[med-svn] [bio-rainbow] 02/11: Imported Debian patch 2.0.4-1
Olivier Sallou
osallou at debian.org
Mon Aug 17 15:09:15 UTC 2015
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch master
in repository bio-rainbow.
commit 54f03648986a57ce3cf1acd20bce166d15a23913
Author: Olivier Sallou <osallou at debian.org>
Date: Mon Aug 17 10:57:33 2015 +0000
Imported Debian patch 2.0.4-1
---
debian/bio-rainbow.install | 4 ++++
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 16 ++++++++++++++
debian/copyright | 44 ++++++++++++++++++++++++++++++++++++++
debian/docs | 2 ++
debian/get-orig-source | 32 +++++++++++++++++++++++++++
debian/patches/add_hardening.patch | 41 +++++++++++++++++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 25 ++++++++++++++++++++++
debian/source/format | 1 +
debian/watch | 3 +++
12 files changed, 175 insertions(+)
diff --git a/debian/bio-rainbow.install b/debian/bio-rainbow.install
new file mode 100644
index 0000000..266807e
--- /dev/null
+++ b/debian/bio-rainbow.install
@@ -0,0 +1,4 @@
+select* usr/bin/
+rbasm usr/bin/
+rainbow usr/bin/
+ezmsim usr/bin/
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..6464ffc
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+bio-rainbow (2.0.4-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn)
+
+ -- Olivier Sallou <osallou at debian.org> Mon, 17 Aug 2015 10:57:33 +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..e7ce413
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,16 @@
+Source: bio-rainbow
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.6
+Homepage: http://sourceforge.net/projects/bio-rainbow/
+#Vcs-Git: git://anonscm.debian.org/collab-maint/bio-rainbow.git
+#Vcs-Browser: https://anonscm.debian.org/gitweb/?p=collab-maint/bio-rainbow.git;a=summary
+
+Package: bio-rainbow
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: clustering and assembling short reads for bioinformatics
+ Efficient tool for clustering and assembling short reads, especially for RAD.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..6166444
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,44 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: bio-rainbow
+Source: http://sourceforge.net/projects/bio-rainbow/
+
+Files: *
+Copyright: 2003-2006, Li Heng <liheng at genomics.org.cn>
+ 2003-2006, Heng Li <liheng at genomics.org.cn>
+ 2011, Jue Ruan <ruanjue at gmail.com>
+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".
+
+
+Files: debian/*
+Copyright: 2015 Olivier Sallou <osallou at 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".
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..fa6b147
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,2 @@
+README.txt
+README.txt
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..3aff321
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,32 @@
+#!/bin/bash
+
+set -e
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`uscan --verbose --force-download --no-symlink |
+ grep "Newest version on remote site is .* local version is .*" |
+ head -n 1 |
+ sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
+
+mkdir -p ../tarballs
+
+cd ../tarballs
+
+UTAR="rainbow_${VERSION}.tar.gz"
+
+mv ../${UTAR} .
+tar -xzf ${UTAR}
+
+mv rainbow_${VERSION} $PKG-${VERSION}.orig
+cd $PKG-${VERSION}.orig
+ rm .*.c
+ rm .*.h
+ rm .*.pl
+ rm .*.bak
+ rm .*.txt
+cd ..
+
+BZIP2="--best" tar -cjf ${PKG}_${VERSION}.orig.tar.bz2 ${PKG}-${VERSION}.orig
+rm -rf ${PKG}-${VERSION}.orig
+
+rm ${UTAR}
diff --git a/debian/patches/add_hardening.patch b/debian/patches/add_hardening.patch
new file mode 100644
index 0000000..8a6e891
--- /dev/null
+++ b/debian/patches/add_hardening.patch
@@ -0,0 +1,41 @@
+From: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Date: Mon, 17 Aug 2015 12:03:40 +0000
+Subject: add_hardening
+
+===================================================================
+---
+ Makefile | 8 +++++++-
+ 1 file changed, 7 insertions(+), 1 deletion(-)
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,5 +1,11 @@
++CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
++CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS)
++CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS)
++LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
++
++
+ CC=gcc
+-CFLAGS= -W -O2 -Wall -Wno-self-assign -Wno-unused-function
++CFLAGS+= -W -O2 -Wall -Wno-self-assign -Wno-unused-function
+ DFLAGS= -D_FILE_OFFSET_BITS=64
+ GLIBS=-lm
+ GENERIC_SRC= string.h bitvec.h file_reader.h hashset.h sort.h list.h dna.h heap.h stdaln.h vector.h
+@@ -13,13 +19,13 @@
+ all: rainbow ezmsim rbasm
+
+ rainbow: main.o divide.o file_reader.o asm_R2.o mergectg.o cluster.o
+- $(CC) $(CFLAGS) -o $@ $^ $(GLIBS)
++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(GLIBS)
+
+ rbasm: asm_R2.o rbasm_main.o file_reader.o
+- $(CC) $(CFLAGS) -o $@ $^ $(GLIBS)
++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(GLIBS)
+
+ ezmsim: ezmsim.o
+- $(CC) $(CFLAGS) -o $@ $^ $(GLIBS)
++ $(CC) $(LDFLAGS)$(CFLAGS) -o $@ $^ $(GLIBS)
+
+ asm_R2.o: asm_R2.c asm_R2.h string.h vector.h hashset.h file_reader.h \
+ dna.h
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..930dd9f
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+add_hardening.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..2eacd3f
--- /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 EXAMPLES in dpkg-buildflags(1) and read /usr/share/dpkg/*
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+# 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
+
+
+# main packaging script based on dh7 syntax
+%:
+ dh $@
+
+get-orig-source:
+ debian/get-orig-source
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..42ca808
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+http://sf.net/bio-rainbow/rainbow_(\d\S*)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bio-rainbow.git
More information about the debian-med-commit
mailing list