Merge security fix into stable.

CITATION

@@ -11,6 +11,7 @@ When using programs that use GNU Parallel to process data for publication please
   url = {http://www.gnu.org/s/parallel},
   year = {2011},
   pages = {42-47}
+  doi = {10.5281/zenodo.16303}
 }
 
 (Feel free to use \nocite{Tange2011a})

NEWS

@@ -2,45 +2,73 @@
 
 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.
+* 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.
+* --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: 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: 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: 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: 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 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: 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/~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:
+  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
+* 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/
+* 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/
+* 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
+* 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
+* 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/
+* 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/
+* 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
+* 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.
 

doc/release_new_version

@@ -58,6 +58,7 @@ pushd
 == Upload ==
 
 export YYYYMMDD=`yyyymmdd`
+eval `gpg-agent --daemon`
 make upload
 
 # Only needed for alpha:
@@ -141,8 +142,7 @@ YYYYMMDD=`yyyymmdd`
 TAG=MyTag
 echo "Released as $YYYYMMDD ('$TAG')."
 
-git commit -a
+git commit -a -m "Released as $YYYYMMDD ('$TAG')"
-
 git tag -s -m "Released as $YYYYMMDD ('$TAG')" $TAG
 git tag -s -m "Released as $YYYYMMDD ('$TAG')" $YYYYMMDD
 
@@ -209,66 +209,43 @@ cc:Tim Cuthbertson <tim3d.junk@gmail.com>,
    Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>,
    Jesse Alama <jesse.alama@gmail.com>
 
-Subject: GNU Parallel 20150422 ('Germanwings') released
+Subject: GNU Parallel 20150522 ('Nepal') released
 
-GNU Parallel 20150422 ('Germanwings') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
+GNU Parallel 20150522 ('Nepal') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
 
 Haiku of the month:
 
-  SSH set up?
+  Many jobs to run.
-  Instant cluster needed now?
+  Idle cores is not your thing.
   Use GNU Parallel.
       -- Ole Tange
 
 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.
-
-* 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
-
 * <<afventer - rykket >> 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
 
 * <<afventer opdatering>> 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
 
+
 * <<afventer opdatering>> GNU Parallel was used (unfortunately without citation) in: MUGBAS: a species free gene-based programme suite for post-GWAS analysis http://www.ncbi.nlm.nih.gov/pubmed/25765345
 
 taxator-tk http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/ (check it)
 
 * << afventer svar fra Rachel >> GNU Parallel was used in: SISRS: Site Identification from Short Read Sequences https://github.com/rachelss/SISRS/
 
-* GNU Parallel was used in: landsat-gifworks https://github.com/KAPPS-/landsat-gifworks
+* 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 used in: https://github.com/exascience/elprep
+* GNU Parallel was cited in: Genome assemblyusing Nanopore-guided long and error-free DNA reads http://www.biomedcentral.com/content/pdf/s12864-015-1519-z.pdf
 
-* GNU Parallel was used in: http://search.cpan.org/~jillrowe/HPC-Runner-GnuParallel-0.01/
+* 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 in: http://search.cpan.org/~ajpage/Bio-Roary-2.0.7/lib/Bio/Roary/JobRunner/Parallel.pm
+* <<kontakt>> GNU Parallel was used (unfortunately with wrong citation) in: TADSim: Discrete Event-Based Performance Prediction for Temperature-Accelerated Dynamics http://vruehle.de/publications/2015c.pdf
 
-* GNU Parallel was used in: Rapid haploid SNP calling https://github.com/tseemann/snippy
+* GNU Parallel was used in: Gene Set Omic Analysis (GSOA) method https://bitbucket.org/srp33/gsoa
 
-* Pictures and Metadata http://www.ozzy.no/2015/02/05/pictures-and-metadata/
+* 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/
 
-* Task automation with bash and parallel https://biowize.wordpress.com/2015/03/23/task-automation-with-bash-and-parallel/
+* Functions and GNU parallel for effective cluster load management http://genomespot.blogspot.dk/2015/04/functions-and-gnu-parallel-for.html
-
-* 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.
 

src/parallel

@@ -725,7 +725,6 @@ sub options_hash {
 	 "use-cpus-instead-of-cores" => \$opt::use_cpus_instead_of_cores,
 	 "shellquote|shell_quote|shell-quote" => \$opt::shellquote,
 	 "nice=i" => \$opt::nice,
-	 "timeout=s" => \$opt::timeout,
 	 "tag" => \$opt::tag,
 	 "tagstring|tag-string=s" => \$opt::tagstring,
 	 "onall" => \$opt::onall,
@@ -751,9 +750,7 @@ sub options_hash {
 	 "compress" => \$opt::compress,
 	 "tty" => \$opt::tty,
 	 "T" => \$opt::retired,
-	 "halt-on-error|halt=s" => \$opt::halt,
 	 "H=i" => \$opt::retired,
-	 "retries=i" => \$opt::retries,
 	 "dry-run|dryrun" => \$opt::dryrun,
 	 "progress" => \$opt::progress,
 	 "eta" => \$opt::eta,
@@ -779,7 +776,11 @@ sub options_hash {
 	 "xapply" => \$opt::xapply,
 	 "bibtex" => \$opt::bibtex,
 	 "wc|willcite|will-cite|nn|nonotice|no-notice" => \$opt::willcite,
+	 # Termination and retries
+	 "halt-on-error|halt=s" => \$opt::halt,
 	 "memfree=s" => \$opt::memfree,
+	 "retries=i" => \$opt::retries,
+	 "timeout=s" => \$opt::timeout,
 	 # xargs-compatibility - implemented, man, testsuite
 	 "max-procs|P=s" => \$opt::jobs,
 	 "delimiter|d=s" => \$opt::d,
@@ -1053,7 +1054,7 @@ sub parse_options {
 
 sub init_globals {
     # Defaults:
-    $Global::version = 20150422;
+    $Global::version = 20150424;
     $Global::progname = 'parallel';
     $Global::infinity = 2**31;
     $Global::debug = 0;

src/parallel.pod

@@ -488,7 +488,7 @@ I<regexp> is a Perl Regular Expression:
 http://perldoc.perl.org/perlre.html
 
 
-=item B<--compress> (beta testing)
+=item B<--compress>
 
 Compress temporary files. If the output is big and very compressible
 this will take up less disk space in $TMPDIR and possibly be faster
@@ -499,9 +499,9 @@ B<plzip>, B<bzip2>, B<lzma>, B<lzip>, B<xz> in that order, and use the
 first available.
 
