optional/R: Package builds without warnings.

doc/release_new_version

@@ -204,112 +204,52 @@ cc:Sandro Cazzaniga <kharec@mandriva.org>,
    Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>,
    Jesse Alama <jesse.alama@gmail.com>
 
-Subject: GNU Parallel 20140122 ('Opportunity') released
+Subject: GNU Parallel 20140222 ('') released
 
-GNU Parallel 20140122 ('Opportunity') has been released. It is
+GNU Parallel 20140222 ('') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
-available for download at: http://ftp.gnu.org/gnu/parallel/
-
-No new functionality was introduced so this is a good candidate for a
-stable release.
 
 New in this release:
 
-* GNU Parallel was cited in: On the likelihood of multiple bit upsets
+* --tollef has been retired.
-  in logic circuits
-  http://arxiv-web3.library.cornell.edu/pdf/1401.1003
 
-* HaploClique uses GNU Parallel
+* GNU Parallel is co-distributed with RepeatExplorer
-  https://github.com/armintoepfer/haploclique
+  http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/repeatexplorer/README.txt
-
-* Scraping NSScreencast
-  https://blog.nicolai86.eu/posts/2014-01-12/scraping-nsscreencast/
-
-* 30 Cool Open Source Software I Discovered in 2013
-  http://www.cyberciti.biz/open-source/30-cool-best-open-source-softwares-of-2013/
-
-* [Unix] 13. The power of doing things in Parallel
-  http://leetaey.tistory.com/384
-
-* Parallel the execution of a job that read from stdin
-  http://www.linuxask.com/questions/parallel-the-execution-of-a-job-that-read-from-stdin
-
-* Mon Make à moi (6:38-11:50)
-  http://videos.rennes.inria.fr/ReNaBI-GO2013/indexPierreLindenbaum.html
-
-* Shell-Abarbeitung beschleunigen: Wie Sie mit parallelen Prozesse
-  effizienter in der Shell arbeiten
-  https://www.hosteurope.ch/blog/shell-abarbeitung-beschleunigen-wie-sie-mit-parallelen-prozesse-effizienter-in-der-shell-arbeiten/
-
-* Summary of GNU Parallel tutorial
-  http://hacktracking.blogspot.dk/2014/01/gnu-parallel-tutorial.html
 
 * Bug fixes and man page updates.
 
 
 = About GNU Parallel =
 
-GNU Parallel is a shell tool for executing jobs in parallel using one
+GNU Parallel is a shell tool for executing jobs in parallel using one or more computers. A job is can be a single command or a small script that has to be run for each of the lines in the input. The typical input is a list of files, a list of hosts, a list of users, a list of URLs, or a list of tables. A job can also be a command that reads from a pipe. GNU Parallel can then split the input and pipe it into commands in parallel.
-or more computers. A job is can be a single command or a small script
-that has to be run for each of the lines in the input. The typical
-input is a list of files, a list of hosts, a list of users, a list of
-URLs, or a list of tables. A job can also be a command that reads from
-a pipe. GNU Parallel can then split the input and pipe it into
-commands in parallel.
 
-If you use xargs and tee today you will find GNU Parallel very easy to
+If you use xargs and tee today you will find GNU Parallel very easy to use as GNU Parallel is written to have the same options as xargs. If you write loops in shell, you will find GNU Parallel may be able to replace most of the loops and make them run faster by running several jobs in parallel. GNU Parallel can even replace nested loops.
-use as GNU Parallel is written to have the same options as xargs. If
-you write loops in shell, you will find GNU Parallel may be able to
-replace most of the loops and make them run faster by running several
-jobs in parallel. GNU Parallel can even replace nested loops.
 
-GNU Parallel makes sure output from the commands is the same output as
+GNU Parallel makes sure output from the commands is the same output as you would get had you run the commands sequentially. This makes it possible to use output from GNU Parallel as input for other programs.
-you would get had you run the commands sequentially. This makes it
-possible to use output from GNU Parallel as input for other programs.
 
-You can find more about GNU Parallel at:
+You can find more about GNU Parallel at: http://www.gnu.org/s/parallel/
-http://www.gnu.org/s/parallel/
 
-You can install GNU Parallel in just 10 seconds with:
+You can install GNU Parallel in just 10 seconds with: (wget -O - pi.dk/3 || curl pi.dk/3/) | bash
-(wget -O - pi.dk/3 || curl pi.dk/3/) | bash
 
-Watch the intro video on
+Watch the intro video on http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1
-http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1
 
-Walk through the tutorial (man parallel_tutorial). Your commandline
+Walk through the tutorial (man parallel_tutorial). Your commandline will love you for it.
-will love you for it.
 
