sebhtml pushed to Ray (el6). "Merge branch 'el6' of ssh://pkgs.fedoraproject.org/Ray into el6 (..more)"
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>From 5a6fbcd95ed30d56349d07d8265c667942aca1c7 Mon Sep 17 00:00:00 2001
From: Till Maas <opensource at till.name>
Date: Sat, 20 Dec 2014 18:37:18 +0100
Subject: 2014-12-20: Retired because of broken deps: unresolved dependencies
for Ray-mpich2-2.3.1-3.el6.i686: mpich2 libmpichcxx.so.1.2 libmpich.so.1.2
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index b1dd56e..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-/Ray-v2.1.0.tar.bz2
-/Ray-2.3.1.tar.bz2
diff --git a/Ray.manpage.patch b/Ray.manpage.patch
deleted file mode 100644
index 35df432..0000000
--- a/Ray.manpage.patch
+++ /dev/null
@@ -1,410 +0,0 @@
---- /dev/null 2012-11-27 10:10:35.990752806 -0500
-+++ Ray.1 2012-11-29 21:48:32.447898203 -0500
-@@ -0,0 +1,407 @@
-+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.12.
-+.TH RAY "1" "November 2012" "Ray 2.1.0" "User Commands"
-+
-+.SH NAME
-+Ray - assemble genomes in parallel using the message-passing interface
-+.SH SYNOPSIS
-+ mpiexec -n NUMBER_OF_RANKS Ray -k KMERLENGTH -p l1_1.fastq l1_2.fastq -p l2_1.fastq l2_2.fastq -o test
-+
-+ mpiexec -n NUMBER_OF_RANKS Ray Ray.conf # with commands in a file
-+.SH DESCRIPTION
-+
-+ The Ray genome assembler is built on top of the RayPlatform, a generic plugin-based
-+ distributed and parallel compute engine that uses the message-passing interface
-+ for passing messages.
-+
-+ Ray targets several applications:
-+
-+ - de novo genome assembly (with Ray vanilla)
-+ - de novo meta-genome assembly (with Ray Méta)
-+ - de novo transcriptome assembly (works, but not tested a lot)
-+ - quantification of contig abundances
-+ - quantification of microbiome consortia members (with Ray Communities)
-+ - quantification of transcript expression
-+ - taxonomy profiling of samples (with Ray Communities)
-+ - gene ontology profiling of samples (with Ray Ontologies)
-+
-+.SH OPTIONS
-+
-+ -help
-+ Displays this help page.
-+
-+ -version
-+ Displays Ray version and compilation options.
-+
-+ Using a configuration file
-+
-+ Ray can be launched with
-+ mpiexec -n 16 Ray Ray.conf
-+ The configuration file can include comments (starting with #).
-+
-+ K-mer length
-+
-+ -k kmerLength
-+ Selects the length of k-mers. The default value is 21.
-+ It must be odd because reverse-complement vertices are stored together.
-+ The maximum length is defined at compilation by MAXKMERLENGTH
-+ Larger k-mers utilise more memory.
-+
-+ Inputs
-+
-+ -p leftSequenceFile rightSequenceFile [averageOuterDistance standardDeviation]
-+ Provides two files containing paired-end reads.
-+ averageOuterDistance and standardDeviation are automatically computed if not provided.
-+
-+ -i interleavedSequenceFile [averageOuterDistance standardDeviation]
-+ Provides one file containing interleaved paired-end reads.
-+ averageOuterDistance and standardDeviation are automatically computed if not provided.
-+
-+ -s sequenceFile
-+ Provides a file containing single-end reads.
-+
-+ Outputs
-+
-+ -o outputDirectory
-+ Specifies the directory for outputted files. Default is RayOutput
-+
-+ Assembly options (defaults work well)
-+
-+ -disable-recycling
-+ Disables read recycling during the assembly
-+ reads will be set free in 3 cases:
-+ 1. the distance did not match for a pair
-+ 2. the read has not met its mate
-+ 3. the library population indicates a wrong placement
-+ see Constrained traversal of repeats with paired sequences.
