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osallou pushed a commit to branch master
in repository bedops.
commit 86cee64fcf47b23f9e3c57a8c92afe7417d57b94
Author: Olivier Sallou <osal...@debian.org>
Date: Fri Jan 13 10:27:13 2017 +0000
Import Debian patch 2.4.20+dfsg-1
---
debian/README.Debian | 6 ++
debian/README.source | 10 ++
debian/bedops-docs.docs | 2 +
debian/bedops.doc-base | 11 ++
debian/changelog | 5 +
debian/compat | 1 +
debian/control | 18 ++++
debian/copyright | 39 +++++++
debian/patches/series | 1 +
debian/patches/use_debian_libs | 226 +++++++++++++++++++++++++++++++++++++++++
debian/rules | 25 +++++
debian/source/format | 1 +
debian/watch | 4 +
13 files changed, 349 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..d6d44b0
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,6 @@
+bedops for Debian
+----------------
+
+<possible notes regarding this package - if none, delete this file>
+
+ -- Olivier Sallou <osal...@debian.org> Fri, 13 Jan 2017 10:27:13 +0000
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..548704d
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,10 @@
+bedops for Debian
+----------------
+
+third-party directory si removed from source as it includes libraries
(jansson, zlib, bz2) available in debian.
+Software is patched to use Debian libs
+
+
+
+ -- Olivier Sallou <osal...@debian.org> Fri, 13 Jan 2017 10:27:13 +0000
+
diff --git a/debian/bedops-docs.docs b/debian/bedops-docs.docs
new file mode 100644
index 0000000..7319041
--- /dev/null
+++ b/debian/bedops-docs.docs
@@ -0,0 +1,2 @@
+README.source
+README.Debian
diff --git a/debian/bedops.doc-base b/debian/bedops.doc-base
new file mode 100644
index 0000000..2dc8e33
--- /dev/null
+++ b/debian/bedops.doc-base
@@ -0,0 +1,11 @@
+Document: bedops
+Title: Debian bedops Manual
+Author: <insert document author here>
+Abstract: This manual describes what bedops is
+ and how it can be used to
+ manage online manuals on Debian systems.
+Section: unknown
+
+Format: HTML
+Index: /usr/share/doc/bedops/html/index.html
+Files: /usr/share/doc/bedops/html/*.html
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..7dae77c
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+bedops (2.4.20+dfsg-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #851256)
+
+ -- Olivier Sallou <osal...@debian.org> Fri, 13 Jan 2017 10:27:13 +0000
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..4046f81
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,18 @@
+Source: bedops
+Section: science
+Priority: optional
+Maintainer: Olivier Sallou <osal...@debian.org>
+Build-Depends: debhelper (>= 9),
+ libbz2-dev,
+ libjansson-dev,
+ zlib1g-dev
+Standards-Version: 3.9.8
+Homepage: <insert the upstream URL, if relevant>
+#Vcs-Git: https://anonscm.debian.org/collab-maint/bedops.git
+#Vcs-Browser: https://anonscm.debian.org/cgit/collab-maint/bedops.git
+
+Package: bedops
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: <insert up to 60 chars description>
+ <insert long description, indented with spaces>
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..80b615e
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,39 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: bedops
+Source: <url://example.com>
+Files-Excluded: third-party
+
+Files: *
+Copyright: <years> <put author's name and email here>
+ <years> <likewise for another author>
+License: <special license>
+ <Put the license of the package here indented by 1 space>
+ <This follows the format of Description: lines in control file>
+ .
+ <Including paragraphs>
+
+# If you want to use GPL v2 or later for the /debian/* files use
+# the following clauses, or change it to suit. Delete these two lines
+Files: debian/*
+Copyright: 2017 Olivier Sallou <osal...@debian.org>
+License: GPL-2+
+ This package 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; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package 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 should have received a copy of the GNU General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
+# Please avoid picking licenses with terms that are more restrictive than the
+# packaged work, as it may make Debian's contributions unacceptable upstream.
