[med-svn] [salmon] 02/02: patch cleanup
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sat Jan 30 17:42:14 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 d5d40a90cbf5065f81e9a3f917f23a90d4d2065e
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Sat Jan 30 09:22:55 2016 -0800
patch cleanup
---
debian/copyright | 61 +++++++++++++++-
debian/patches/use-system-cppformat | 121 -------------------------------
debian/patches/use-system-pkg-config-tbb | 2 +
3 files changed, 62 insertions(+), 122 deletions(-)
diff --git a/debian/copyright b/debian/copyright
index 6a339e6..2d47792 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -39,7 +39,7 @@ License: BSL-1.0
Files: include/btree*.h
include/safe_btree*.h
Copyright: 2013 Google Inc.
-License: apache-2.0
+License: Apache-2.0
Files: include/ezETAProgressBar.hpp
include/fastapprox.h
@@ -89,6 +89,26 @@ License: BSD-cameron-descrochers
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: Expat
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
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
@@ -106,3 +126,42 @@ License: GPL-3+
On Debian systems, the full text of the GNU General Public
License version 3 can be found in the file
`/usr/share/common-licenses/GPL-3'.
+
+License: BSL-1.0
+ Permission is hereby granted, free of charge, to any person or organization
+ obtaining a copy of the software and accompanying documentation covered by this
+ license (the "Software") to use, reproduce, display, distribute, execute, and
+ transmit the Software, and to prepare derivative works of the Software, and to
+ permit third-parties to whom the Software is furnished to do so, all subject to
+ the following:
+ .
+ The copyright notices in the Software and this entire statement, including the
+ above license grant, this restriction and the following disclaimer, must be
+ included in all copies of the Software, in whole or in part, and all derivative
+ works of the Software, unless such copies or derivative works are solely in the
+ form of machine-executable object code generated by a source language
+ processor.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL
+ THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY
+ DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
+License: Apache-2.0
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+ .
+ http://www.apache.org/licenses/LICENSE-2.0
+ .
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+ .
+ On Debian systems, the full text of the Apache License, Version 2.0 can be
+ found in the file `/usr/share/common-licenses/Apache-2.0'
diff --git a/debian/patches/use-system-cppformat b/debian/patches/use-system-cppformat
deleted file mode 100644
index 4101785..0000000
--- a/debian/patches/use-system-cppformat
+++ /dev/null
@@ -1,121 +0,0 @@
---- 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
index 4d47f6c..c272275 100644
--- a/debian/patches/use-system-pkg-config-tbb
+++ b/debian/patches/use-system-pkg-config-tbb
@@ -1,3 +1,5 @@
+Description: Use pkgconfig to find the system library for tbb
+Author: Michael R. Crusoe <crusoe at ucdavis.edu>
--- salmon.orig/CMakeLists.txt
+++ salmon/CMakeLists.txt
@@ -169,6 +169,9 @@
--
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