Released as 20160522 ('TTIPleaks')

NEWS

@@ -1,3 +1,96 @@
+20160522
+
+* niceload --net pauses the program if the internet connection is overloaded.
+
+* Vote for GNU Parallel's community ad on https://meta.askubuntu.com/questions/14925/community-promotion-ads-2016/15046#15046
+
+* Updated speed comparison between versions https://www.gnu.org/software/parallel/process-time-j2-1700MHz-3000-1000.pdf
+
+* GNU Parallel was cited in: Improving computation efficiency by parallel programming http://www.irbis-nbuv.gov.ua/cgi-bin/irbis_nbuv/cgiirbis_64.exe?C21COM=2&I21DBN=UJRN&P21DBN=UJRN&IMAGE_FILE_DOWNLOAD=1&Image_file_name=PDF/ape_2013_3_44.pdf
+
+* GNU Parallel was cited in: A supernova feedback implementation for the astrophysical simulation software Arepo https://arxiv.org/abs/1604.06071
+
+* GNU Parallel was cited in: Lorenz-Mie theory for 2D scattering and resonance calculations https://arxiv.org/pdf/1505.07691v2.pdf
+
+* GNU Parallel was cited in: Host-pathogen co-evolution and the emergence of broadly neutralizing antibodies in chronic infections https://arxiv.org/abs/1512.06296
+
+* GNU Parallel was cited in: Pacific People, Metabolic Disease and Evolutionary Processes: a mitochondrial DNA study https://otago.ourarchive.ac.nz/handle/10523/6340
+
+* GNU Parallel was cited in: The effect of domain modeling on efficiency of planning: Lessons from the Nomystery domain http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=7407131
+
+* GNU Parallel was cited in: Oops, my tests broke the build: An analysis of Travis CI buildswith GitHub https://peerj.com/preprints/1984/
+
+* GNU Parallel was cited in: Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution http://www.g3journal.org/content/5/5/719.full.pdf+html
+
+* GNU Parallel was cited in: An Empirical Comparison of Neural Architectures for Reinforcement Learning in Partially Observable Environments http://biorxiv.org/content/biorxiv/early/2016/03/24/022707.full.pdf
+
+* GNU Parallel was cited in: Functional enrichments of disease variants across thousands of independent loci in eight diseases http://biorxiv.org/content/early/2016/04/11/048066.abstract
+
+* GNU Parallel was cited in: PleaseTM: Enabling Transaction Conflict Management in Requester-wins Hardware Transactional Memory http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7446072
+
+* GNU Parallel was cited in: EASE-MM: Sequence-Based Prediction of Mutation-Induced Stability Changes with Feature-Based Multiple Models http://www.sciencedirect.com/science/article/pii/S0022283616000310
+
+* GNU Parallel was cited in: A new orthology assessment method for phylogenomic data: Unrooted Phylogenetic Orthology http://mbe.oxfordjournals.org/content/early/2016/04/06/molbev.msw069.short https://github.com/ballesterus/UPhO
+
+* GNU Parallel was cited in: Distinctive Interest Point Selection for Efficient Near-duplicate Image Retrieval http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7459172
+
+* GNU Parallel was cited in: The Evolution of C Programming Practices: A Study of the Unix Operating System 1973–2015 https://dl.acm.org/citation.cfm?id=2884799 (It has the cutest thumbnail graphs I have ever seen scattered all over the text)
+
+* GNU Parallel was cited in: StrAuto: Automation and Parallelization of STRUCTURE Analysis http://vchhatre.w3.uvm.edu/download/strauto/strauto_doc.pdf
+
+* GNU Parallel was cited in: Data processing pipeline for serial femtosecond crystallography at SACLA http://journals.iucr.org/j/issues/2016/03/00/zw5001/index.html
+
+* GNU Parallel was cited in: Reconstruction of Fine-Scale Auroral Dynamics http://arxiv.org/pdf/1512.01460.pdf
+
+* GNU Parallel was cited in: The Outer Solar System Origins Survey: I. Design and First-Quarter Discoveries http://arxiv.org/pdf/1511.02895.pdf
+
+* GNU Parallel was cited in: Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1004381.PDF
+
+* GNU Parallel was cited in: Genomic legacy of the African cheetah, Acinonyx jubatus https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676127/pdf/13059_2015_Article_837.pdf
+
+* GNU Parallel was cited in: Don’t Forget to Lock the Back Door! A Characterization of IPv6 Network Security Policy http://benign-research-probe2.eecs.umich.edu/ndss16_ipv6_final.pdf
+
+* GNU Parallel was cited in: Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics http://journals.plos.org/plosone/article/asset?id=10.1371%2Fjournal.pone.0147221.PDF
+
+* GNU Parallel was cited in: Stride Search: a general algorithm for storm detection in high-resolution climate data http://www.geosci-model-dev-discuss.net/8/7727/2015/gmdd-8-7727-2015.pdf
+
+* GNU Parallel was cited in: How attention influences perceptual decision making: Single-trial EEG correlates of drift-diffusion model parameters http://www.cidlab.com/prints/nunez2016attention.pdf
+
+* GNU Parallel was cited in: Telomere And Proximal Sequence Analysis Using High-Throughput Sequencing Reads http://repository.upenn.edu/edissertations/1460/
+
+* GNU Parallel was cited in: AT-GIS: Highly Parallel Spatial Query Processing with Associative Transducers http://lsds.doc.ic.ac.uk/sites/default/files/ATGIS-SIGMOD16.pdf
+
+* GNU Parallel was cited in: PVAIR: Partial Variable Assignment InterpolatoR http://verify.inf.usi.ch/sites/default/files/main-2.pdf
+
+* GNU Parallel was cited in: Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life http://opus.bath.ac.uk/43955/ 
+
+* GNU Parallel was cited in: Shannon: An Information-Optimal de NovoRNA-Seq Assembler http://biorxiv.org/content/biorxiv/early/2016/02/09/039230.full.pdf
+
+* GNU Parallel was cited in: Adaptive Measure-Theoretic Parameter Estimation for Coastal Ocean Modeling https://repositories.lib.utexas.edu/handle/2152/32435
+
+* GNU Parallel was cited in: Computational Design of DNA-Binding Proteins http://link.springer.com/protocol/10.1007/978-1-4939-3569-7_16
+
+* GNU Parallel was cited in: Reference genotype and exome data from an Australian Aboriginal population for health-based research http://www.nature.com/articles/sdata201623
+
+* GNU Parallel was cited in: Computational Design of DNA-Binding Proteins http://link.springer.com/protocol/10.1007/978-1-4939-3569-7_16
+
+* GNU Parallel was cited in: Do aye-ayes echolocate? http://biorxiv.org/content/biorxiv/early/2016/04/11/048165.full.pdf
+
+* GNU Parallel was cited in: Functional enrichments of disease variants across thousands of independent loci in eight diseases http://biorxiv.org/content/biorxiv/early/2016/04/11/048066.full.pdf
+
+* GNU Parallel was cited in: From genomes to phenotypes: Traitar, the microbial trait analyzer http://biorxiv.org/content/biorxiv/early/2016/03/12/043315.full.pdf
+
+* GNU Parallel was mentioned in: Fast Playback Framework for Analysis of Ground-Based Doppler Radar Observations Using MapReduce Technology http://journals.ametsoc.org/doi/pdf/10.1175/JTECH-D-15-0118.1
+
+* NCBI blast tutorial https://github.com/enormandeau/ncbi_blast_tutorial
+
+* Distributed Preservation Made Simple https://blog.archive.org/2016/02/26/distributed-preservation-made-simple/
+
+* Parallel Jobs in Luigi http://rjbaxley.com/posts/2016/03/13/parallel_jobs_in_luigi.html
+
+* Bug fixes and man page updates.
+
+
 20160422
 
