[med-svn] [Git][med-team/salmon][master] 9 commits: More cmake changes to find Debian packaged libraries
Andreas Tille
gitlab at salsa.debian.org
Thu Dec 13 14:52:14 GMT 2018
Andreas Tille pushed to branch master at Debian Med / salmon
Commits:
65a93665 by Andreas Tille at 2018-12-13T10:15:54Z
More cmake changes to find Debian packaged libraries
- - - - -
13d7dee3 by Andreas Tille at 2018-12-13T13:56:10Z
Cleanup d/copyright
- - - - -
22579f90 by Andreas Tille at 2018-12-13T13:57:07Z
Make sure libs are linked dynamically
- - - - -
c47c766e by Andreas Tille at 2018-12-13T13:57:33Z
Try hard to use dynamic libs (but this does not seem to help much actually
- - - - -
901341b5 by Andreas Tille at 2018-12-13T14:08:30Z
Use python3-sphinx exclusively
- - - - -
d69a68ea by Andreas Tille at 2018-12-13T14:10:49Z
Do not parse d/changelog
- - - - -
f1fdf056 by Andreas Tille at 2018-12-13T14:12:41Z
More cleanup of d/copyright
- - - - -
d4f10761 by Andreas Tille at 2018-12-13T14:50:52Z
Enforce dynamic linking
- - - - -
c4041866 by Andreas Tille at 2018-12-13T14:51:56Z
Close bug
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/use_debian_packaged_libs.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -2,11 +2,14 @@ salmon (0.12.0+ds1-1) UNRELEASED; urgency=medium
* Team upload.
* New upstream version
+ Closes: #909767
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Remove debian/gbp.conf
* Build-Depends: libbz2-dev, liblzma-dev
+ * Use python3-sphinx exclusively
+ * Do not parse d/changelog
-- Andreas Tille <tille at debian.org> Tue, 11 Dec 2018 19:29:39 +0100
=====================================
debian/control
=====================================
@@ -27,8 +27,8 @@ Build-Depends: debhelper (>= 11~),
libtclap-dev,
help2man,
sphinx-doc,
- python-sphinx | python3-sphinx,
- python-sphinx-rtd-theme | python3-sphinx-rtd-theme,
+ python3-sphinx,
+ python3-sphinx-rtd-theme,
zlib1g-dev,
libeigen3-dev,
libbz2-dev,
=====================================
debian/copyright
=====================================
@@ -36,15 +36,8 @@ Copyright: (c) 2014 Thomas Heller
(c) 2003-2012 Christopher M. Kohlhoff <chris at kohlhoff.com>
License: BSL-1.0
-Files: include/btree*.h
- include/safe_btree*.h
-Copyright: 2013 Google Inc.
-License: Apache-2.0
-
Files: include/ezETAProgressBar.hpp
include/fastapprox.h
- src/bwtindex.c
- src/is.c
Copyright: 2011, 2012 Remik Ziemlinski
2011, 2012 Paul Mineiro <paul at mineiro.com>
(c) 2008 Genome Research Ltd (GRL)
@@ -52,53 +45,15 @@ Copyright: 2011, 2012 Remik Ziemlinski
License: Expat
Files: include/format.h
- src/format.cc
Copyright: (c) 2012 - 2015, Victor Zverovich
License: BSD-2-clause
-Files: src/QSufSort.c
-Copyright: 1999, N. Jesper Larsson <jesper at cs.lth.se>
-License: other
- This software may be used freely for any purpose. However, when distributed,
- the original source must be clearly stated, and, when the source code is
- distributed, the copyright notice must be retained and any alterations in
- the code must be clearly marked. No warranty is given regarding the quality
- of this software
-
Files: include/atomicops.h
include/concurrentqueue.h
include/readerwriterqueue.h
Copyright: ©2013 Cameron Desrochers
License: BSD-cameron-descrochers
-Files: debian/rapmap/*
-Copyright: (c) 2014-2016 COMputational BIology and Network Evolution lab
-License: GPL-3+
-Comment:
- Taken from RapMap (https://github.com/COMBINE-lab/RapMap) with the following
- license statement:
- Since RapMap uses Jellyfish, it must be released under the GPL.
- However, this is currently the only GPL dependency. If it can be
- replaced, I'd like to re-license RapMap under the BSD license. I'd be
- happy to accept pull-requests that replace the Jellyfish components
- with a library released under a more liberal license (BSD-compatible).