-+ Sébastien Boisvert, Élénie Godzaridis, François Laviolette & Jacques Corbeil.
-+ First Annual RECOMB Satellite Workshop on Massively Parallel Sequencing, March 26-27 2011, Vancouver, BC, Canada.
-+
-+ -disable-scaffolder
-+ Disables the scaffolder.
-+
-+ -minimum-contig-length minimumContigLength
-+ Changes the minimum contig length, default is 100 nucleotides
-+
-+ -color-space
-+ Runs in color-space
-+ Needs csfasta files. Activated automatically if csfasta files are provided.
-+
-+ -use-maximum-seed-coverage maximumSeedCoverageDepth
-+ Ignores any seed with a coverage depth above this threshold.
-+ The default is 4294967295.
-+
-+ -use-minimum-seed-coverage minimumSeedCoverageDepth
-+ Sets the minimum seed coverage depth.
-+ Any path with a coverage depth lower than this will be discarded. The default is 0.
-+
-+ Distributed storage engine (all these values are for each MPI rank)
-+
-+ -bloom-filter-bits bits
-+ Sets the number of bits for the Bloom filter
-+ Default is 268435456 bits, 0 bits disables the Bloom filter.
-+
-+ -hash-table-buckets buckets
-+ Sets the initial number of buckets. Must be a power of 2 !
-+ Default value: 268435456
-+
-+ -hash-table-buckets-per-group buckets
-+ Sets the number of buckets per group for sparse storage
-+ Default value: 64, Must be between >=1 and <= 64
-+
-+ -hash-table-load-factor-threshold threshold
-+ Sets the load factor threshold for real-time resizing
-+ Default value: 0.75, must be >= 0.5 and < 1
-+
-+ -hash-table-verbosity
-+ Activates verbosity for the distributed storage engine
-+
-+ Biological abundances
-+
-+ -search searchDirectory
-+ Provides a directory containing fasta files to be searched in the de Bruijn graph.
-+ Biological abundances will be written to RayOutput/BiologicalAbundances
-+ See Documentation/BiologicalAbundances.txt
-+
-+ -one-color-per-file
-+ Sets one color per file instead of one per sequence.
-+ By default, each sequence in each file has a different color.
-+ For files with large numbers of sequences, using one single color per file may be more efficient.
-+
-+ Taxonomic profiling with colored de Bruijn graphs
-+
-+ -with-taxonomy Genome-to-Taxon.tsv TreeOfLife-Edges.tsv Taxon-Names.tsv
-+ Provides a taxonomy.
-+ Computes and writes detailed taxonomic profiles.
-+ See Documentation/Taxonomy.txt for details.
-+
-+ -gene-ontology OntologyTerms.txt Annotations.txt
-+ Provides an ontology and annotations.
-+ OntologyTerms.txt is fetched from http://geneontology.org
-+ Annotations.txt is a 2-column file (EMBL_CDS handle & gene ontology identifier)
-+ See Documentation/GeneOntology.txt
-+ Other outputs
-+
-+ -enable-neighbourhoods
-+ Computes contig neighborhoods in the de Bruijn graph
-+ Output file: RayOutput/NeighbourhoodRelations.txt
-+
-+ -amos
-+ Writes the AMOS file called RayOutput/AMOS.afg
-+ An AMOS file contains read positions on contigs.
-+ Can be opened with software with graphical user interface.
-+
-+ -write-kmers
-+ Writes k-mer graph to RayOutput/kmers.txt
-+ The resulting file is not utilised by Ray.
-+ The resulting file is very large.
-+
-+ -write-read-markers
-+ Writes read markers to disk.
-+
-+ -write-seeds
-+ Writes seed DNA sequences to RayOutput/Rank<rank>.RaySeeds.fasta
-+
-+ -write-extensions
-+ Writes extension DNA sequences to RayOutput/Rank<rank>.RayExtensions.fasta
-+
-+ -write-contig-paths
-+ Writes contig paths with coverage values
-+ to RayOutput/Rank<rank>.RayContigPaths.txt
-+
-+ -write-marker-summary
-+ Writes marker statistics.
