat", intern=TRUE)[-1]
+} else
+{
+ statusList = system("ps -o s", intern=TRUE)[-1]
+}
+
+zombies = grep("[Zz]", statusList, value=TRUE)
+if(length(zombies)>50)
+ stop(length(zombies), " Zombie Processes Present!")
+else
+ cat("Done. No Zombies present.\n")
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|
|
From: <wa...@us...> - 2007-03-06 21:01:39
|
Revision: 1062
http://svn.sourceforge.net/r-gregmisc/?rev=1062&view=rev
Author: warnes
Date: 2007-03-06 13:01:38 -0800 (Tue, 06 Mar 2007)
Log Message:
-----------
This is a test commit.
Modified Paths:
--------------
trunk/fork/DESCRIPTION
Modified: trunk/fork/DESCRIPTION
===================================================================
--- trunk/fork/DESCRIPTION 2007-03-01 22:43:18 UTC (rev 1061)
+++ trunk/fork/DESCRIPTION 2007-03-06 21:01:38 UTC (rev 1062)
@@ -1,6 +1,6 @@
Package: fork
Title: R functions for handling multiple processes.
-Version: 1.1.0
+Version: 1.1.1
Author: Gregory R. Warnes <wa...@bs...>
Description: These functions provides simple wrappers around the Unix process
management API calls: fork, wait, waitpid, kill, and _exit. This
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|
|
From: <wa...@us...> - 2007-03-01 22:43:20
|
Revision: 1061
http://svn.sourceforge.net/r-gregmisc/?rev=1061&view=rev
Author: warnes
Date: 2007-03-01 14:43:18 -0800 (Thu, 01 Mar 2007)
Log Message:
-----------
Fix typo
Modified Paths:
--------------
trunk/PathwayModeling/thesispaper/priorPlot.Snw
Modified: trunk/PathwayModeling/thesispaper/priorPlot.Snw
===================================================================
--- trunk/PathwayModeling/thesispaper/priorPlot.Snw 2007-03-01 22:42:15 UTC (rev 1060)
+++ trunk/PathwayModeling/thesispaper/priorPlot.Snw 2007-03-01 22:43:18 UTC (rev 1061)
@@ -2,7 +2,7 @@
\centering
<<priorPlot,echo=F,eval=T,fig=T,width=3,height=3>>=4
-f20 <- function(x) dchisq(3*x/20, df=5)
+f <- function(x, mu=20) dchisq(3*x/mu, df=5)
plot( f, from=0, to=150, xlab=expression(mu[i]), ylab="density", lwd=2)
abline(v=20,lty=2,lwd=2)
mtext(text="20", side=1, at=20, line=0.5)
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