-
-Files: debian/rapmap/BooPHF.hpp
-Copyright: ©2015 Guillaume Rizk
-License: Expat
-Comment:
- This project is now BBHash, see
- https://github.com/rizkg/BBHash/blob/master/LICENSE.
-
-Files: debian/rapmap/kseq.h
-Copyright: (c) 2008, 2009, 2011 Attractive Chaos <attractor at live.co.uk>
-License: Expat
-
-Files: debian/rapmap/macros.h
- debian/rapmap/rank9b.*
-Copyright: ©2007-2013 Sebastiano Vigna
-License: LGPL-3+
-
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:
@@ -159,23 +114,6 @@ License: GPL-3+
License version 3 can be found in the file
`/usr/share/common-licenses/GPL-3'.
-License: LGPL-3+
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published by the
- Free Software Foundation; either version 3 of the License, or (at your option)
- any later version.
- .
- This library 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 Lesser General Public License
- for more details.
- .
- You should have received a copy of the GNU Lesser General Public License
- along with this program; if not, see <http://www.gnu.org/licenses/>.
- .
- On Debian systems, the full text of the GNU Lesser General Public License
- version 3 can be found in the file `/usr/share/common-licenses/LGPL-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
@@ -199,22 +137,6 @@ License: BSL-1.0
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'
-
License: BSD-2-clause
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
=====================================
debian/patches/use_debian_packaged_libs.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 11 Dec 2018 19:29:39 +0100
+Description: Use Debian packaged libraries and make sure these are linked dynamically
+
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -477,6 +477,7 @@ message("BOOST LIBRARIES = ${Boost_LIBRA
@@ -76,3 +80,85 @@
set(FAST_MALLOC_LIB "")
set(HAVE_FAST_MALLOC FALSE)
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -1,6 +1,6 @@
+ include_directories(
+ ${GAT_SOURCE_DIR}/include
+-${GAT_SOURCE_DIR}/include/eigen3
++/usr/include/eigen3
+ ${GAT_SOURCE_DIR}/external
+ ${GAT_SOURCE_DIR}/external/cereal/include
+ ${GAT_SOURCE_DIR}/external/install/include
+@@ -8,8 +8,8 @@ ${GAT_SOURCE_DIR}/external/install/inclu
+ ${ZLIB_INCLUDE_DIR}
+ ${TBB_INCLUDE_DIRS}
+ ${Boost_INCLUDE_DIRS}
+-${GAT_SOURCE_DIR}/external/install/include/rapmap
+-${GAT_SOURCE_DIR}/external/install/include/rapmap/digestpp
++/usr/include/rapmap
++/usr/include/rapmap/digestpp
+ ${ICU_INC_DIRS}
+ )
+
+@@ -199,8 +199,8 @@ add_executable(unitTests ${UNIT_TESTS_SR
+ #set_target_properties(salmon_core salmon PROPERTIES LINK_SEARCH_END_STATIC TRUE)
+
+ # our suffix array construction libraries
+-set (SUFFARRAY_LIB ${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort.a)
+-set (SUFFARRAY64_LIB ${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort64.a)
++set (SUFFARRAY_LIB divsufsort)
++set (SUFFARRAY64_LIB divsufsort64)
+
+
+ # Link the executable
+@@ -209,20 +209,20 @@ target_link_libraries(salmon
+ salmon_core
+ alevin_core
+ gff
+- ${Boost_LIBRARIES}
++ boost_iostreams boost_filesystem boost_system boost_timer boost_chrono boost_program_options boost_regex
+ ${ICU_LIBS}
+- ${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a
+- ${ZLIB_LIBRARY}
++ staden-read
++ z
+ ${SUFFARRAY_LIB}
+ ${SUFFARRAY64_LIB}
+ #${GAT_SOURCE_DIR}/external/install/lib/libbwa.a
+ m
+- ${LIBLZMA_LIBRARIES}
++ lzma
+ ${BZIP2_LIBRARIES}
+- ${TBB_LIBRARIES}