-+
-+ Memory usage
-+
-+ -show-memory-usage
-+ Shows memory usage. Data is fetched from /proc on GNU/Linux
-+ Needs __linux__
-+
-+ -show-memory-allocations
-+ Shows memory allocation events
-+
-+ Algorithm verbosity
-+
-+ -show-extension-choice
-+ Shows the choice made (with other choices) during the extension.
-+
-+ -show-ending-context
-+ Shows the ending context of each extension.
-+ Shows the children of the vertex where extension was too difficult.
-+
-+ -show-distance-summary
-+ Shows summary of outer distances used for an extension path.
-+
-+ -show-consensus
-+ Shows the consensus when a choice is done.
-+
-+ Checkpointing
-+
-+ -write-checkpoints checkpointDirectory
-+ Write checkpoint files
-+
-+ -read-checkpoints checkpointDirectory
-+ Read checkpoint files
-+
-+ -read-write-checkpoints checkpointDirectory
-+ Read and write checkpoint files
-+
-+ Message routing for large number of cores
-+
-+ -route-messages
-+ Enables the Ray message router. Disabled by default.
-+ Messages will be routed accordingly so that any rank can communicate directly with only a few others.
-+ Without -route-messages, any rank can communicate directly with any other rank.
-+ Files generated: Routing/Connections.txt, Routing/Routes.txt and Routing/RelayEvents.txt
-+ and Routing/Summary.txt
-+
-+ -connection-type type
-+ Sets the connection type for routes.
-+ Accepted values are debruijn, hypercube, polytope, group, random, kautz and complete. Default is debruijn.
-+ debruijn: a full de Bruijn graph a given alphabet and diameter
-+ hypercube: a hypercube, alphabet is {0,1} and the vertices is a power of 2
-+ polytope: a convex regular polytope, alphabet is {0,1,...,B-1} and the vertices is a power of B
-+ group: silly model where one representative per group can communicate with outsiders
-+ random: Erdős-Rényi model
-+ kautz: a full de Kautz graph, which is a subgraph of a de Bruijn graph
-+ complete: a full graph with all the possible connections
-+ With the type debruijn, the number of ranks must be a power of something.
-+ Examples: 256 = 16*16, 512=8*8*8, 49=7*7, and so on.
-+ Otherwise, don't use debruijn routing but use another one
-+ With the type kautz, the number of ranks n must be n=(k+1)*k^(d-1) for some k and d
-+
-+ -routing-graph-degree degree
-+ Specifies the outgoing degree for the routing graph.
-+ See Documentation/Routing.txt
-+
-+ Hardware testing
-+
-+ -test-network-only
-+ Tests the network and returns.
-+
-+ -write-network-test-raw-data
-+ Writes one additional file per rank detailing the network test.
-+
-+ -exchanges NumberOfExchanges
-+ Sets the number of exchanges
-+
-+ -disable-network-test
-+ Skips the network test.
-+
-+ Debugging
-+
-+ -verify-message-integrity
-+ Checks message data reliability for any non-empty message.
-+ add '-D CONFIG_SSE_4_2' in the Makefile to use hardware instruction (SSE 4.2)
-+
-+ -run-profiler
-+ Runs the profiler as the code runs. By default, only show granularity warnings.
-+ Running the profiler increases running times.
-+
-+ -with-profiler-details
-+ Shows number of messages sent and received in each methods during in each time slices (epochs). Needs -run-profiler.
-+
-+ -show-communication-events
-+ Shows all messages sent and received.
-+
-+ -show-read-placement
-+ Shows read placement in the graph during the extension.
-+
-+ -debug-bubbles
-+ Debugs bubble code.