 * :::+ and ::::+ work like ::: and :::: but links this input source to

README

@@ -40,9 +40,9 @@ document.
 
 Full installation of GNU Parallel is as simple as:
 
-    wget http://ftpmirror.gnu.org/parallel/parallel-20160422.tar.bz2
+    wget http://ftpmirror.gnu.org/parallel/parallel-20160522.tar.bz2
-    bzip2 -dc parallel-20160422.tar.bz2 | tar xvf -
+    bzip2 -dc parallel-20160522.tar.bz2 | tar xvf -
-    cd parallel-20160422
+    cd parallel-20160522
     ./configure && make && sudo 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-20160422.tar.bz2
+    wget http://ftpmirror.gnu.org/parallel/parallel-20160522.tar.bz2
-    bzip2 -dc parallel-20160422.tar.bz2 | tar xvf -
+    bzip2 -dc parallel-20160522.tar.bz2 | tar xvf -
-    cd parallel-20160422
+    cd parallel-20160522
     ./configure --prefix=$HOME && make && make install
 
 Or if your system lacks 'make' you can simply copy src/parallel

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for parallel 20160422.
+# Generated by GNU Autoconf 2.69 for parallel 20160522.
 #
 # Report bugs to <bug-parallel@gnu.org>.
 #
@@ -579,8 +579,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='parallel'
 PACKAGE_TARNAME='parallel'
-PACKAGE_VERSION='20160422'
+PACKAGE_VERSION='20160522'
-PACKAGE_STRING='parallel 20160422'
+PACKAGE_STRING='parallel 20160522'
 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 20160422 to adapt to many kinds of systems.
+\`configure' configures parallel 20160522 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 20160422:";;
+     short | recursive ) echo "Configuration of parallel 20160522:";;
    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 20160422
+parallel configure 20160522
 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 20160422, which was
+It was created by parallel $as_me 20160522, 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='20160422'
+ VERSION='20160522'
 
 
 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 20160422, which was
+This file was extended by parallel $as_me 20160522, 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 20160422
+parallel config.status 20160522
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -1,4 +1,4 @@
-AC_INIT([parallel], [20160422], [bug-parallel@gnu.org])
+AC_INIT([parallel], [20160522], [bug-parallel@gnu.org])
 AM_INIT_AUTOMAKE([-Wall -Werror foreign])
 AC_CONFIG_HEADERS([config.h])
 AC_CONFIG_FILES([

packager/obs/home:tange/parallel/parallel.spec

@@ -1,6 +1,6 @@
 Summary:	Shell tool for executing jobs in parallel
 Name: 		parallel
-Version: 	20160422
+Version: 	20160522
 Release: 	1.1
 License: 	GPL
 Group: 		Productivity/File utilities

src/niceload

@@ -24,7 +24,7 @@
 use strict;
 use Getopt::Long;
 $Global::progname="niceload";
-$Global::version = 20160423;
+$Global::version = 20160522;
 Getopt::Long::Configure("bundling","require_order");
 get_options_from_array(\@ARGV) || die_usage();
 if($opt::version) {

src/parallel

@@ -1183,7 +1183,7 @@ sub check_invalid_option_combinations {
 
 sub init_globals {
     # Defaults:
-    $Global::version = 20160423;
+    $Global::version = 20160522;
     $Global::progname = 'parallel';
     $Global::infinity = 2**31;
     $Global::debug = 0;

src/sql

@@ -566,7 +566,7 @@ $Global::Initfile && unlink $Global::Initfile;
 exit ($err);
 
 sub parse_options {
-    $Global::version = 20160423;
+    $Global::version = 20160522;
     $Global::progname = 'sql';
 
     # This must be done first as this may exec myself