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..356d8eb
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+use_debian_libs
diff --git a/debian/patches/use_debian_libs b/debian/patches/use_debian_libs
new file mode 100644
index 0000000..071c3c5
--- /dev/null
+++ b/debian/patches/use_debian_libs
@@ -0,0 +1,226 @@
+--- a/applications/bed/bedops/src/Makefile
++++ b/applications/bed/bedops/src/Makefile
+@@ -22,11 +22,11 @@
+ LOCALZLIBLIB = ${LOCALZLIBDIR}/${LIBZLIB}
+ LOCALZLIBINCDIR = ${LOCALZLIBDIR}
+ OBJDIR = objects
+-INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR}
-I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+-LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR}
-L${LOCALZLIBDIR}
+-LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
++INCLUDES = -iquote$(HEAD)
++LIBLOCATION =
++LIBRARIES =
+ BLDFLAGS = -Wall -pedantic -O3 -std=c++11
+-SFLAGS = -static
++SFLAGS = -ljansson -lz -lbz2
+
+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers
starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+ dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o,
$(dependency_names)))
+--- a/interfaces/src/data/starch/starchFileHelpers.c
++++ b/interfaces/src/data/starch/starchFileHelpers.c
+@@ -178,7 +178,7 @@
+ /* deflateInit2 allows creation of archive with gzip header, i.e. a gzip
file */
+ /* cf. http://www.zlib.net/manual.html */
+ #ifdef __cplusplus
+- ret = deflateInit2cpp(&strm, level, Z_DEFLATED, (15+16), 8,
Z_DEFAULT_STRATEGY);
++ ret = deflateInit2(&strm, level, Z_DEFLATED, (15+16), 8,
Z_DEFAULT_STRATEGY);
+ #else
+ ret = deflateInit2(&strm, level, Z_DEFLATED, (15+16), 8,
Z_DEFAULT_STRATEGY);
+ #endif
+--- a/applications/bed/bedextract/src/Makefile
++++ b/applications/bed/bedextract/src/Makefile
+@@ -21,11 +21,11 @@
+ LOCALZLIBDIR = ${PARTY3}/zlib
+ LOCALZLIBLIB = ${LOCALZLIBDIR}/${LIBZLIB}
+ LOCALZLIBINCDIR = ${LOCALZLIBDIR}
+-INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR}
-I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+-LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR}
-L${LOCALZLIBDIR}
+-LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
++INCLUDES = -iquote$(HEAD)
++LIBLOCATION =
++LIBRARIES =
+ BLDFLAGS = -Wall -pedantic -O3 -std=c++11
+-SFLAGS = -static
++SFLAGS = -ljansson -lz -lbz2
+
+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers
starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+ dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o,
$(dependency_names)))
+@@ -64,4 +64,4 @@
+ rm -rf $(OBJDIR)
+ rm -f $(BINDIR)/$(PROG)
+ rm -f $(BINDIR)/*.$(PROG)
+- rm -rf $(BINDIR)
+\ No newline at end of file
++ rm -rf $(BINDIR)
+--- a/applications/bed/bedmap/src/Makefile
++++ b/applications/bed/bedmap/src/Makefile
+@@ -20,11 +20,11 @@
+ LOCALZLIBLIB = ${LOCALZLIBDIR}/${LIBZLIB}
+ LOCALZLIBINCDIR = ${LOCALZLIBDIR}
+ OBJDIR = objects
+-INCLUDES = -iquote${HEAD} -I${PARTY3} -I${LOCALJANSSONINCDIR}
-I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+-LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR}
-L${LOCALZLIBDIR}
+-LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
++INCLUDES = -iquote${HEAD}
++LIBLOCATION =
++LIBRARIES =
+ BLDFLAGS = -Wall -pedantic -O3 -std=c++11
+-SFLAGS = -static
++SFLAGS = -ljansson -lz -lbz2
+
+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers
starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+ dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o,
$(dependency_names)))
+--- a/system.mk/Makefile.linux
++++ b/system.mk/Makefile.linux
+@@ -155,13 +155,13 @@
+ support: $(LIBS)
+
+ ${PARTY3}/jansson/lib/libjansson.a: $(WHICHJANSSON).tar.bz2
+- bzcat $^ | tar -x -C ${PARTY3}
+- cd ${PARTY3}/${JANSSONVERSION} && ./configure
--prefix=${WDIR}/${PARTY3}/${JANSSONVERSION} && $(MAKE) && $(MAKE) install &&
cd ${WDIR} && rm -f jansson && ln -sf ${JANSSONVERSION} ${PARTY3}/jansson
++ #bzcat $^ | tar -x -C ${PARTY3}
++ #cd ${PARTY3}/${JANSSONVERSION} && ./configure