-+ Bubbles can be due to heterozygous sites or sequencing errors or other (unknown) events
-+
-+ -debug-seeds
-+ Debugs seed code.
-+ Seeds are paths in the graph that are likely unique.
-+
-+ -debug-fusions
-+ Debugs fusion code.
-+
-+ -debug-scaffolder
-+ Debug the scaffolder.
-+.SH FILES
-+
-+ Input files
-+
-+ Note: file format is determined with file extension.
-+
-+ .fasta
-+ .fasta.gz (needs HAVE_LIBZ=y at compilation)
-+ .fasta.bz2 (needs HAVE_LIBBZ2=y at compilation)
-+ .fastq
-+ .fastq.gz (needs HAVE_LIBZ=y at compilation)
-+ .fastq.bz2 (needs HAVE_LIBBZ2=y at compilation)
-+ .sff (paired reads must be extracted manually)
-+ .csfasta (color-space reads)
-+
-+ Outputted files
-+
-+ Scaffolds
-+
-+ RayOutput/Scaffolds.fasta
-+ The scaffold sequences in FASTA format
-+ RayOutput/ScaffoldComponents.txt
-+ The components of each scaffold
-+ RayOutput/ScaffoldLengths.txt
-+ The length of each scaffold
-+ RayOutput/ScaffoldLinks.txt
-+ Scaffold links
-+
-+ Contigs
-+
-+ RayOutput/Contigs.fasta
-+ Contiguous sequences in FASTA format
-+ RayOutput/ContigLengths.txt
-+ The lengths of contiguous sequences
-+
-+ Summary
-+
-+ RayOutput/OutputNumbers.txt
-+ Overall numbers for the assembly
-+
-+ de Bruijn graph
-+
-+ RayOutput/CoverageDistribution.txt
-+ The distribution of coverage values
-+ RayOutput/CoverageDistributionAnalysis.txt
-+ Analysis of the coverage distribution
-+ RayOutput/degreeDistribution.txt
-+ Distribution of ingoing and outgoing degrees
-+ RayOutput/kmers.txt
-+ k-mer graph, required option: -write-kmers
-+ The resulting file is not utilised by Ray.
-+ The resulting file is very large.
-+
-+ Assembly steps
-+
-+ RayOutput/SeedLengthDistribution.txt
-+ Distribution of seed length
-+ RayOutput/Rank<rank>.OptimalReadMarkers.txt
-+ Read markers.
-+ RayOutput/Rank<rank>.RaySeeds.fasta
-+ Seed DNA sequences, required option: -write-seeds
-+ RayOutput/Rank<rank>.RayExtensions.fasta
-+ Extension DNA sequences, required option: -write-extensions
-+ RayOutput/Rank<rank>.RayContigPaths.txt
-+ Contig paths with coverage values, required option: -write-contig-paths
-+
-+ Paired reads
-+
-+ RayOutput/LibraryStatistics.txt
-+ Estimation of outer distances for paired reads
-+ RayOutput/Library<LibraryNumber>.txt
-+ Frequencies for observed outer distances (insert size + read lengths)
-+
-+ Partition
-+
-+ RayOutput/NumberOfSequences.txt
-+ Number of reads in each file
-+ RayOutput/SequencePartition.txt
-+ Sequence partition
-+
-+ Ray software
-+
-+ RayOutput/RayVersion.txt
-+ The version of Ray
-+ RayOutput/RayCommand.txt
-+ The exact same command provided
-+
-+ AMOS
-+
-+ RayOutput/AMOS.afg
-+ Assembly representation in AMOS format, required option: -amos
-+
-+ Communication
-+
-+ RayOutput/MessagePassingInterface.txt
-+ Number of messages sent
-+ RayOutput/NetworkTest.txt
-+ Latencies in microseconds
-+ RayOutput/Rank<rank>NetworkTestData.txt
-+ Network test raw data
-+.SH DOCUMENTATION
-+
-+ - mpiexec -n 1 Ray -help|less (always up-to-date)
-+ - This help page (always up-to-date)
-+ - The directory Documentation/
-+ - Manual (Portable Document Format): InstructionManual.tex (in Documentation)
-+ - Mailing list archives: http://sourceforge.net/mailarchive/forum.php?forum_name=denovoassembler-users
-+.SH AUTHOR
-+ Written by Sébastien Boisvert.
