[med-svn] [salmon] 02/05: use more system libs, update copyrights
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sat Jan 30 16:18:45 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository salmon.
commit 73d7ff1175c9dbfaba580b04db8a335d901e858c
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Sat Jan 30 07:55:16 2016 -0800
use more system libs, update copyrights
---
debian/TODO | 1 +
debian/copyright | 49 +++++++++++++
debian/patches/series | 2 +-
debian/patches/use-system-cppformat | 121 +++++++++++++++++++++++++++++++
debian/patches/use-system-pkg-config-tbb | 22 ++++++
5 files changed, 194 insertions(+), 1 deletion(-)
diff --git a/debian/TODO b/debian/TODO
new file mode 100644
index 0000000..c75fb17
--- /dev/null
+++ b/debian/TODO
@@ -0,0 +1 @@
+migrate from customized/old include/format.h to libcppformat2-dev
diff --git a/debian/copyright b/debian/copyright
index d73ccaf..90a906b 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -6,15 +6,64 @@ Files-Excluded: doc/build/*
src/SalmonQuantify.cpp.bak
include/eigen3
include/obsolete
+ cmake/Modules/FindTBB.cmake
Files: *
Copyright: © 2015 The Salmon Authors
+ (c) 2013, 2014 Rob Patro <robp at cs.cmu.edu>
+ 2013 Adam Roberts
License: GPL-3+
Files: debian/*
Copyright: © 2015 Michael R. Crusoe <crusoe at ucdavis.edu>
License: GPL-3+
+Files: cmake/Modules/FindJemalloc.cmake
+ include/VersionChecker.hpp
+Copyright: (c) 2014 Thomas Heller
+ (c) 2007-2012 Hartmut Kaiser
+ (c) 2010-2011 Matt Anderson
+ (c) 2011 Bryce Lelbach
+ (c) 2003-2012 Christopher M. Kohlhoff <chris at kohlhoff.com>
+License: BSL-1.0
+
+Files: include/btree*.h
+Copyright: 2013 Google Inc.
+License: apache-2.0
+
+Files: include/ezETAProgressBar.hpp
+ include/fastapprox.h
+ include/format.h
+Copyright: 2011, 2012 Remik Ziemlinski
+ 2011, 2012 Paul Mineiro <paul at mineiro.com>
+ (c) 2012 - 2015, Victor Zverovich
+License: Expat
+
+Files: include/atomicops.h
+ include/concurrentqueue.h
+Copyright: ©2013 Cameron Desrochers
+License: BSD-cameron-descrochers
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+ .
+ Redistributions in binary form must reproduce the above copyright notice, this
+ list of conditions and the following disclaimer in the documentation and/or
+ other materials provided with the distribution.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
License: GPL-3+
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
diff --git a/debian/patches/series b/debian/patches/series
index e08a900..36557a7 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,4 +4,4 @@ cmake-adj
drop-mathjax
cmake-typo-fixes
disable-version-check
-system-eigen3
+use-system-pkg-config-tbb
diff --git a/debian/patches/use-system-cppformat b/debian/patches/use-system-cppformat
new file mode 100644
index 0000000..4101785
--- /dev/null
+++ b/debian/patches/use-system-cppformat
@@ -0,0 +1,121 @@
+--- salmon.orig/include/ReadPair.hpp
++++ salmon/include/ReadPair.hpp
+@@ -6,7 +6,7 @@
+ #include "LibraryFormat.hpp"
+ #include "SalmonUtils.hpp"
+
+-#include "format.h"
++#include <cppformat/format.h>
+
+ struct ReadPair {
+ bam_seq_t* read1 = nullptr;
+--- salmon.orig/include/SalmonUtils.hpp
++++ salmon/include/SalmonUtils.hpp
+@@ -18,7 +18,7 @@
+ #include <boost/filesystem.hpp>
+ #include <boost/program_options.hpp>
+
+-#include "format.h"
