Author: lkajan Date: 2013-05-08 18:43:34 +0000 (Wed, 08 May 2013) New Revision: 13523
Added: trunk/packages/dssp/trunk/debian/patches/thread_include Removed: trunk/packages/dssp/trunk/debian/patches/src-matrix.h Modified: trunk/packages/dssp/trunk/debian/changelog trunk/packages/dssp/trunk/debian/control trunk/packages/dssp/trunk/debian/patches/makefile trunk/packages/dssp/trunk/debian/patches/series trunk/packages/dssp/trunk/debian/rules Log: updated Debianization to upstream 2.1.0, but this will fail to build until boost >=1.53.0 becomes the standard in unstable, because of a libc update (see http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=703980); it may work (backports) with older boost, though, as long as the libc is older too, so I am not requiring boost >=1.53.0 in d/control Modified: trunk/packages/dssp/trunk/debian/changelog =================================================================== --- trunk/packages/dssp/trunk/debian/changelog 2013-05-08 15:56:54 UTC (rev 13522) +++ trunk/packages/dssp/trunk/debian/changelog 2013-05-08 18:43:34 UTC (rev 13523) @@ -1,3 +1,9 @@ +dssp (2.1.0-1) UNRELEASED; urgency=low + + * New upstream release. + + -- Laszlo Kajan <[email protected]> Wed, 08 May 2013 18:20:06 +0200 + dssp (2.0.4-2) unstable; urgency=low [ Laszlo Kajan ] Modified: trunk/packages/dssp/trunk/debian/control =================================================================== --- trunk/packages/dssp/trunk/debian/control 2013-05-08 15:56:54 UTC (rev 13522) +++ trunk/packages/dssp/trunk/debian/control 2013-05-08 18:43:34 UTC (rev 13523) @@ -5,16 +5,15 @@ Laszlo Kajan <[email protected]>, Andreas Tille <[email protected]> Build-Depends: debhelper (>= 7.0.50~), - libboost-filesystem-dev (>= 1.42.0.1), - libboost-iostreams-dev (>= 1.42.0.1), - libboost-program-options-dev (>= 1.42.0.1), - libboost-system-dev (>= 1.42.0.1), - libboost-thread-dev (>= 1.42.0.1) -Standards-Version: 3.9.3 + libboost-filesystem-dev (>= 1.42.0), + libboost-iostreams-dev (>= 1.42.0), + libboost-program-options-dev (>= 1.42.0), + libboost-system-dev (>= 1.42.0), + libboost-thread-dev (>= 1.42.0) +Standards-Version: 3.9.4 Section: science Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/dssp/trunk/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/dssp/trunk/ -DM-Upload-Allowed: yes Homepage: http://www.cmbi.ru.nl/dssp.html Package: dssp Modified: trunk/packages/dssp/trunk/debian/patches/makefile =================================================================== --- trunk/packages/dssp/trunk/debian/patches/makefile 2013-05-08 15:56:54 UTC (rev 13522) +++ trunk/packages/dssp/trunk/debian/patches/makefile 2013-05-08 18:43:34 UTC (rev 13523) @@ -12,95 +12,57 @@ Author: Laszlo Kajan <[email protected]> --- a/makefile +++ b/makefile -@@ -9,37 +9,36 @@ - # new one if it doesn't exist. In this make.config you can set site - # specific variables like the Boost library location. +@@ -11,18 +11,16 @@ --firstTarget: mkdssp -- + all: mkdssp + -include make.config -+all: mkdssp +- + VERSION = 2.1.0 - VERSION = 2.0.4 + DEST_DIR ?= /usr/local + LIB_DIR = $(BOOST_LIB_DIR) + INC_DIR = $(BOOST_INC_DIR) +-BIN_DIR = $(DEST_DIR)/bin +-MAN_DIR = $(DEST_DIR)/man/man1 ++BIN_DIR = $(DESTDIR)$(DEST_DIR)/bin ++MAN_DIR = $(DESTDIR)$(DEST_DIR)/share/man/man1 --DEST_DIR ?