-+.SH "REPORTING BUGS"
-+ Report bugs to denovoassembler-users at lists.sourceforge.net
-+ Home page: <http://denovoassembler.sourceforge.net/>
-+.SH COPYRIGHT
-+ 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, version 3 of the License.
-+
-+ 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 have received a copy of the GNU General Public License
-+ along with this program (see LICENSE).
-+
diff --git a/Ray.spec b/Ray.spec
deleted file mode 100644
index af1f763..0000000
--- a/Ray.spec
+++ /dev/null
@@ -1,264 +0,0 @@
-Name: Ray
-Version: 2.3.1
-Release: 6%{?dist}
-Summary: Parallel genome assemblies for parallel DNA sequencing
-
-Group: Applications/Engineering
-License: GPLv3
-URL: http://denovoassembler.sourceforge.net/
-Source0: http://downloads.sourceforge.net/denovoassembler/%{name}-%{version}.tar.bz2
-Patch0: Ray.manpage.patch
-
-%global useMpich 1
-%ifarch ppc64
-%if 0%{?rhel}==5 || 0%{?rhel} == 6
-%global useMpich 0
-%endif
-%endif
-
-%define mpichName mpich
-
-# el5 still uses the old name MPICH2
-%if 0%{?rhel}==5
- %define mpichName mpich2
-%endif
-
-BuildRequires: openmpi-devel, bzip2-devel, zlib-devel
-
-%if %useMpich
-BuildRequires: %{mpichName}-devel
-%endif
-
-%description
-%{name} is a parallel software that computes de novo genome assemblies with
-next-generation sequencing data.
-%{name} is written in C++ and can run in parallel on numerous interconnected
-computers using the message-passing interface (MPI) standard.
-Included:
- - %{name} de novo assembly of single genomes
- - %{name} Méta de novo assembly of metagenomes
- - %{name} Communities microbe abundance + taxonomic profiling
- - %{name} Ontologies gene ontology profiling
-
-%package common
-Summary: Parallel genome assemblies for parallel DNA sequencing
-Group: Applications/Engineering
-
-%description common
-%{name} is a parallel software that computes de novo genome assemblies with
-next-generation sequencing data.
-%{name} is written in C++ and can run in parallel on numerous interconnected
-computers using the message-passing interface (MPI) standard.
-This sub-package contains common files for Ray.
-
-%package openmpi
-Summary: %{name} package for Open-MPI
-Group: Applications/Engineering
-Requires: openmpi, %{name}-common
-
-%description openmpi
-%{name} is a parallel software that computes de novo genome assemblies with
-next-generation sequencing data.
-%{name} is written in C++ and can run in parallel on numerous interconnected
-computers using the message-passing interface (MPI) standard.
-This sub-package enables parallel computation using openmpi.
-
-
-%if %useMpich
-%package %{mpichName}
-Summary: %{name} package for MPICH
-Group: Applications/Engineering
-Requires: %{mpichName}, %{name}-common
-%if %{mpichName} == "mpich"
-Obsoletes: %{name}-mpich2 < 2.3.1-4
-Conflicts: %{name}-mpich2 < 2.3.1-4
-%endif
-
-%description %{mpichName}
-%{name} is a parallel software that computes de novo genome assemblies with
-next-generation sequencing data.
-%{name} is written in C++ and can run in parallel on numerous interconnected
-computers using the message-passing interface (MPI) standard.
-This sub-package enables parallel computation using mpich.
-%endif
-
-%package doc
-Summary: Documentation files
-Group: Documentation
-Requires: %{name}-common
-
-%description doc
-%{name} is a parallel software that computes de novo genome assemblies with
-next-generation sequencing data.