-When using programs that use GNU Parallel to process data for
+When using programs that use GNU Parallel to process data for publication please cite:
-publication please cite:
 
-O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login:
+O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47.
-The USENIX Magazine, February 2011:42-47.
 
 
 = About GNU SQL =
 
-GNU sql aims to give a simple, unified interface for accessing
+GNU sql aims to give a simple, unified interface for accessing databases through all the different databases' command line clients. So far the focus has been on giving a common way to specify login information (protocol, username, password, hostname, and port number), size (database and table size), and running queries.
-databases through all the different databases' command line
-clients. So far the focus has been on giving a common way to specify
-login information (protocol, username, password, hostname, and port
-number), size (database and table size), and running queries.
 
-The database is addressed using a DBURL. If commands are left out you
+The database is addressed using a DBURL. If commands are left out you will get that database's interactive shell.
-will get that database's interactive shell.
 
 When using GNU SQL for a publication please cite:
 
-O. Tange (2011): GNU SQL - A Command Line Tool for Accessing Different
+O. Tange (2011): GNU SQL - A Command Line Tool for Accessing Different Databases Using DBURLs, ;login: The USENIX Magazine, April 2011:29-32.
-Databases Using DBURLs, ;login: The USENIX Magazine, April 2011:29-32.
 
 
 = About GNU Niceload =
 
-GNU niceload slows down a program when the computer load average (or
+GNU niceload slows down a program when the computer load average (or other system activity) is above a certain limit. When the limit is reached the program will be suspended for some time. If the limit is a soft limit the program will be allowed to run for short amounts of time before being suspended again. If the limit is a hard limit the program will only be allowed to run when the system is below the limit.
-other system activity) is above a certain limit. When the limit is
-reached the program will be suspended for some time. If the limit is a
-soft limit the program will be allowed to run for short amounts of
-time before being suspended again. If the limit is a hard limit the
-program will only be allowed to run when the system is below the
-limit.
-
->>>>>

src/optional/R/gnuparallel/DESCRIPTION

@@ -0,0 +1,15 @@
+Package: gnuparallel
+Type: Package
+Title: Loading of GNU Parallel --results output
+Version: 0.1
+Date: 2014-01-22
+Author: Ole Tange
+Maintainer: Ole Tange <tange@gnu.org>
+Description: Load GNU Parallel --results output as R objects
+License: GPL (>= 3)
+LazyLoad: yes
+Collate: 'gnuparallel.R'
+Date/Publication: 2014-01-22 21:19:14
+Packaged: 2014-01-21 02:35:20 UTC; tange
+NeedsCompilation: no
+Depends: R (>= 2.12.1), data.table, plyr

src/optional/R/gnuparallel/MD5

@@ -0,0 +1,4 @@
+c521738aeecfa8e237500f4a3263143e  DESCRIPTION
+d186dcbdce42279894f9241df00ed5a2  NAMESPACE
+55cef8c319d20ad1a7825e2bafb52a34  R/gnuparallel.R
+2fbd375e38ecad68a4e96c80ebad2143  man/gnuparallel-package.Rd

src/optional/R/gnuparallel/NAMESPACE

@@ -0,0 +1,7 @@
+export(heckbert)
+export(gnu.parallel.filenames)
+export(gnu.parallel.load)
+export(gnu.parallel.load.lines)
+export(gnu.parallel.load.data.frame)
+export(gnu.parallel.load.data.table)
+