= /usr/local/ --LIB_DIR = $(BOOST_LIB_DIR) --INC_DIR = $(BOOST_INC_DIR) --MAN_DIR = $(DEST_DIR)man/man1/ -+CXXFLAGS := $(shell dpkg-buildflags --get CXXFLAGS) -+LDFLAGS := $(shell dpkg-buildflags --get LDFLAGS) -+ -+BIN_DIR = $(DESTDIR)/usr/bin -+MAN_DIR = $(DESTDIR)/usr/share/man/man1 - --BOOST_LIBS = thread regex filesystem program_options date_time iostreams math_c99 system +-BOOST_LIBS = thread filesystem program_options iostreams system -LIBS = $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) z bz2 +BOOST_LIBS = thread program_options iostreams system -+LIBS = $(BOOST_LIBS:%=boost_%) ++LIBS = $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) DEFINES = USE_COMPRESSION LINUX VERSION='"$(VERSION)"' --CC = c++ -+CXX = g++ + CXX = g++ +@@ -49,22 +47,19 @@ + OBJECTS = $(OBJ_DIR)/mkdssp.o $(OBJ_DIR)/dssp.o $(OBJ_DIR)/primitives-3d.o $(OBJ_DIR)/structure.o $(OBJ_DIR)/utils.o $(OBJ_DIR)/mas.o --CFLAGS = $(INC_DIR:%=-I%) -iquote src -g -Wall -Wno-multichar -pthread --LDOPTS = $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -g -pthread -+CXXFLAGS += -I $(HOME)/projects/boost/include -iquote src -g -Wall -Wno-multichar -pthread -+LDOPTS += -L $(HOME)/projects/boost/lib $(LIBS:%=-l%) -g -pthread + mkdssp: $(OBJECTS) +- @ echo linking $@ +- @ $(CXX) -static -o $@ $^ $(LDOPTS) ++ $(CXX) -o $@ $^ $(LDOPTS) - OBJ_DIR = obj +-include $(OBJECTS:%.o=%.d) ++-include $(OBJECTS:%.o=%.d) - ifeq ($(DEBUG),1) - OBJ_DIR := $(OBJ_DIR).dbg --CFLAGS += -g3 -+CXXFLAGS += -g3 - else - DEFINES += NDEBUG --CFLAGS += -O3 -+CXXFLAGS += -O3 - endif + $(OBJECTS:.o=.d): --CFLAGS += $(DEFINES:%=-D%) -+CXXFLAGS += $(DEFINES:%=-D%) + $(OBJ_DIR): +- @ mkdir -p $(OBJ_DIR) ++ mkdir -p $(OBJ_DIR) - DIST_NAME = dssp-$(VERSION) - -@@ -48,25 +47,21 @@ - OBJECTS = $(OBJ_DIR)/mkdssp.o $(OBJ_DIR)/dssp.o $(OBJ_DIR)/primitives-3d.o $(OBJ_DIR)/structure.o $(OBJ_DIR)/utils.o - - mkdssp: $(OBJECTS) -- @ echo linking $@ -- @ $(CC) -static -o $@ $^ $(LDOPTS) -- @ echo OK -- --include $(OBJECTS:%.o=%.d) -- --$(OBJECTS:.o=.d): -- --$(OBJ_DIR)/%.o: %.cpp -- @ if [ ! -d $(OBJ_DIR) ]; then mkdir $(OBJ_DIR); fi + $(OBJ_DIR)/%.o: %.cpp | $(OBJ_DIR) - @ echo compiling $@ -- @ $(CC) -MD -c -o $@ $< $(CFLAGS) -+ $(CXX) -o $@ $^ $(LDOPTS) -+ -+$(OBJ_DIR): -+ mkdir -p $(OBJ_DIR) -+ -+$(OBJ_DIR)/%.o: %.cpp | $(OBJ_DIR) -+ $(CXX) -MD -c -o $@ $< $(CXXFLAGS) +- @ $(CXX) -MD -c -o $@ $< $(CFLAGS) ++ $(CXX) -MD -c -o $@ $< $(CFLAGS) clean: +- install -d $(BIN_DIR) $(MAN_DIR) rm -rf $(OBJ_DIR)/* mkdssp install: mkdssp -- sudo install -m 755 mkdssp $(DEST_DIR)bin/mkdssp -- sudo install doc/mkdssp.1 $(MAN_DIR)mkdssp.1 -+ install -d $(BIN_DIR) $(MAN_DIR) -+ install -m 755 mkdssp $(BIN_DIR)/mkdssp -+ install doc/mkdssp.1 $(MAN_DIR)/mkdssp.1 - - dist: $(OBJECTS) - @ rm -rf $(DIST_NAME) -@@ -81,11 +76,3 @@ +@@ -85,11 +80,3 @@ @ cp doc/mkdssp.1 $(DIST_NAME)/doc/mkdssp.1 tar czf $(DIST_NAME).tgz $(DIST_NAME) cp $(DIST_NAME).tgz dssp_$(VERSION).orig.tar.gz @@ -112,23 +74,3 @@ - @echo "#BOOST_LIB_DIR = $(HOME)/projects/boost/lib" >> make.config - @echo "#BOOST_INC_DIR = $(HOME)/projects/boost/include" >> make.config - ---- a/doc/mkdssp.1 -+++ b/doc/mkdssp.1 -@@ -13,7 +13,7 @@ - Please note that \fImkdssp\fP \fBdoes not predict\fP secondary structure. - .SH OPTIONS - If you invoke \fImkdssp\fP with only one parameter, it will be --interpreted as the PDB file to process and output will be send to -+interpreted as the PDB file to process and output will be sent to - stdout. If a second parameter is specified this is interpreted as - the name of the DSSP file to create. Both the input and the output - file names may have either \.gz or \.bz2 as extension resulting in -@@ -159,7 +159,7 @@ - .SH TODO - The code desperately needs an update. The first thing that needs - implementing is the improved recognition of pi\-helices. A second --improvement would be to use angle