-%{name} is written in C++ and can run in parallel on numerous interconnected
-computers using the message-passing interface (MPI) standard.
-This sub-package includes documentation files.
-
-%package extra
-Summary: Scripts and XSL sheets for post-processing
-Group: Applications/Engineering
-Requires: python, R, %{name}-common
-
-%description extra
-%{name} is a parallel software that computes de novo genome assemblies with
-next-generation sequencing data.
-%{name} is written in C++ and can run in parallel on numerous interconnected
-computers using the message-passing interface (MPI) standard.
-This sub-package contains scripts and XSL sheets for post-processing.
-
-%prep
-%setup -q -n %{name}-%{version}
-%patch0
-
-%build
-CXXFLAGS="%{optflags}"
-
-%{_openmpi_load}
-make CXXFLAGS="$CXXFLAGS" HAVE_LIBBZ2=y HAVE_LIBZ=y
-cp %{name} %{name}$MPI_SUFFIX
-
-cp README.md README
-cp %{name}Platform/README.md README.%{name}Platform
-cp %{name}Platform/AUTHORS AUTHORS.%{name}Platform
-
-make clean
-%{_openmpi_unload}
-
-%if %useMpich
- # %{_%{mpichName}_load} does not work
- %if %mpichName == "mpich"
- %{_mpich_load}
- %else
- %{_mpich2_load}
- %endif
-make CXXFLAGS="$CXXFLAGS" HAVE_LIBBZ2=y HAVE_LIBZ=y
-cp %{name} %{name}$MPI_SUFFIX
-make clean
- %if %mpichName == "mpich"
- %{_mpich_unload}
- %else
- %{_mpich2_unload}
- %endif
-%endif
-
-%install
-rm -rf %{buildroot}
-
-# Ray-common
-mkdir -p %{buildroot}%{_mandir}/man1
-install -m 0644 %{name}.1 %{buildroot}%{_mandir}/man1/%{name}.1
-
-# Ray-openmpi
-%{_openmpi_load}
-mkdir -p %{buildroot}$MPI_BIN
-install -m 0755 %{name}$MPI_SUFFIX %{buildroot}$MPI_BIN
-%{_openmpi_unload}
-
-%if %useMpich
-# Ray-mpich
- %if %mpichName == "mpich"
- %{_mpich_load}
- %else
- %{_mpich2_load}
- %endif
-mkdir -p %{buildroot}$MPI_BIN
-install -m 0755 %{name}$MPI_SUFFIX %{buildroot}$MPI_BIN
- %if %mpichName == "mpich"
- %{_mpich_unload}
- %else
- %{_mpich2_unload}
- %endif
-%endif
-
-# Ray-doc
-mkdir doc
-cp -ar %{name}Platform/Documentation/ doc/%{name}Platform
-chmod 644 doc/%{name}Platform/*
-chmod 644 Documentation/*
-
-# Ray-extra
-mkdir -p %{buildroot}%{_datadir}/%{name}
-cp -r scripts %{buildroot}%{_datadir}/%{name}
-chmod 0755 %{buildroot}%{_datadir}/%{name}/scripts
-
-%clean
-rm -rf %{buildroot}
-
-%files common
-%doc MANUAL_PAGE.txt gpl-3.0.txt LICENSE.txt
-%doc %{name}Platform/lgpl-3.0.txt
-%doc AUTHORS AUTHORS.%{name}Platform
-%doc README README.%{name}Platform
-%{_mandir}/man1/%{name}.1*
-
-%files openmpi
-%{_libdir}/openmpi/bin/%{name}*
-
-%if %useMpich
-%files %{mpichName}
-%{_libdir}/%{mpichName}/bin/%{name}*
-%endif
-
-%files doc
-%doc Documentation/*
-%doc doc/%{name}Platform/
-
-%files extra
-%{_datadir}/%{name}/
-
-%changelog
-* Fri Aug 15 2014 Fedora Release Engineering <rel-eng at lists.fedoraproject.org> - 2.3.1-5
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
-
-* Fri Jun 06 2014 Fedora Release Engineering <rel-eng at lists.fedoraproject.org> - 2.3.1-4
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
-
-* Sun Mar 2 2014 Sébastien Boisvert <sebastien.boisvert.3 at ulaval.ca> - 2.3.2-3
-- use correct macro name to load/unload mpich2
-
-* Mon Feb 24 2014 Sébastien Boisvert <sebastien.boisvert.3 at ulaval.ca> - 2.3.1-2
-- add a variable for mpich package name (mpich or mpich2)
-
-* Mon Feb 24 2014 Sébastien Boisvert <sebastien.boisvert.3 at ulaval.ca> - 2.3.1-1
-- Fix days of week in spec changelog (rpmlint warning)
-- Update version with upstream.