src/optional/R/gnuparallel/R/gnuparallel.R

@@ -0,0 +1,224 @@
+## Copyright (C) 2014 Ole Tange, David Rosenberg, and Free Software
+## Foundation, Inc.
+##
+## This program is free software; you can redistribute it and/or modify
+## it under the terms of the GNU General Public License as published by
+## the Free Software Foundation; either version 3 of the License, or
+## (at your option) any later version.
+##
+## This program is distributed in the hope that it will be useful, but
+## WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+## General Public License for more details.
+##
+## You should have received a copy of the GNU General Public License
+## along with this program; if not, see <http://www.gnu.org/licenses/>
+## or write to the Free Software Foundation, Inc., 51 Franklin St,
+## Fifth Floor, Boston, MA 02110-1301 USA
+
+#' Functions for reading GNU Parallel results dir
+#'
+#' \tabular{ll}{
+#' Package: \tab gnuparallel\cr
+#' Type: \tab Package\cr
+#' Version: \tab 0.1\cr
+#' Date: \tab 2014-01-22\cr
+#' License: \tab GPL >= 3\cr
+#' LazyLoad: \tab no\cr
+#' }
+#' 
+#' Implements a number of functions for reading GNU Parallel results dir
+#'
+#' @name gnuparallel-package
+#' @aliases gnuparallel
+#' @docType package
+#' @title Results dir loading
+#' @author Ole Tange \email{tange@@gnu.org}
+#' @references
+#' Tange, O. (2011) GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47.
+#' Talbot, J. (2011) labeling R-package, CRAN 2011.
+#' @keywords parallel
+#' @seealso \code{\link{heckbert}}, \code{\link{gnu.parallel.filenames}}
+#' @examples
+#' heckbert(8.1, 14.1, 4)	# 5 10 15
+
+#' # When plotting, extend the plot range to include the labeling
+#' # Should probably have a helper function to make this easier
+#' data(iris)
+#' x <- iris$Sepal.Width
+#' y <- iris$Sepal.Length
+#' xl <- extended(min(x), max(x), 6)
+#' yl <- extended(min(y), max(y), 6)
+#' plot(x, y, 
+#'     xlim=c(min(x,xl),max(x,xl)), 
+#'     ylim=c(min(y,yl),max(y,yl)), 
+#'     axes=FALSE, main="Extended labeling")
+#' axis(1, at=xl)
+#' axis(2, at=yl)
+c()
+
+
+#' Find the filenames in a results dir
+#'
+#' @param resdir results dir from GNU Parallel's --results
+#' @return filenametable with a column for each of GNU Parallel's input sources and a column for file name of both stdout and stderr
+#' @export
+gnu.parallel.filenames <- function(resdir) {
+  ## Find files called .../stdout
+  stdoutnames <- list.files(path=resdir, pattern="stdout", recursive=T);
+  ## Find files called .../stderr
+  stderrnames <- list.files(path=resdir, pattern="stderr", recursive=T);
+  if(length(stdoutnames) == 0) {
+    ## Return empty data frame if no files found
+    return(data.frame());
+  }
+  ## The argument names are every other dir level
+  ## The argument values are every other dir level
+  ## e.g. my/results/dir/age/18/chromosome/20/stdout
+  m <- matrix(unlist(strsplit(stdoutnames, "/")),nrow = length(stdoutnames),byrow=T);
+  filenametable <- as.table(m[,c(F,T)]);
+  ## Append the stdout and stderr filenames
+  filenametable <- cbind(filenametable,
+                         paste(resdir,unlist(stdoutnames),sep="/"),
+                         paste(resdir,unlist(stderrnames),sep="/"));
+  colnames(filenametable) <- c(strsplit(stdoutnames[1],"/")[[1]][c(T,F)],"stderr");
+  return(filenametable);
+}
+
+#' Read the contents of the stdout and stderr files as 1 field each
+#'
+#' @param filenametable from gnu.parallel.filenames
+#' @return table with a column for each of GNU Parallel's input sources and 2 columns for content of stdout and stderr
+#' @export
+gnu.parallel.load <- function(filenametable) {
+  ## Read the files given in column stdout
+  stdoutcontents <-
+    lapply(filenametable[,c("stdout")],
+           function(filename) {
+             return(readChar(filename, file.info(filename)$size));
+           } );
+  ## Read the files given in column stderr
+  stderrcontents <-
+    lapply(filenametable[,c("stderr")],
+           function(filename) {