dependant H\-bond energy calculation. -+improvement would be to use angle dependent H\-bond energy calculation. - .SH BUGS - If you find any, please let me know. - .SH AUTHOR Modified: trunk/packages/dssp/trunk/debian/patches/series =================================================================== --- trunk/packages/dssp/trunk/debian/patches/series 2013-05-08 15:56:54 UTC (rev 13522) +++ trunk/packages/dssp/trunk/debian/patches/series 2013-05-08 18:43:34 UTC (rev 13523) @@ -1,2 +1,2 @@ +thread_include makefile -src-matrix.h Deleted: trunk/packages/dssp/trunk/debian/patches/src-matrix.h =================================================================== --- trunk/packages/dssp/trunk/debian/patches/src-matrix.h 2013-05-08 15:56:54 UTC (rev 13522) +++ trunk/packages/dssp/trunk/debian/patches/src-matrix.h 2013-05-08 18:43:34 UTC (rev 13523) @@ -1,23 +0,0 @@ -Description: fix for compiling with gcc 4.7 - [Julian Taylor <[email protected]>] - * Include algorithm and added std:: -Author: Julian Taylor <[email protected]> ---- a/src/matrix.h -+++ b/src/matrix.h -@@ -14,6 +14,7 @@ - #include <istream> - #include <cassert> - #include <stdexcept> -+#include <algorithm> - - // -------------------------------------------------------------------- - // uBlas compatible matrix types -@@ -310,7 +311,7 @@ matrix<T> operator*(const matrix_base<T> - template<typename T> - matrix<T> operator-(const matrix_base<T>& lhs, const matrix_base<T>& rhs) - { -- matrix<T> result(min(lhs.dim_m(), rhs.dim_m()), min(lhs.dim_n(), rhs.dim_n())); -+ matrix<T> result(std::min(lhs.dim_m(), rhs.dim_m()), std::min(lhs.dim_n(), rhs.dim_n())); - - for (uint32 i = 0; i < result.dim_m(); ++i) - { Added: trunk/packages/dssp/trunk/debian/patches/thread_include =================================================================== --- trunk/packages/dssp/trunk/debian/patches/thread_include (rev 0) +++ trunk/packages/dssp/trunk/debian/patches/thread_include 2013-05-08 18:43:34 UTC (rev 13523) @@ -0,0 +1,23 @@ +Description: moving boost thread include out of header that does not use it + Patch is not yet forwarded upstream. +Author: Laszlo Kajan <[email protected]> +--- a/src/utils.h ++++ b/src/utils.h +@@ -10,7 +10,6 @@ + #endif + + #include <time.h> +-#include <boost/thread.hpp> + #include <boost/lexical_cast.hpp> + #include <boost/format.hpp> + #include <boost/filesystem.hpp> +--- a/src/structure.cpp ++++ b/src/structure.cpp +@@ -18,6 +18,7 @@ + #define foreach BOOST_FOREACH + #include <boost/algorithm/string.hpp> + #include <boost/math/special_functions/round.hpp> ++#include <boost/thread.hpp> + + #include "align-2d.h" + #include "utils.h" Modified: trunk/packages/dssp/trunk/debian/rules =================================================================== --- trunk/packages/dssp/trunk/debian/rules 2013-05-08 15:56:54 UTC (rev 13522) +++ trunk/packages/dssp/trunk/debian/rules 2013-05-08 18:43:34 UTC (rev 13523) @@ -1,10 +1,12 @@ #!/usr/bin/make -f +#DH_VERBOSE := 1 +export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) +export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) +export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) +export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) -DH_VERBOSE := 1 -PPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) -CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) -CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) -LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) +export DEST_DIR:=/usr +export LDOPTS:=$(LDFLAGS) %: dh $@ --parallel _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