-
-* Wed Sep 04 2013 Sébastien Boisvert <sebastien.boisvert.3 at ulaval.ca> - 2.1.0-8
-- Change dependency name from mpich2 to mpich
-
-* Fri Aug 02 2013 Fedora Release Engineering <rel-eng at lists.fedoraproject.org> - 2.1.0-7
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
-
-* Mon Jul 15 2013 Sébastien Boisvert <sebastien.boisvert.3 at ulaval.ca> - 2.1.0-6
-- Skip mpich2 on el5 and el6 for ppc64
-
-* Thu Nov 29 2012 Sébastien Boisvert <sebastien.boisvert.3 at ulaval.ca> - 2.1.0-5
-- Added a patch for the man page
-
-* Mon Nov 5 2012 Sébastien Boisvert <sebastien.boisvert.3 at ulaval.ca> - 2.1.0-4
-- The man page encoding is en_US.UTF-8
-- Added more specific descriptions
-
-* Sun Nov 4 2012 Sébastien Boisvert <sebastien.boisvert.3 at ulaval.ca> - 2.1.0-3
-- Changed the package name from ray to Ray
-- Renamed README.md to README
-- Added AUTHORS, README.RayPlatform, AUTHORS.RayPlatform
-
-* Sun Nov 4 2012 Sébastien Boisvert <sebastien.boisvert.3 at ulaval.ca> - 2.1.0-2
-- Added build dependency help2man
-- Added OMPI_MCA_orte_rsh_agent to pass mock builds
-
-* Sat Nov 3 2012 Sébastien Boisvert <sebastien.boisvert.3 at ulaval.ca> - 2.1.0-1
-
-- The Spec file was (informally) reviewed by Jussi Lehtola
-- Moved sub-package declarations to the top
-- Added sub-packages common, openmpi, mpich2
-- Removed useless '/' after buildroot
-- Fixed the packaging of Documentation
-- Removed symbols that are not U.S. American English from man page
-- Added Fedora compilation flags (optflags)
-- The Spec file was (informally) reviewed a second time by Jussi Lehtola
-- CXXFLAGS was shortened
-- Replacement of non-ASCII symbols is more compact with sed
-- ray-extra now ships _datadir/ray/ instead of _datadir/ray/scripts/.
-- This is the initial Ray package for Fedora
diff --git a/dead.package b/dead.package
new file mode 100644
index 0000000..2f17425
--- /dev/null
+++ b/dead.package
@@ -0,0 +1,6 @@
+2014-12-20: Retired because of broken deps:
+unresolved dependencies for Ray-mpich2-2.3.1-3.el6.i686:
+mpich2
+libmpichcxx.so.1.2
+libmpich.so.1.2
+
diff --git a/sources b/sources
deleted file mode 100644
index d41ecb1..0000000
--- a/sources
+++ /dev/null
@@ -1 +0,0 @@
-82f693c4db60af4328263c9279701009 Ray-2.3.1.tar.bz2
--
cgit v0.10.2
http://pkgs.fedoraproject.org/cgit/Ray.git/commit/?h=el6&id=e7622771e4e419386ab6008172e0f4507618898a
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