--prefix=${WDIR}/${PARTY3}/${JANSSONVERSION} && $(MAKE) && $(MAKE) install &&
cd ${WDIR} && rm -f jansson && ln -sf ${JANSSONVERSION} ${PARTY3}/jansson
+
+ $(PARTY3)/bzip2/libbz2.a: $(WHICHBZIP2).tar.bz2
+- bzcat $^ | tar -x -C ${PARTY3}
+- cd ${PARTY3}/${BZIP2VERSION} && $(MAKE) libbz2.a && cd ${WDIR} && rm -f
bzip2 && ln -sf ${BZIP2VERSION} ${PARTY3}/bzip2
++ #bzcat $^ | tar -x -C ${PARTY3}
++ #cd ${PARTY3}/${BZIP2VERSION} && $(MAKE) libbz2.a && cd ${WDIR} && rm
-f bzip2 && ln -sf ${BZIP2VERSION} ${PARTY3}/bzip2
+
+ ${PARTY3}/zlib/libz.a: $(WHICHZLIB).tar.bz2
+- bzcat $^ | tar -x -C ${PARTY3}
+- cd ${PARTY3}/${ZLIBVERSION} && ./configure --static && $(MAKE) && cd
${WDIR} && rm -f zlib && ln -sf ${ZLIBVERSION} ${PARTY3}/zlib
++ #bzcat $^ | tar -x -C ${PARTY3}
++ #cd ${PARTY3}/${ZLIBVERSION} && ./configure --static && $(MAKE) && cd
${WDIR} && rm -f zlib && ln -sf ${ZLIBVERSION} ${PARTY3}/zlib
+--- a/applications/bed/closestfeats/src/Makefile
++++ b/applications/bed/closestfeats/src/Makefile
+@@ -20,11 +20,11 @@
+ LOCALZLIBLIB = ${LOCALZLIBDIR}/${LIBZLIB}
+ LOCALZLIBINCDIR = ${LOCALZLIBDIR}
+ OBJDIR = objects
+-INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR}
-I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+-LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR}
-L${LOCALZLIBDIR}
+-LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
++INCLUDES = -iquote$(HEAD)
++LIBLOCATION =
++LIBRARIES =
+ BLDFLAGS = -Wall -pedantic -O3 -std=c++11
+-SFLAGS = -static
++SFLAGS = -ljansson -lz -lbz2
+
+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers
starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+ dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o,
$(dependency_names)))
+--- a/applications/bed/conversion/src/Makefile
++++ b/applications/bed/conversion/src/Makefile
+@@ -10,7 +10,7 @@
+ WRAPPERDIR = wrappers
+ PROG = convert2bed
+ SOURCE = convert2bed.c
+-SFLAGS = -static
++SFLAGS =
+
+ all: build
+
+--- a/applications/bed/sort-bed/src/Makefile
++++ b/applications/bed/sort-bed/src/Makefile
+@@ -4,7 +4,7 @@
+ LIB2 = $(MAIN)/interfaces/src/utility
+ LIB3 = $(MAIN)/interfaces/src/data/starch
+ THISDIR = ${shell pwd}
+-INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR}
-I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
++INCLUDES = -iquote$(HEAD)
+
+ PARTY3 = ${THISDIR}/$(MAIN)/third-party
+ LIBJANSSON = libjansson.a
+@@ -22,15 +22,15 @@
+ LOCALZLIBLIB = ${LOCALZLIBDIR}/${LIBZLIB}
+ LOCALZLIBINCDIR = ${LOCALZLIBDIR}
+
+-LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR}
-L${LOCALZLIBDIR}
+-LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
++LIBLOCATION =
++LIBRARIES =
+
+ PROG = sort-bed
+ BINDIR = ../bin
+ OBJDIR = objects
+ WARNINGS = -Wall -Wextra -pedantic
+ BLDFLAGS = ${WARNINGS} -O3 -std=c++11
+-SFLAGS = -static
++SFLAGS = -ljansson -lz -lbz2
+
+ dependency_names = starchConstants starchFileHelpers starchHelpers
starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
SortDetails Sort CheckSort
+ dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o,
$(dependency_names)))
+--- a/applications/bed/starch/src/Makefile
++++ b/applications/bed/starch/src/Makefile
+@@ -29,15 +29,15 @@
+ LOCALZLIBINCDIR = ${LOCALZLIBDIR}
+ OBJDIR = ${INTERFACES}/src/data/starch
+ LOCALOBJDIR = objects
+-INCLUDES = -iquote${MAIN} -iquote${HEAD} -iquote${PARTY3}
-I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+-LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB}
${LOCALZLIBLIB}
++INCLUDES = -iquote${MAIN} -iquote${HEAD}
++LIBRARIES =
+ ARCH_VERSION = v2.1
+ BIN_VERSION = v2.4.16
+ TEST = ../test
+ TEST_LINUX_BINDIR = ${TEST}/binaries/linux/${ARCH_VERSION}/bin
+ TEST_OSX_BINDIR = ${TEST}/binaries/osx/${ARCH_VERSION}/bin
+ AR = ar
+-SFLAGS = -static
++SFLAGS = -ljansson -lz -lbz2
+ CXXFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64
-D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra
-Wswitch-enum -std=c++11 ${SFLAGS} -s
+ CXXDFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64
-D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O0 -g -Wformat -Wall -Wextra
-Wswitch-enum -std=c++11 -DDEBUG_VERBOSE=1 ${SFLAGS}
+ CXXGFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64
-D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O -Wformat -Wall -Wextra
-Wswitch-enum -std=c++11 -DDEBUG_VERBOSE=1 ${SFLAGS} -pg
+--- a/applications/bed/starch/src/starchcat.c
++++ b/applications/bed/starch/src/starchcat.c
+@@ -4870,7 +4870,7 @@
+
+ /* cf. http://www.zlib.net/manual.html for level information */
+ #ifdef __cplusplus
+- zError = deflateInit2cpp(zStreamPtr, STARCH_Z_COMPRESSION_LEVEL,
Z_DEFLATED, STARCH_Z_WINDOW_BITS, STARCH_Z_MEMORY_LEVEL, Z_DEFAULT_STRATEGY);
++ zError = deflateInit2(zStreamPtr, STARCH_Z_COMPRESSION_LEVEL, Z_DEFLATED,
STARCH_Z_WINDOW_BITS, STARCH_Z_MEMORY_LEVEL, Z_DEFAULT_STRATEGY);
+ #else
+ zError = deflateInit2(zStreamPtr, STARCH_Z_COMPRESSION_LEVEL, Z_DEFLATED,
STARCH_Z_WINDOW_BITS, STARCH_Z_MEMORY_LEVEL, Z_DEFAULT_STRATEGY);
+ #endif
+--- a/docs/conf.py
++++ b/docs/conf.py
+@@ -12,7 +12,6 @@
+ # serve to show the default.
+
+ import sys, os
+-from better import better_theme_path
+
+ # If extensions (or modules to document with autodoc) are in another
directory,
+ # add these directories to sys.path here. If the directory is relative to the
+@@ -26,7 +25,7 @@
+
+ # Add any Sphinx extension module names here, as strings. They can be
extensions
+ # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest',
'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage',
'sphinx.ext.pngmath', 'sphinx.ext.mathjax', 'sphinx.ext.ifconfig',
'sphinx.ext.viewcode']
++extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest',
'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage',
'sphinx.ext.imgmath', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode']
+ #, 'sphinx.ext.mathbase']
+
+ # Add any paths that contain templates here, relative to this directory.
+@@ -96,8 +95,8 @@
+
+ # The theme to use for HTML and HTML Help pages. See the documentation for
+ # a list of builtin themes.
+-#html_theme = 'default'
+-html_theme = 'better'
++html_theme = 'default'
++#html_theme = 'better'
+
+ # Theme options are theme-specific and customize the look and feel of a theme
+ # further. For a list of options available for each theme, see the
+@@ -110,8 +109,8 @@
+ }
+
+ # Add any paths that contain custom themes here, relative to this directory.
+-#html_theme_path = []
+-html_theme_path = [better_theme_path]
++html_theme_path = []
++#html_theme_path = [better_theme_path]
+
+ # The name for this set of Sphinx documents. If None, it defaults to
+ # "<project> v<release> documentation".
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..e1c367c
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,25 @@
+#!/usr/bin/make -f
+# See debhelper(7) (uncomment to enable)
+# output every command that modifies files on the build system.
+#export DH_VERBOSE = 1
+
+
+# see FEATURE AREAS in dpkg-buildflags(1)
+#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+# see ENVIRONMENT in dpkg-buildflags(1)
+# package maintainers to append CFLAGS
+#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
+# package maintainers to append LDFLAGS
+#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+
+
+%:
+ dh $@
+
+
+# dh_make generated override targets
+# This is example for Cmake (See https://bugs.debian.org/641051 )
+#override_dh_auto_configure:
+# dh_auto_configure -- # -DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH)
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..113a8a9
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=4
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz,filenamemangle=s/.+\/v?(\d\S+)\.tar\.gz/bedops-$1\.tar\.gz/"
\
+ https://github.com/bedops/bedops/tags .*/v?(\d\S+)\.tar\.gz
--
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