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Merge branch 'master' of ssh://git.sv.gnu.org/srv/git/parallel

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Conflicts:
	doc/release_new_version
	src/parallel
	testsuite/wanted-results/parallel-tutorial
This commit is contained in:
Ole Tange 2015-05-25 20:26:53 +02:00
parent 6a6a5e4d01 1b0c5d4ca7
commit ee7ad814aa
10 changed files with 296 additions and 415 deletions
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41
NEWS
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@ -1,3 +1,44 @@
20150522
* Security: The security issue for --sshlogin + --fifo/--cat has been fixed. Thereby all issues with http://lists.gnu.org/archive/html/parallel/2015-04/msg00045.html have been fixed.
* Security: After further security analysis the issue fixed in 20150422 also fixed the problem for --tmux.
* GNU Parallel was cited in: CIDER: a pipeline for detecting waves of coordinated transcriptional regulation in gene expression time-course data http://biorxiv.org/content/biorxiv/early/2015/03/17/012518.full.pdf
* GNU Parallel was cited in: Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq http://biorxiv.org/content/biorxiv/early/2015/05/05/018085.full.pdf
* GNU Parallel was cited in: Toward Enhanced Metadata Quality of Large-Scale Digital Libraries: Estimating Volume Time Range https://www.ideals.illinois.edu/bitstream/handle/2142/73656/186_ready.pdf
* GNU Parallel was cited in: Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation http://nar.oxfordjournals.org/content/early/2015/04/20/nar.gkv333.full.pdf
* GNU Parallel was cited in: Genome assembly using Nanopore-guided long and error-free DNA reads http://www.biomedcentral.com/content/pdf/s12864-015-1519-z.pdf
* GNU Parallel was cited in: Contrasting regional architectures of schizophrenia and other complex diseases using fast variance components analysis http://biorxiv.org/content/biorxiv/early/2015/03/13/016527.full.pdf
* GNU Parallel was used (unfortunately with wrong citation) in: Comparing the CarbonTracker and TM5-4DVar data assimilation systems for CO2 surface flux inversions http://www.atmos-chem-phys-discuss.net/15/8883/2015/acpd-15-8883-2015-discussion.html
* GNU Parallel was used in: Gene Set Omic Analysis (GSOA) method https://bitbucket.org/srp33/gsoa
* A Quick and Neat :) Orchestrator using GNU Parallel http://www.elsotanillo.net/2015/05/a-quick-and-neat-orchestrator-using-gnu-parallel/
* Execute commands on multiple computers using GNU Parallel (setting up a cluster on the cheap) https://spectraldifferences.wordpress.com/2015/04/26/execute-commands-on-multiple-computers-using-gnu-parallel-setting-up-a-cluster-on-the-cheap/
* Functions and GNU parallel for effective cluster load management http://genomespot.blogspot.dk/2015/04/functions-and-gnu-parallel-for.html
* Use parallel processing to save time importing databases http://drupalsun.com/node/41854
* Run multiple ssh commands in parallel with GNU Parallel http://www.ameir.net/blog/archives/380-run-multiple-ssh-commands-in-parallel-with-gnu-parallel.html
* Importing huge databases faster https://www.lullabot.com/blog/article/importing-huge-databases-faster
* Run multiple ssh commands in parallel with GNU Parallel https://www.ameir.net/blog/archives/380-run-multiple-ssh-commands-in-parallel-with-gnu-parallel.html/comment-page-1
* Parallel? Gnu parallel! https://debian.pro/1834
* Bug fixes and man page updates.
20150422
New in this release:

12
README
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@ -40,9 +40,9 @@ document.
Full installation of GNU Parallel is as simple as:
wget http://ftpmirror.gnu.org/parallel/parallel-20150422.tar.bz2
bzip2 -dc parallel-20150422.tar.bz2 | tar xvf -
cd parallel-20150422
wget http://ftpmirror.gnu.org/parallel/parallel-20150522.tar.bz2
bzip2 -dc parallel-20150522.tar.bz2 | tar xvf -
cd parallel-20150522
./configure && make && make install
@ -51,9 +51,9 @@ Full installation of GNU Parallel is as simple as:
If you are not root you can add ~/bin to your path and install in
~/bin and ~/share:
wget http://ftpmirror.gnu.org/parallel/parallel-20150422.tar.bz2
bzip2 -dc parallel-20150422.tar.bz2 | tar xvf -
cd parallel-20150422
wget http://ftpmirror.gnu.org/parallel/parallel-20150522.tar.bz2
bzip2 -dc parallel-20150522.tar.bz2 | tar xvf -
cd parallel-20150522
./configure --prefix=$HOME && make && make install
Or if your system lacks 'make' you can simply copy src/parallel

