Passes testsuite.

This commit is contained in:
Ole Tange 2015-04-23 01:12:00 +02:00
parent 4e3e0867b9
commit 53ebf4dcd0
6 changed files with 62 additions and 15 deletions

47
NEWS
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@ -1,3 +1,50 @@
20150422
New in this release:
* Security fix. An attacker on the local system could make you overwrite one of your own files with a single byte. The problem exist when you use --compress or --tmux or --pipe or --cat or --fifo. The attacker must figure out the randomly chosen file name and create a symlink within a time window of 15 ms.
* --shuf will generate all jobs, and shuffle them before running them. This is useful to get a quick preview of the results before running the full batch.
* GNU Parallel now has a DOI: https://dx.doi.org/10.5281/zenodo.16303
* GNU Parallel was cited in: Scaling Machine Learning for Target Prediction in Drug Discovery using Apache Spark https://cris.cumulus.vub.ac.be/portal/files/5147244/spark.pdf
* GNU Parallel was cited in: Bayesian inference of protein structure from chemical shift data https://peerj.com/articles/861/
* 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: 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 cited in: Experimental study on the Wind Farm Substation Cable Installation Problem http://i11www.iti.uni-karlsruhe.de/_media/teaching/theses/ma-schmitz-14.pdf
* GNU Parallel was used in: landsat-gifworks https://github.com/KAPPS-/landsat-gifworks
* GNU Parallel was used in: https://github.com/exascience/elprep
* GNU Parallel was used in: http://search.cpan.org/~jillrowe/HPC-Runner-GnuParallel-0.01/
* GNU Parallel was used in: http://search.cpan.org/~ajpage/Bio-Roary-2.0.7/lib/Bio/Roary/JobRunner/Parallel.pm
* GNU Parallel was used in: Rapid haploid SNP calling https://github.com/tseemann/snippy
* Pictures and Metadata http://www.ozzy.no/2015/02/05/pictures-and-metadata/
* Task automation with bash and parallel https://biowize.wordpress.com/2015/03/23/task-automation-with-bash-and-parallel/
* How To: Speed Up File Transfers in Linux using RSync with GNU Parallel http://www.yourownlinux.com/2015/04/speed-up-file-transfers-using-rsync-with-gnu-parallel.html
* Mirroring a Git Repository https://avacariu.me/articles/mirroring-a-git-repository.html
* Add an ENVI header to JAXA Global Mangrove Watch PALSAR tiles https://spectraldifferences.wordpress.com/2015/03/24/add-an-envi-header-to-jaxa-global-mangrove-watch-palsar-tiles/
* GNU Parallel (Sebuah Uji Coba) http://kaka.prakasa.my.id/2014/09/04/gnu-parallel-sebuah-uji-coba/
* 你见过的最牛逼的命令行程序是什么? http://www.zhihu.com/question/29257300
* Bug fixes and man page updates.
20150322 20150322
New in this release: New in this release:

20
configure vendored
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@ -1,6 +1,6 @@
#! /bin/sh #! /bin/sh
# Guess values for system-dependent variables and create Makefiles. # Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.69 for parallel 20150322. # Generated by GNU Autoconf 2.69 for parallel 20150422.
# #
# Report bugs to <bug-parallel@gnu.org>. # Report bugs to <bug-parallel@gnu.org>.
# #
@ -579,8 +579,8 @@ MAKEFLAGS=
# Identity of this package. # Identity of this package.
PACKAGE_NAME='parallel' PACKAGE_NAME='parallel'
PACKAGE_TARNAME='parallel' PACKAGE_TARNAME='parallel'
PACKAGE_VERSION='20150322' PACKAGE_VERSION='20150422'
PACKAGE_STRING='parallel 20150322' PACKAGE_STRING='parallel 20150422'
PACKAGE_BUGREPORT='bug-parallel@gnu.org' PACKAGE_BUGREPORT='bug-parallel@gnu.org'
PACKAGE_URL='' 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. # 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. # This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF cat <<_ACEOF
\`configure' configures parallel 20150322 to adapt to many kinds of systems. \`configure' configures parallel 20150422 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]... Usage: $0 [OPTION]... [VAR=VALUE]...
@ -1269,7 +1269,7 @@ fi
if test -n "$ac_init_help"; then if test -n "$ac_init_help"; then
case $ac_init_help in case $ac_init_help in
short | recursive ) echo "Configuration of parallel 20150322:";; short | recursive ) echo "Configuration of parallel 20150422:";;
esac esac
cat <<\_ACEOF cat <<\_ACEOF
@ -1345,7 +1345,7 @@ fi
test -n "$ac_init_help" && exit $ac_status test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then if $ac_init_version; then
cat <<\_ACEOF cat <<\_ACEOF
parallel configure 20150322 parallel configure 20150422
generated by GNU Autoconf 2.69 generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc. Copyright (C) 2012 Free Software Foundation, Inc.
@ -1362,7 +1362,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake. running configure, to aid debugging if configure makes a mistake.
It was created by parallel $as_me 20150322, which was It was created by parallel $as_me 20150422, which was
generated by GNU Autoconf 2.69. Invocation command line was generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@ $ $0 $@
@ -2225,7 +2225,7 @@ fi
# Define the identity of the package. # Define the identity of the package.
PACKAGE='parallel' PACKAGE='parallel'
VERSION='20150322' VERSION='20150422'
cat >>confdefs.h <<_ACEOF cat >>confdefs.h <<_ACEOF
@ -2867,7 +2867,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their # report actual input values of CONFIG_FILES etc. instead of their
# values after options handling. # values after options handling.
ac_log=" ac_log="
This file was extended by parallel $as_me 20150322, which was This file was extended by parallel $as_me 20150422, which was
generated by GNU Autoconf 2.69. Invocation command line was generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES CONFIG_FILES = $CONFIG_FILES
@ -2929,7 +2929,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\ ac_cs_version="\\
parallel config.status 20150322 parallel config.status 20150422
configured by $0, generated by GNU Autoconf 2.69, configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\" with options \\"\$ac_cs_config\\"

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@ -1,6 +1,6 @@
Summary: Shell tool for executing jobs in parallel Summary: Shell tool for executing jobs in parallel
Name: parallel Name: parallel
Version: 20150322 Version: 20150422
Release: 1 Release: 1
License: GPL License: GPL
Group: Productivity/File utilities Group: Productivity/File utilities

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@ -3719,7 +3719,7 @@ sub reap_usleep {
$SIG{CHLD} = sub { kill "ALRM", $$ }; $SIG{CHLD} = sub { kill "ALRM", $$ };
usleep($ms); usleep($ms);
# --compress needs $SIG{CHLD} undefined # --compress needs $SIG{CHLD} undefined
$SIG{CHLD} = undef; delete $SIG{CHLD};
exit_if_disk_full(); exit_if_disk_full();
if($opt::linebuffer) { if($opt::linebuffer) {
for my $job (values %Global::running) { for my $job (values %Global::running) {

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@ -1,7 +1,7 @@
#!/bin/bash #!/bin/bash
make stopvm make stopvm
mkdir -p $TMPDIR
# Jobs that eat more than 2 GB RAM # Jobs that eat more than 2 GB RAM
cat <<'EOF' | sed -e 's/;$/; /;s/$SERVER1/'$SERVER1'/;s/$SERVER2/'$SERVER2'/' | stdout parallel -vj1 -k --joblog /tmp/jl-`basename $0` -L1 cat <<'EOF' | sed -e 's/;$/; /;s/$SERVER1/'$SERVER1'/;s/$SERVER2/'$SERVER2'/' | stdout parallel -vj1 -k --joblog /tmp/jl-`basename $0` -L1
echo '### Trouble reading a record > 2 GB for certain versions of Perl (substr($a,0,2G+1)="fails")' echo '### Trouble reading a record > 2 GB for certain versions of Perl (substr($a,0,2G+1)="fails")'

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@ -931,7 +931,7 @@ 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. If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
parallel --version parallel --version
GNU parallel 20150419 GNU parallel 20150422
Copyright (C) 2007,2008,2009,2010,2011,2012,2013,2014,2015 Ole Tange Copyright (C) 2007,2008,2009,2010,2011,2012,2013,2014,2015 Ole Tange
and Free Software Foundation, Inc. and Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
@ -943,7 +943,7 @@ Web site: http://www.gnu.org/software/parallel
When using programs that use GNU Parallel to process data for publication When using programs that use GNU Parallel to process data for publication
please cite as described in 'parallel --bibtex'. please cite as described in 'parallel --bibtex'.
parallel --minversion 20130722 && echo Your version is at least 20130722. parallel --minversion 20130722 && echo Your version is at least 20130722.
20150419 20150422
Your version is at least 20130722. Your version is at least 20130722.
parallel --bibtex parallel --bibtex
Academic tradition requires you to cite works you base your article on. Academic tradition requires you to cite works you base your article on.