[med-svn] r13523 - in trunk/packages/dssp/trunk/debian: . patches
Laszlo Kajan
lkajan at alioth.debian.org
Wed May 8 18:43:34 UTC 2013
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 <lkajan at rostlab.org> 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 <lkajan at rostlab.org>,
Andreas Tille <tille at debian.org>
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 <lkajan at rostlab.org>
--- 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 <jtaylor.debian at googlemail.com>]
- * Include algorithm and added std::
-Author: Julian Taylor <jtaylor.debian at googlemail.com>
---- 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 <lkajan at rostlab.org>
+--- 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
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