20
configure vendored
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@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.69 for parallel 20150422.
# Generated by GNU Autoconf 2.69 for parallel 20150522.
#
# Report bugs to <bug-parallel@gnu.org>.
#
@ -579,8 +579,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='parallel'
PACKAGE_TARNAME='parallel'
PACKAGE_VERSION='20150422'
PACKAGE_STRING='parallel 20150422'
PACKAGE_VERSION='20150522'
PACKAGE_STRING='parallel 20150522'
PACKAGE_BUGREPORT='bug-parallel@gnu.org'
PACKAGE_URL=''
@ -1203,7 +1203,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
\`configure' configures parallel 20150422 to adapt to many kinds of systems.
\`configure' configures parallel 20150522 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@ -1269,7 +1269,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
short | recursive ) echo "Configuration of parallel 20150422:";;
short | recursive ) echo "Configuration of parallel 20150522:";;
esac
cat <<\_ACEOF
@ -1345,7 +1345,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
parallel configure 20150422
parallel configure 20150522
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@ -1362,7 +1362,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by parallel $as_me 20150422, which was
It was created by parallel $as_me 20150522, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@ -2225,7 +2225,7 @@ fi
# Define the identity of the package.
PACKAGE='parallel'
VERSION='20150422'
VERSION='20150522'
cat >>confdefs.h <<_ACEOF
@ -2867,7 +2867,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
This file was extended by parallel $as_me 20150422, which was
This file was extended by parallel $as_me 20150522, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@ -2929,7 +2929,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
parallel config.status 20150422
parallel config.status 20150522
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"

2
configure.ac
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@ -1,4 +1,4 @@
AC_INIT([parallel], [20150422], [bug-parallel@gnu.org])
AC_INIT([parallel], [20150522], [bug-parallel@gnu.org])
AM_INIT_AUTOMAKE([-Wall -Werror foreign])
AC_CONFIG_HEADERS([config.h])
AC_CONFIG_FILES([

2
doc/release_new_version
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@ -213,6 +213,8 @@ Subject: GNU Parallel 20150622 ('<<>>') released
GNU Parallel 20150622 ('<<>>') has been released. It is 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.
Haiku of the month:
Programs very slow.

2
packager/obs/home:tange/parallel/parallel.spec
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@ -1,6 +1,6 @@
Summary: Shell tool for executing jobs in parallel
Name: parallel
Version: 20150422
Version: 20150522
Release: 1
License: GPL
Group: Productivity/File utilities

2
src/niceload
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@ -24,7 +24,7 @@
use strict;
use Getopt::Long;
$Global::progname="niceload";
$Global::version = 20150422;
$Global::version = 20150522;
Getopt::Long::Configure("bundling","require_order");
get_options_from_array(\@ARGV) || die_usage();
if($opt::version) {

582
src/parallel
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File diff suppressed because it is too large Load diff

2
src/sql
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@ -566,7 +566,7 @@ $Global::Initfile && unlink $Global::Initfile;
exit ($err);
sub parse_options {
$Global::version = 20150422;
$Global::version = 20150522;
$Global::progname = 'sql';
# This must be done first as this may exec myself

10
testsuite/wanted-results/parallel-tutorial
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@ -614,7 +614,7 @@ foo
3
parallel --filter-hosts -S 173.194.32.46,$SERVER1 echo ::: bar
bar
parallel: Warning: Removed 173.194.32.46.
parallel: Warning: Removed 173.194.32.46
parallel --onall -S $SERVER1,$SERVER2 echo ::: foo bar
foo
bar
@ -982,7 +982,7 @@ This helps funding further development; and it won't cost you a cent.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
parallel --version
GNU parallel VERSION
GNU parallel 20150522
Copyright (C) 2007,2008,2009,2010,2011,2012,2013,2014,2015 Ole Tange
and Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
@ -993,9 +993,9 @@ Web site: http://www.gnu.org/software/parallel
When using programs that use GNU Parallel to process data for publication
please cite as described in 'parallel --bibtex'.
parallel --minversion VERSION && echo Your version is at least VERSION.
VERSION
Your version is at least VERSION.
parallel --minversion 20130722 && echo Your version is at least 20130722.
20150522
Your version is at least 20130722.
parallel --bibtex
Academic tradition requires you to cite works you base your article on.
When using programs that use GNU Parallel to process data for publication