+             return(readChar(filename, file.info(filename)$size));
+           } );
+  ## Replace filenames with file contents
+  filenametable[,c("stdout","stderr")] <-
+    c(as.character(stdoutcontents),as.character(stderrcontents));
+  return(filenametable);
+}
+
+#' Read the contents of the stdout and produce a row for each line of stdout
+#'
+#' @param filenametable from gnu.parallel.filenames
+#' @return table with a column for each of GNU Parallel's input sources and a column for content of stdout
+#' @export
+gnu.parallel.load.lines <- function(filenametable,split="\n") {
+  raw <- gnu.parallel.load(filenametable);
+  ## Keep all columns except stdout and stderr
+  varnames = setdiff(colnames(raw), c("stdout","stderr"))
+  ## Find the id of the non-stdout and non-stderr columns
+  header_cols = which(colnames(raw) %in% varnames)
+  ## Split stdout on \n
+  splits = strsplit(raw[,"stdout"], split)
+  ## Compute lengths of all the lines
+  lens = sapply(splits, length)
+  ## The arguments should be repeated as many times as there are lines
+  reps = rep(1:nrow(raw), lens)
+  ## Merge the repeating argument and the lines into a matrix
+  m = cbind(raw[reps, header_cols], unlist(splits))
+  return(m)
+}
+
+#' Read the contents of the stdout and produce a row for each line of stdout split into columns on \t
+#'
+#' @param filenametable from gnu.parallel.filenames
+#' @return table with a column for each of GNU Parallel's input sources and stdout split by \t
+#' @export
+gnu.parallel.load.data.table <- function(filenametable, ...) {
+  raw <- gnu.parallel.load(filenametable);
+  require(data.table)
+  ## Keep all columns except stdout and stderr
+  varnames = setdiff(colnames(raw), c("stdout","stderr"))  
+  ## after data.table feature request the as.data.frame can be skipped
+  ## and will thus be much faster
+  ddt = as.data.table(as.data.frame(raw,stringsAsFactors=FALSE))
+  ## ensure fread knows stdout is string and not filename by appending \n
+  ddt[, stdout := paste0(stdout,"\n")]
+  ## drop files with empty stdout
+  ddd = ddt[nchar(stdout)>1,fread(stdout, header=FALSE, ...), by=varnames]
+  return(ddd)
+}
+
+#' Read the contents of the stdout and produce a row for each line of stdout split into columns on \t
+#'
+#' @param filenametable from gnu.parallel.filenames
+#' @return table with a column for each of GNU Parallel's input sources and stdout split by \t
+#' @export
+gnu.parallel.load.data.frame <- function(filenametable, ...) {
+  raw <- gnu.parallel.load(filenametable);
+  require(plyr)
+  ## Convert to data.frame without factors
+  raw = as.data.frame(raw, stringsAsFactors = FALSE)
+  ## Keep all columns except stdout and stderr
+  varnames = setdiff(colnames(raw), c("stdout","stderr"))  
+  
+  dd = ddply(raw, .variables=varnames, function(row) {
+    ## Ignore empty stdouts
+    if (nchar(row[,"stdout"]) == 0) {
+      return(NULL)
+    }
+    ## Read stdout with read.table
+    con <- textConnection(row[,"stdout"], open = "r")
+    d = read.table(con, header=FALSE, ...)
+    return(d)
+  })
+  return(dd)
+}
+
+
+#' Heckbert's labeling algorithm
+#'
+#' @param dmin minimum of the data range
+#' @param dmax maximum of the data range
+#' @param m number of axis labels
+#' @return vector of axis label locations
+#' @references
+#' Heckbert, P. S. (1990) Nice numbers for graph labels, Graphics Gems I, Academic Press Professional, Inc.
+#' @author Justin Talbot \email{jtalbot@@stanford.edu}
+#' @export
+heckbert <- function(dmin, dmax, m)
+{
+    range <- .heckbert.nicenum((dmax-dmin), FALSE)
+    lstep <- .heckbert.nicenum(range/(m-1), TRUE)
+    lmin <- floor(dmin/lstep)*lstep
+    lmax <- ceiling(dmax/lstep)*lstep
+    seq(lmin, lmax, by=lstep)
+}
+    
+.heckbert.nicenum <- function(x, round)
+{
+	e <- floor(log10(x))
+	f <- x / (10^e)
+	if(round)
+	{
+		if(f < 1.5) nf <- 1
+		else if(f < 3) nf <- 2
+		else if(f < 7) nf <- 5
+		else nf <- 10
+	}
+	else
+	{
+		if(f <= 1) nf <- 1
+		else if(f <= 2) nf <- 2
+		else if(f <= 5) nf <- 5
+		else nf <- 10
+	}
+	nf * (10^e)
+}
+
+
+
+
+