++#include <cppformat/format.h>
+
+ #include "SalmonOpts.hpp"
+ #include "SalmonMath.hpp"
+--- salmon.orig/include/Sampler.hpp
++++ salmon/include/Sampler.hpp
+@@ -9,7 +9,7 @@
+ }
+
+ // for cpp-format
+-#include "format.h"
++#include <cppformat/format.h>
+
+ #include "spdlog/spdlog.h"
+
+--- salmon.orig/include/posix.h
++++ salmon/include/posix.h
+@@ -39,7 +39,7 @@
+
+ #include <cstddef>
+
+-#include "format.h"
++#include <cppformat/format.h>
+
+ #ifdef FMT_INCLUDE_POSIX_TEST
+ # include "test/posix-test.h"
+--- salmon.orig/src/BuildSalmonIndex.cpp
++++ salmon/src/BuildSalmonIndex.cpp
+@@ -43,7 +43,7 @@
+ #include "Transcript.hpp"
+ #include "SalmonUtils.hpp"
+ #include "GenomicFeature.hpp"
+-#include "format.h"
++#include <cppformat/format.h>
+ #include "spdlog/spdlog.h"
+
+ using my_mer = jellyfish::mer_dna_ns::mer_base_static<uint64_t, 1>;
+--- salmon.orig/src/CollapsedEMOptimizer.cpp
++++ salmon/src/CollapsedEMOptimizer.cpp
+@@ -13,7 +13,7 @@
+ #include <boost/math/special_functions/digamma.hpp>
+
+ // C++ string formatting library
+-#include "format.h"
++#include <cppformat/format.h>
+
+ #include "cuckoohash_map.hh"
+ #include "Eigen/Dense"
+--- salmon.orig/src/CollapsedGibbsSampler.cpp
++++ salmon/src/CollapsedGibbsSampler.cpp
+@@ -15,7 +15,7 @@
+ #include <boost/filesystem.hpp>
+
+ // C++ string formatting library
+-#include "format.h"
++#include <cppformat/format.h>
+
+ #include "cuckoohash_map.hh"
+ #include "Eigen/Dense"
+--- salmon.orig/src/SalmonQuantify.cpp
++++ salmon/src/SalmonQuantify.cpp
+@@ -40,7 +40,7 @@
+ #include "btree_set.h"
+
+ // C++ string formatting library
+-#include "format.h"
++#include <cppformat/format.h>
+
+ // C Includes for BWA
+ #include <cstdio>
+--- salmon.orig/src/SalmonQuantifyAlignments.cpp
++++ salmon/src/SalmonQuantifyAlignments.cpp
+@@ -5,7 +5,7 @@
+ }
+
+ // for cpp-format
+-#include "format.h"
++#include <cppformat/format.h>
+
+ // are these used?
+ #include <boost/dynamic_bitset.hpp>
+--- salmon.orig/src/SequenceBiasModel.cpp
++++ salmon/src/SequenceBiasModel.cpp
+@@ -3,7 +3,7 @@
+
+ #include <boost/config.hpp> // for BOOST_LIKELY/BOOST_UNLIKELY
+
+-#include "format.h"
++#include <cppformat/format.h>
+ #include "SequenceBiasModel.hpp"
+ #include "LibraryFormat.hpp"
+ #include "Transcript.hpp"
+--- salmon.orig/src/format.cc
++++ salmon/src/format.cc
+@@ -25,7 +25,7 @@
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+-#include "format.h"
++#include <cppformat/format.h>
+
+ #include <string.h>
+
diff --git a/debian/patches/use-system-pkg-config-tbb b/debian/patches/use-system-pkg-config-tbb
new file mode 100644
index 0000000..4d47f6c
--- /dev/null
+++ b/debian/patches/use-system-pkg-config-tbb
@@ -0,0 +1,22 @@
+--- salmon.orig/CMakeLists.txt
++++ salmon/CMakeLists.txt
+@@ -169,6 +169,9 @@
+ set (Boost_USE_MULTITHREADED ON)
+ #set (Boost_USE_STATIC_RUNTIME OFF)
+
++find_package (PkgConfig)
++pkg_check_modules(TBB REQUIRED tbb)
++
+ find_package (ZLIB)
+ if (NOT ZLIB_FOUND)
+ message (FATAL_ERROR "zlib must be installed before configuration & building can proceed")
+@@ -370,7 +373,8 @@
+ # cp config.h <INSTALL_DIR>/include/
+ #)
+
+-find_package(TBB)
++#find_package(TBB)
++
+
+ ##
+ #
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/salmon.git
More information about the debian-med-commit
mailing list