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commit 54f03648986a57ce3cf1acd20bce166d15a23913 Author: Olivier Sallou <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Olivier Sallou <[email protected]> +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 <[email protected]> + 2003-2006, Heng Li <[email protected]> + 2011, Jue Ruan <[email protected]> +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 <[email protected]> +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 ${UTAR} diff --git a/debian/patches/add_hardening.patch b/debian/patches/add_hardening.patch new file mode 100644 index 0000000..8a6e891 --- /dev/null +++ b/debian/patches/add_hardening.patch @@ -0,0 +1,41 @@ +From: Debian Med Packaging Team <[email protected]> +Date: Mon, 17 Aug 2015 12:03:40 +0000 +Subject: add_hardening + +=================================================================== +--- + Makefile | 8 +++++++- + 1 file changed, 7 insertions(+), 1 deletion(-) + +--- a/Makefile ++++ b/Makefile +@@ -1,5 +1,11 @@ ++CPPFLAGS:=$(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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