src/optional/R/gnuparallel/man/gnu.parallel.filenames.Rd

@@ -0,0 +1,23 @@
+\name{gnu.parallel.filenames}
+\alias{gnu.parallel.filenames}
+\title{Find the filenames in a GNU Parallel results dir}
+\usage{
+  gnu.parallel.filenames(resdir)
+}
+\arguments{
+  \item{resdir}{results dir from GNU Parallel's --results}
+}
+\value{
+  filenametable with a column for each of GNU Parallel's input sources
+  and a column for file name of both stdout and stderr
+}
+\description{
+  Find the filenames in a GNU Parallel results dir
+}
+\author{
+  Ole Tange \email{tange@gnu.org}, David Rosenberg
+}
+\references{
+  Tange, O. (2011) \emph{GNU Parallel - The Command-Line Power Tool} ;login:
+  The USENIX Magazine, February 2011:42-47.
+}

src/optional/R/gnuparallel/man/gnu.parallel.load.Rd

@@ -0,0 +1,22 @@
+\name{gnu.parallel.load}
+\alias{gnu.parallel.load}
+\title{Read the contents of the stdout and stderr files as 1 field each}
+\usage{
+  gnu.parallel.load(filenametable)
+}
+\arguments{
+  \item{filenametable}{filenametable from gnu.parallel.filenames}
+}
+\value{
+  table with a column for each of GNU Parallel's input sources and 2 columns for content of stdout and stderr
+}
+\description{
+  Read the contents of the stdout and stderr files as 1 field each.
+}
+\author{
+  Ole Tange \email{tange@gnu.org}
+}
+\references{
+  Tange, O. (2011) \emph{GNU Parallel - The Command-Line Power Tool} ;login:
+  The USENIX Magazine, February 2011:42-47.
+}

src/optional/R/gnuparallel/man/gnu.parallel.load.data.frame.Rd

@@ -0,0 +1,25 @@
+\name{gnu.parallel.load.data.frame}
+\alias{gnu.parallel.load.data.frame}
+\title{Read the contents of the stdout and produce a row for each line of stdout split into columns on TAB}
+\usage{
+  gnu.parallel.load.data.frame(filenametable,...)
+}
+\arguments{
+  \item{filenametable}{filenametable from gnu.parallel.filenames}
+  \item{...}{passed on}
+}
+\value{
+  table with a column for each of GNU Parallel's input sources and
+  stdout split by TAB.
+}
+\description{
+  Read the contents of the stdout and produce a row for each line of
+  stdout split into columns on TAB.
+}
+\author{
+  Ole Tange \email{tange@gnu.org}, David Rosenberg
+}
+\references{
+  Tange, O. (2011) \emph{GNU Parallel - The Command-Line Power Tool} ;login:
+  The USENIX Magazine, February 2011:42-47.
+}

src/optional/R/gnuparallel/man/gnu.parallel.load.data.table.Rd

@@ -0,0 +1,25 @@
+\name{gnu.parallel.load.data.table}
+\alias{gnu.parallel.load.data.table}
+\title{Read the contents of the stdout and produce a row for each line of stdout split into columns on TAB}
+\usage{
+  gnu.parallel.load.data.table(filenametable,...)
+}
+\arguments{
+  \item{filenametable}{filenametable from gnu.parallel.filenames}
+  \item{...}{passed on}
+}
+\value{
+  table with a column for each of GNU Parallel's input sources and
+  stdout split by TAB.
+}
+\description{
+  Read the contents of the stdout and produce a row for each line of
+  stdout split into columns on TAB.
+}
+\author{
+  Ole Tange \email{tange@gnu.org}, David Rosenberg
+}
+\references{
+  Tange, O. (2011) \emph{GNU Parallel - The Command-Line Power Tool} ;login:
+  The USENIX Magazine, February 2011:42-47.
+}

src/optional/R/gnuparallel/man/gnu.parallel.load.lines.Rd

@@ -0,0 +1,24 @@
+\name{gnu.parallel.load.lines}
+\alias{gnu.parallel.load.lines}
+\title{Read the contents of the stdout and produce a row for each line of stdout}
+\usage{
+  gnu.parallel.load.lines(filenametable,split="\n")
+}
+\arguments{
+  \item{filenametable}{filenametable from gnu.parallel.filenames}
+  \item{split}{defaults to newline}
+}
+\value{
+  table with a column for each of GNU Parallel's input sources and a
+  column for content of stdout
+}
+\description{
+  Read the contents of the stdout and produce a row for each line of stdout.
+}
+\author{
+  Ole Tange \email{tange@gnu.org}, David Rosenberg
+}
+\references{
+  Tange, O. (2011) \emph{GNU Parallel - The Command-Line Power Tool} ;login:
+  The USENIX Magazine, February 2011:42-47.
+}