 
-=item B<--compress-program> I<prg> (beta testing)
+=item B<--compress-program> I<prg>
 
-=item B<--decompress-program> I<prg> (beta testing)
+=item B<--decompress-program> I<prg>
 
 Use I<prg> for (de)compressing temporary files. It is assumed that I<prg
 -dc> will decompress stdin (standard input) to stdout (standard
@@ -514,9 +514,9 @@ If receiving SIGNING, GNU B<parallel> will send SIGINT to tasks
 running on remote computers thus killing them.
 
 
-=item B<--delimiter> I<delim> (beta testing)
+=item B<--delimiter> I<delim>
 
-=item B<-d> I<delim> (beta testing)
+=item B<-d> I<delim>
 
 Input items are terminated by I<delim>.  Quotes and backslash are not
 special; every character in the input is taken literally.  Disables
@@ -568,7 +568,7 @@ If I<eof-str> is omitted, there is no end of file string.  If neither
 B<-E> nor B<-e> is used, no end of file string is used.
 
 
-=item B<--env> I<var> (alpha testing)
+=item B<--env> I<var> (beta testing)
 
 Copy environment variable I<var>. This will copy I<var> to the
 environment that the command is run in. This is especially useful for
@@ -782,7 +782,7 @@ specified, and for B<-I>{} otherwise.  This option is deprecated;
 use B<-I> instead.
 
 
-=item B<--joblog> I<logfile> (beta testing)
+=item B<--joblog> I<logfile>
 
 Logfile for executed jobs. Save a list of the executed jobs to
 I<logfile> in the following TAB separated format: sequence number,
@@ -1039,9 +1039,9 @@ of each job is saved in a file and the filename is then printed.
 
 See also: B<--results>
 
-=item B<--pipe> (beta testing)
+=item B<--pipe>
 
-=item B<--spreadstdin> (beta testing)
+=item B<--spreadstdin>
 
 Spread input to jobs on stdin (standard input). Read a block of data
 from stdin (standard input) and give one block of data as input to one
@@ -1068,7 +1068,7 @@ B<--files> is often used with B<--pipe>.
 See also: B<--recstart>, B<--recend>, B<--fifo>, B<--cat>, B<--pipepart>.
 
 
-=item B<--pipepart> (alpha testing)
+=item B<--pipepart> (beta testing)
 
 Pipe parts of a physical file. B<--pipepart> works similar to
 B<--pipe>, but is much faster. It has a few limitations:
@@ -1162,13 +1162,13 @@ exit (used by GNU B<parallel> itself to determine the line length
 on remote computers).
 
 
-=item B<--number-of-cpus> (beta testing)
+=item B<--number-of-cpus>
 
 Print the number of physical CPUs and exit (used by GNU B<parallel>
 itself to determine the number of physical CPUs on remote computers).
 
 
-=item B<--number-of-cores> (beta testing)
+=item B<--number-of-cores>
 
 Print the number of CPU cores and exit (used by GNU B<parallel> itself
 to determine the number of CPU cores on remote computers).
@@ -1180,7 +1180,7 @@ Overrides an earlier B<--keep-order> (e.g. if set in
 B<~/.parallel/config>).
 
 
-=item B<--nice> I<niceness> (beta testing)
+=item B<--nice> I<niceness>
 
 Run the command at this niceness. For simple commands you can just add
 B<nice> in front of the command. But if the command consists of more
@@ -1441,7 +1441,7 @@ B<--keep-order> will not work with B<--round-robin> as it is
 impossible to track which input block corresponds to which output.
 
 
-=item B<--rpl> 'I<tag> I<perl expression>' (beta testing)
+=item B<--rpl> 'I<tag> I<perl expression>'
 
 Use I<tag> as a replacement string for I<perl expression>. This makes
 it possible to define your own replacement strings. GNU B<parallel>'s
@@ -1616,7 +1616,7 @@ Does not run the command but quotes it. Useful for making quoted
 composed commands for GNU B<parallel>.
 
 
-=item B<--shuf> (alpha testing)
+=item B<--shuf> (beta testing)
 
 Shuffle jobs. When having multiple input sources it is hard to
 randomize jobs. --shuf will generate all jobs, and shuffle them before
@@ -1781,7 +1781,7 @@ the lines will be prepended with the sshlogin instead.
 B<--tag> is ignored when using B<-u>.
 
 
-=item B<--tagstring> I<str> (beta testing)
+=item B<--tagstring> I<str>
 
 Tag lines with a string. Each output line will be prepended with
 I<str> and TAB (\t). I<str> can contain replacement strings such as
@@ -1798,7 +1798,7 @@ different dir for the files. Setting B<--tmpdir> is equivalent to
 setting $TMPDIR.
 
 
-=item B<--tmux> (beta testing)
+=item B<--tmux>
 
 Use B<tmux> for output. Start a B<tmux> session and run each job in a
 window in that session. No other output will be produced.