++ tbb tbbmalloc
+ ${LIBSALMON_LINKER_FLAGS}
+ ${NON_APPLECLANG_LIBS}
+- ${FAST_MALLOC_LIB}
++ jemalloc
+ ${LIBRT}
+ ksw2pp
+ ${CMAKE_DL_LIBS}
+@@ -234,17 +234,17 @@ target_link_libraries(unitTests
+ salmon_core
+ alevin_core
+ gff
+- ${Boost_LIBRARIES}
++ boost_iostreams boost_filesystem boost_system boost_timer boost_chrono boost_program_options boost_regex
+ ${ICU_LIBS}
+- ${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a
+- ${ZLIB_LIBRARY}
++ staden-read
++ z
+ ${SUFFARRAY_LIB}
+ ${SUFFARRAY64_LIB}
+ #${GAT_SOURCE_DIR}/external/install/lib/libbwa.a
+ m
+- ${LIBLZMA_LIBRARIES}
++ lzma
+ ${BZIP2_LIBRARIES}
+- ${TBB_LIBRARIES}
++ tbb tbbmalloc
+ ${LIBSALMON_LINKER_FLAGS}
+ ${NON_APPLECLANG_LIBS}
+ ${LIBRT}
=====================================
debian/rules
=====================================
@@ -2,8 +2,7 @@
# DH_VERBOSE := 1
-DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+include /usr/share/dpkg/default.mk
# Fails to build when trying to enhance hardening
export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
@@ -14,11 +13,13 @@ CMAKE_EXTRA_FLAGS += -DDEBIAN_BUILD=1 \
-DBZIP2_LIBRARIES=-lbz2 \
-DBZIP2_INCLUDE_DIR=/usr/include \
-DLIBLZMA_INCLUDE_DIR=/usr/include/ \
- -DLIBLZMA_LIBRARY=-llzma \
+ -DLIBLZMA_LIBRARY=lzma \
-DLIBLZMA_HAS_AUTO_DECODER=1 \
-DLIBLZMA_HAS_EASY_ENCODER=1 \
-DLIBLZMA_HAS_LZMA_PRESET=1 \
- -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules
+ -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules \
+ -DTBB_WILL_RECONFIGURE=FALSE \
+ -DBOOST_WILL_RECONFIGURE=FALSE
%:
dh $@ --with sphinxdoc
@@ -28,31 +29,6 @@ override_dh_auto_configure:
cp -av /usr/share/rapmap/src/* $(CURDIR)/external/install/src/rapmap
dh_auto_configure -- $(CMAKE_EXTRA_FLAGS)
-__override_dh_auto_configure:
- cp -rv debian/rapmap/RapMap*.h* \
- debian/rapmap/*Boo???.hpp \
- debian/rapmap/IndexHeader.hpp \
- debian/rapmap/HitManager.hpp \
- debian/rapmap/JFRaw.hpp \
- debian/rapmap/SA*.hpp \
- debian/rapmap/kseq.h \
- debian/rapmap/SpinLock.hpp \
- debian/rapmap/ScopedTimer.hpp \
- debian/rapmap/bit_*.h \
- debian/rapmap/rank9b.h \
- debian/rapmap/macros.h \
- debian/rapmap/PairAlignmentFormatter.hpp \
- debian/rapmap/SingleAlignmentFormatter.hpp \
- debian/rapmap/SparseHashSerializer.hpp \
- debian/rapmap/sparsepp \
- include/
- cp -v debian/rapmap/bit_array.c \
- debian/rapmap/rank9b.cpp \
- debian/rapmap/RapMap*.cpp \
- debian/rapmap/HitManager.cpp \
- src/
- dh_auto_configure
-
override_dh_auto_build:
dh_auto_build
mv doc/source/license.rst doc/ # unused
@@ -62,7 +38,7 @@ override_dh_auto_build:
help2man --no-discard-stderr --no-info --name="highly-accurate, transcript-level quantification estimates from RNA-seq data"\
./salmon > ../../debian/salmon.1 && \
for option in index quant swim; do help2man --no-discard-stderr \
- --version-string="${VERSION}" --no-info "./salmon --no-version-check $${option}" \
+ --version-string="$(DEB_VERSION_UPSTREAM)" --no-info "./salmon --no-version-check $${option}" \
--include=../../debian/salmon-$${option}-man-include \
> ../../debian/salmon-$${option}.1; done
View it on GitLab: https://salsa.debian.org/med-team/salmon/compare/3b2376fd1da6af3c4dbb54a1a9e3b29064a66a7b...c4041866181b5b6daa8453289e01621fd30488e7
--
View it on GitLab: https://salsa.debian.org/med-team/salmon/compare/3b2376fd1da6af3c4dbb54a1a9e3b29064a66a7b...c4041866181b5b6daa8453289e01621fd30488e7
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