src/optional/R/gnuparallel/man/gnuparallel-package.Rd

@@ -0,0 +1,53 @@
+\docType{package}
+\name{gnuparallel-package}
+\alias{gnuparallel}
+\alias{gnuparallel-package}
+\title{GNU Parallel}
+\description{
+  Loading of GNU Parallel --results output
+}
+\details{
+  \tabular{ll}{ Package: \tab gnuparallel\cr Type: \tab
+  Package\cr Version: \tab 2014.01.22\cr Date: \tab 2014-01-22\cr
+  License: \tab GPL (>= 3)\cr LazyLoad: \tab yes\cr }
+
+  Implements a number of functions for reading GNU Parallel results dir.
+}
+\examples{
+library(gnuparallel)
+system("parallel --header : --results foobar printf out{1}\\\\\\\\tout{2}\\\\\\\\nline2{1}\\\\\\\\t{2}\\\\\\\\n ::: letters a b c ::: numbers 4 5 6")
+fn <- gnu.parallel.filenames("foobar")
+gnu.parallel.load(fn)
+gnu.parallel.load.lines(fn)
+gnu.parallel.load.data.frame(fn)
+gnu.parallel.load.data.table(fn)
+
+heckbert(8.1, 14.1, 4)	# 5 10 15
+# When plotting, extend the plot range to include the labeling
+# Should probably have a helper function to make this easier
+data(iris)
+x <- iris$Sepal.Width
+y <- iris$Sepal.Length
+xl <- heckbert(min(x), max(x), 6)
+yl <- heckbert(min(y), max(y), 6)
+plot(x, y,
+    xlim=c(min(x,xl),max(x,xl)),
+    ylim=c(min(y,yl),max(y,yl)),
+    axes=FALSE, main="Extended labeling")
+axis(1, at=xl)
+axis(2, at=yl)
+}
+\author{
+  Ole Tange \email{tange@gnu.org}, David Rosenberg
+}
+\references{
+  Tange, O. (2011) GNU Parallel - The Command-Line Power Tool,
+  ;login: The USENIX Magazine, February 2011:42-47.
+}
+\seealso{
+  \code{\link{gnu.parallel.filenames}}, \code{\link{gnu.parallel.load}},
+  \code{\link{gnu.parallel.load.data.frame}}, \code{\link{gnu.parallel.load.data.table}},
+  \code{\link{gnu.parallel.load.lines}}
+}
+\keyword{parallel}
+

src/parallel

@@ -1649,11 +1649,12 @@ sub progress {
 	    if($opt::bar) {
 		my $arg = $Global::newest_job ? 
 		    $Global::newest_job->{'commandline'}->simple_replace_placeholders($Global::replace{"{}"}) : "";
-		my $bar = sprintf("%d%% %ds %s", $pctcomplete*100, $this_eta, $arg);
+		my $bar_text = sprintf("%d%% %d:%d=%ds %s", 
+				  $pctcomplete*100, $completed, $left, $this_eta, $arg);
 		my $rev = '';
 		my $reset = '';
 		my $terminal_width = terminal_columns();
-		my $s = sprintf("%-${terminal_width}s",$bar);
+		my $s = sprintf("%-${terminal_width}s",$bar_text);
 		my $width = int($terminal_width * $pctcomplete);
 		$s =~ s/^(.{$width})/$1$reset/;
 		$s = "\r#   ".int($this_eta)." sec $arg" . "\r". $pctcomplete*100 # Prefix with zenity header

src/parallel_tutorial.1

@@ -124,7 +124,7 @@
 .\" ========================================================================
 .\"
 .IX Title "PARALLEL_TUTORIAL 1"
-.TH PARALLEL_TUTORIAL 1 "2014-01-14" "20140122" "parallel"
+.TH PARALLEL_TUTORIAL 1 "2014-01-25" "20140122" "parallel"
 .\" For nroff, turn off justification.  Always turn off hyphenation; it makes
 .\" way too many mistakes in technical documents.
 .if n .ad l
@@ -2213,6 +2213,7 @@ job by matching the header with \-\-header. If headers start with \f(CW%:\fR
 Output (the order may be different):
 .PP
 .Vb 10
+\&  JOB1
 \&  %head1
 \&  %head2
 \&  1

src/parallel_tutorial.html

@@ -1528,6 +1528,7 @@ job by matching the header with --header. If headers start with %:</p>
   cat num_%header | parallel --header '(%.*\n)*' --pipe -N3 echo JOB{#}\;cat</pre>
 <p>Output (the order may be different):</p>
 <pre>
+  JOB1
   %head1
   %head2
   1

src/parallel_tutorial.pod

@@ -1650,6 +1650,7 @@ job by matching the header with --header. If headers start with %:
 
 Output (the order may be different):
 
+  JOB1
   %head1
   %head2
   1